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Title:
OLIGONUCLEOTIDE COMPOSITIONS AND METHODS OF USE THEREOF
Document Type and Number:
WIPO Patent Application WO/2019/200185
Kind Code:
A1
Abstract:
Among other things, the present disclosure provides designed oligonucleotides, compositions, and methods of use thereof. In some embodiments, the present disclosure provides technologies useful for reducing levels of transcripts. In some embodiments, the present disclosure provides technologies useful for modulating transcript splicing. In some embodiments, provided technologies can alter splicing of a dystrophin (DMD) transcript. In some embodiments, the present disclosure provides methods for treating diseases, such as Duchenne muscular dystrophy, Becker's muscular dystrophy, etc.

Inventors:
ZHANG, Jason Jingxin (733 Concord AvenueCambridge, Massachusetts, 02138, US)
VARGEESE, Chandra (733 Concord AvenueCambridge, Massachusetts, 02138, US)
IWAMOTO, Naoki (733 Concord AvenueCambridge, Massachusetts, 02138, US)
SHIVALILA, Chikdu Shakti (733 Concord AvenueCambridge, Massachusetts, 02138, US)
KOTHARI, Nayantara (733 Concord AvenueCambridge, Massachusetts, 02138, US)
DURBIN, Ann Fiegen (733 Concord AvenueCambridge, Massachusetts, 02138, US)
RAMASAMY, Selvi (733 Concord AvenueCambridge, Massachusetts, 02138, US)
KANDASAMY, Pachamuthu (733 Concord AvenueCambridge, Massachusetts, 02138, US)
KUMARASAMY, Jayakanthan (733 Concord AvenueCambridge, Massachusetts, 02138, US)
BOMMINENI, Gopal Reddy (733 Concord AvenueCambridge, Massachusetts, 02138, US)
MARAPPAN, Subramanian (733 Concord AvenueCambridge, Massachusetts, 02138, US)
DIVAKARAMENON, Sethumadhavan (733 Concord AvenueCambridge, Massachusetts, 02138, US)
BUTLER, David Charles Donnell (733 Concord AvenueCambridge, Massachusetts, 02138, US)
LU, Genliang (733 Concord AvenueCambridge, Massachusetts, 02138, US)
YANG, Hailin (733 Concord AvenueCambridge, Massachusetts, 02138, US)
SHIMIZU, Mamoru (733 Concord AvenueCambridge, Massachusetts, 02138, US)
MONIAN, Prashant (733 Concord AvenueCambridge, Massachusetts, 02138, US)
Application Number:
US2019/027109
Publication Date:
October 17, 2019
Filing Date:
April 11, 2019
Export Citation:
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Assignee:
WAVE LIFE SCIENCES LTD. (7 Straits View #12-00, Marina One East Tower, Singapore 6, 018936, SG)
ZHANG, Jason Jingxin (733 Concord AvenueCambridge, Massachusetts, 02138, US)
VARGEESE, Chandra (733 Concord AvenueCambridge, Massachusetts, 02138, US)
IWAMOTO, Naoki (733 Concord AvenueCambridge, Massachusetts, 02138, US)
SHIVALILA, Chikdu Shakti (733 Concord AvenueCambridge, Massachusetts, 02138, US)
KOTHARI, Nayantara (733 Concord AvenueCambridge, Massachusetts, 02138, US)
DURBIN, Ann Fiegen (733 Concord AvenueCambridge, Massachusetts, 02138, US)
RAMASAMY, Selvi (733 Concord AvenueCambridge, Massachusetts, 02138, US)
KANDASAMY, Pachamuthu (733 Concord AvenueCambridge, Massachusetts, 02138, US)
KUMARASAMY, Jayakanthan (733 Concord AvenueCambridge, Massachusetts, 02138, US)
BOMMINENI, Gopal Reddy (733 Concord AvenueCambridge, Massachusetts, 02138, US)
MARAPPAN, Subramanian (733 Concord AvenueCambridge, Massachusetts, 02138, US)
DIVAKARAMENON, Sethumadhavan (733 Concord AvenueCambridge, Massachusetts, 02138, US)
BUTLER, David Charles Donnell (733 Concord AvenueCambridge, Massachusetts, 02138, US)
LU, Genliang (733 Concord AvenueCambridge, Massachusetts, 02138, US)
YANG, Hailin (733 Concord AvenueCambridge, Massachusetts, 02138, US)
SHIMIZU, Mamoru (733 Concord AvenueCambridge, Massachusetts, 02138, US)
MONIAN, Prashant (733 Concord AvenueCambridge, Massachusetts, 02138, US)
International Classes:
C12N15/11; C07C317/28; C07H21/02; C07H21/04; C12Q1/68
Attorney, Agent or Firm:
LI, Xiaodong et al. (Choate, Hall & Stewart LLPTwo International Plac, Boston Massachusetts, 02110, US)
Download PDF:
Claims:
CLAIMS

1. An oligonucleotide composition, comprising a plurality of oligonucleotides of a particular

oligonucleotide type defined by:

1 ) base sequence;

2) pattern of backbone linkages;

3) pattern of backbone chiral centers; and

4) pattern of backbone phosphorus modifi cations,

wherein:

oligonucleotides of the plurality comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 clurally controlled intemucleotidic linkages; and

oligonucleotides of the plurality comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 non-negatively charged intemucleotidic linkages.

2. An oligonucleotide composition, comprising a plurality of oligonucleotides of a particular oligonucleotide type defined by:

1) base sequence;

2) pattern of backbone linkages;

3) pattern of backbone chiral centers; and

4) pattern of backbone phosphorus modifications,

wherein:

oligonucleotides of the plurality comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 chi rally controlled intemucleotidic linkages; and

the oligonucleotide composition being characterized in that, when it is contacted with a transcript m a transcript splicing system, splicing of the transcript is altered relative to that observed under a reference condition selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof.

3. The oligonucleotide of claim 2, wherein the pattern of backbone linkages comprises at least one non-negatively charged intemucleotidic linkage.

4. The oligonucleotide composition of claim 1, wherein when the oligonucleotide composition is contacted with a transcript in a transcript splicing system, splicing of the transcript is altered relative to that observed under a reference condition selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof.

5. The oligonucleotide of any one of claims 1-4, wherein one or more non-negatively charged intemucleotidic linkage are independently chiraily controlled.

6. The composi tion of claim 5, wherein a non-negatively charged intemucleotidic linkage has the structure of formula I:

or a salt form thereof, wherein:

each ofR1 and IIs is independently -H, -L~R’, halogen, -CN, --N02, -L-Si(R ) , -OR’, -SR, or -N(R’)2;

X is N( I. R ) :

each of Y and Z is independently -0-, -S-, -N(-L-R3)-, or L;

each L is independently a covalent bond, or a bivalent, optionally substituted, linear or branched group selected from a C]-3o aliphatic group and a Ci_3o heteroaliphatic group having 1-10 heteroatoms, wherein one or more methylene units are optionally and independently replaced with Cj 6 alkylene, Ci-6 alkenyl ene, a bivalent Ci-C6 heteroaliphatic group having 1-5 heteroatoms, -C(R’)2-, -Cy-, -O-, S . S S . -N(R’)-, ( {()) . C(S) . -C(NR’)-, -C(0)N(R’)-, -N(R’)C(0)N(R’)- N(R )( (())() . S(O) . -S(0 )2-, S(0)-\(R ) . -C(0)S- -C(0)0-, -P(0)(OR’)-, -P(0)(SR’)-, -P(0)(R’)- -P(0)(NR’)-, PcSKOin . -P(S)(SR’)-, -P(S)(R’)-, -P(S)(NR’)-, -P(R’)- -P(OR’)- -P(SR’)-, -P(NR’)-, -P(OR’)[B(R’)3]-, -0P(0)(0R’)0-, -0P(0)(SR’)0-, -OP(0)(R’)0- -0P(0)(NR’)0 , OP(OR’)0~, -OP(SR’)0-, -0P(NR’)0~, -OP(R’)0-, or -OP(OR’)[B(R’)3]0-, and one or more CH or carbon atoms are optionally and independently replaced with Cy1 ;

each -Cy- is independently an optionally substituted bivalent group selected from a C3-2o cycloaliphatic ring, a C6.2o aryl ring, a 5-20 membered heteroaryl ring having 1-10 heteroatoms, and a 3- 20 membered heterocyclyl ring having 1-10 heteroatoms;

each CyL is independently an optionally substituted trivalent or tetravalent group selected from a C3-2o cycloaliphatic ring, a C6-2o aryl ring, a 5-20 membered heteroaryl ring having 1-10 heteroatoms, and a 3-20 membered heterocyclyl ring having 1-10 heteroatoms;

each R’ is independently -R, ~C(0)R, ~C(0)OR, or -S(0)2R;

each R is independently -H, or an optionally substituted group selected from C;i-3o aliphatic, C]-3o heteroaliphatic having 1-10 heteroatoms, C6-3o aryl, C6-3o arylahphatic, C6.3o aiylheteroaliphatic having 1- 10 heteroatoms, 5-30 membered heteroaryl having 1-10 heteroatoms, and 3-30 membered heterocyclyl having 1-10 heteroatoms, or

two R groups are optionally and independently taken together to form a covalent bond, or two or more R groups on the same atom are optionally and independently taken together with the atom to form an optionally substituted, 3-30 membered, monocyclic, bicyciic or polycyclic ring having, in addition to the atom, 0-10 heteroatoms, or

two or more R groups on two or more atoms are optionally and independently taken together with their intervening atoms to form an optionally substituted, 3-30 membered, monocyclic, bicyciic or polycyclic ring having, in addition to the intervening atoms, 0-10 heteroatoms.

7. The composition of claim 5, wherein a non-negatively charged intemucleotidic linkage has the structure of formula I~n~3:

I~n~3

or a salt form thereof, wherein:

PL is P( W). P, or P B(R’)3;

W is O, N(-L R5), S or Sc.

each of R1 and R5 is independently -H, -L-R’, halogen, -CN, -N02, ---L-Si(R/):;, OR . -SR’, or N( R o.

each of Y and Z is independently -O-, -S-, -N(-L-R:’)-, or L;

each L is independently a covalent bond, or a bivalent, optionally substituted, linear or branched group selected from a Ci-30 aliphatic group and a Ci-3o heteroaliphatic group having 1-10 heteroatoms, wherein one or more methylene units are optionally and independently replaced with C _6 alkylene, C..6 alkenylene, C=C a bivalent C -C6 heteroaliphatic group having 1-5 heteroatoms, -C(R’)2-, -Cy-, -0-, -S-, -S-S-, Ni R . -C(O)-, -C(S)-, -C(NR’)-, -C(0)N(R’)-, -N(R’)C(0)N(R’)-,

-N(R)C(0)0-, SiO) . -S(0)2-, -S(0)2N(R’)-, -C(0)S-, -C(0)0-, -P(0)(OR’)-, -P(0)(SR’)-, -P(0)(R’)-, -P(0)(NR’)-, -P(S)(OR )-, -P(S)(SR’)-, P(S)(R ) . -P(S)(NR’)-, P(R ) . -P(OR’)- -P(SR’)-, P( NR ) . -P(OR’)[B(R’)3]-, -0P(0)(0R’)0- -0P(0)(SR’)0-, -0P(0)(R’)0- -0P(0)(NR’)0-, -0P(0R’)0-, -0P(SR’)0- -0P(NR’)0- -OP(R’)0- or -OP(OR’)[B(R’)3]0-, and one or more CH or carbon atoms are optionally and independently replaced with CyL;

each -Cy- is independently an optionally substituted bivalent group selected from a C3-2o cycloaliphatic ring, a C6-2o aryl ring, a 5-20 membered heteroaryl ring having 1-10 heteroatoms, and a 3- 20 membered heterocyclyl ring having 1-10 heteroatoms;

each CyL is independently an optionally substituted bivalent or tetravalent group selected from a C3-20 cycloaliphatic ring, a C6-2o aryl ring, a 5-20 membered heteroaryl ring having 1-10 heteroatoms, and a 3-20 membered heterocyclyl ring having 1-10 heteroatoms;

each R is independently R. -C(Q)R, -C(0)OR, or -S(0)2R;

each R is independently -H, or an optionally substituted group selected from Ci-30 aliphatic, C1-30 heteroahphatic having 1-10 heteroatoms, C6-3o aryl, C¾-3o arylaliphatic, C6 3o arylheteroaliphatic having 1 - 10 heteroatoms, 5-30 membered heteroaryl having 1-10 heteroatoms, and 3-30 rnernbered heterocyclyl having 1-10 heteroatoms, or

two R groups are optionally and independently taken together to fonn a covalent bond, or two or more R groups on the same atom are optionally and independently taken together with the atom to form an optionally substituted, 3-30 membered, monocyclic, bicydic or polycyclic ring having, in addition to the atom, 0-10 heteroatoms, or

two or more R groups on two or more atoms are optionally and independently taken together with their intervening atoms to form an optionally substituted, 3-30 membered, monocyclic, bicydic or polycyclic ring having, in addition to tire intervening atoms, 0-10 heteroatoms.

8. The composition of claim 5, wherein a non-negatively charged intemucleotidic linkage has tire

structure

9. The composition of claim 8, wherein the non-negatively charged intemucleotidic linkage chirally controlled and is tip

10. The composition of claim 8, wherein the transcript is a Dystrophin transcript.

1 1. The composition of claim 10, wherein splicing of the transcript is altered such that the level of skipping of exon 45, 51, or 53, or multiple exons is increased.

12. The composition of claim 8, wherein each chiral intemucleotidic linkage of the oligonucleotides of the plurality is independently a chirally controlled intemucleotidic linkage.

13. The composition of claim 8, wherein the base sequence is or comprises or comprises 15 contiguous bases of the base sequence of any oligonucleotide in Table Al.

14. The composition of claim 11, wherein the oligonucleotide type comprises any of: cholesterol; L- camitine (amide and carbamate bond); Folic acid; Gambogic acid; Cleavable lipid (1,2-dilaurin and ester bond); Insulin receptor ligand; CPP; Glucose (tri- and hex-antennary); or Mannose (tri- and hex- antennary, alpha and beta).

15. The composition of claim 11, wherein each non-negatively charged intemucleotidic linkage is independently an intemucleotidic linkage at least 50% of which exists in its non-negatively charged form at pH 7.4.

16. The composition of claim 11, wherein the oligonucleotides of the plurality each comprise one or more sugar modifications.

17. The composition of claim 16, wherein one or more sugar modifications are 2'-F modifications.

18. The composition of any one of the preceding claims, wheretn each heteroatom is independently boron, nitrogen, oxygen, silicon, sulfur, or phosphorus.

19. A pharmaceutical composition comprising an oligonucleotide composition of any one of the preceding claims and a pharmaceutically acceptable carrier.

20. A method for altering splicing of a target transcript, comprising administering an oligonucleotide composition of any one of the preceding claims.

21 . The method of claim 20, wherein the target transcript is pre-m NA of dystrophin.

22. The method of claim 21, wherein exon 45 of dystrophin is skipped at an increased level relative to absence of the composition.

23. The method of claim 21, wherein exon 51 of dystrophin is skipped at an increased level relative to absence of the composition.

24. The method of claim 21, wherein exon 53 of dystrophin is skipped at an increased level relative to absence of the composition.

25. A method for treating muscular dystrophy, Duchenne (Duchenne’s) muscular dystrophy (DMD), or Becker (Becker’s) muscular dystrophy (BMD), comprising administering to a subject susceptible thereto or suffering therefrom a composi tion of any one of the preceding claims.

26. A method for preparing an oligonucleotide or an oligonucleotide composition thereof, wherein the oligonucleotide comprises one or more non-negatively charged intemucleotidic linkages, comprising providing a phosphoramidite compound having the structure of:

wherein:

RSs is independently R’ or -OR’;

each BA is independently an optionally substituted group selected from C3-30 cycloaliphatic, C6-3o aryl, C5.3o heteroaryl having 1-10 heteroatoms, C3.30 heterocyclyl having 1-10 heteroatoms, a natural nucleobase moiety, and a modified nueleobase moiety;

each R is independently 1 1. halogen, -CN, -N3, NO. NO , ! . It. -L-Si(R)3s 1. OR . -L-SR’, -L-N(R’)2, -O-L-R’, -Q-L-Si(R)3, O 1. OR . O 1 SR . or -0-L-N(R’)2;

each s is independently 0-20;

each Ls is independently -C(R5s)2-, or L;

each L is independently a covalent bond, or a bivalent, optionally substituted, linear or branched group selected from a C1-30 aliphatic group and a C!-30 heteroaliphatic group having 1 -10 heteroatoms, wherein one or more methylene units are optionally and independently replaced with Cj .6 alkylene, Ci.6

one or more CH or carbon atoms are optionally and independently replaced with Cy1';

each— Cy— is independently an optionally substituted bivalent group selected from a C3.2o cycloaliphatic ring, a C6.2o aryl ring, a 5-20 membered heteroaryl ring having 1-10 heteroatoms, and a 3- 20 membered heterocyclyl ring having 1-10 heteroatoms; each CyL is independently an optionally substituted trivalent or tetravalent group selected from a C3-20 cycloaliphatic ring, a C6-2o aryl ring, a 5-20 membered heteroaryl ring having 1-10 heteroatoms, and a 3-20 membered heteroeyclyi ring having 1-10 heteroatoms;

each Ring A is independently an optionally substituted 3-20 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon;

each of G1, G2, G3, G4, G5, and G8 is independently R1;

each R1 is independently -H, -L-R’, halogen, -CN, -N02, -L-Si(R’)3, -OR’, -SR’, or -N(R’)2; each R is independently -R, -C(0)R, C(0)0R. or S{(>) R;

each R is independently -H, or an optionally substituted group selected from Ci-30 aliphatic, Ci-30 heteroaiiphatic having 1-10 heteroatoms, C6-30 aryl, C6-30 arylaliphatic, C6-30 arylheteroaliphatic having 1 - 10 heteroatoms, 5-30 membered heteroaryl having 1-10 heteroatoms, and 3-30 membered heteroeyclyi having 1-10 heteroatoms, or

two R groups are optionally and independently taken together to form a covalent bond, or two or more R groups on tire same atom are optionally and independently taken together with the atom to form an optionally substituted, 3-30 membered, monocyclic, bicyclic or polycyclic ring having, in addition to the atom, 0-10 heteroatoms, or

two or more R groups on two or more atoms are optionally and independently taken together with their intervening atoms to form an optionally substituted, 3-30 membered, monocyclic, bicyclic or polycyclic ring having, in addition to the intervening atoms, 0-10 heteroatoms; and

wherein G2 comprises an electron-withdrawing group.

27. The method of claim 26, wherein G' and one of G3 and G4 are taken together to form an optionally substituted 3-8 membered saturated ring having 0-3 heteroatoms in addition to the nitrogen of -NG5-

28 The method of claim 26, wherein the oligonucleotide comprises an interaucleotidic linkage

having the structure

29. The method of any one of claims 26-28, wherein G2 comprises an electron-withdrawing group.

30. The method of claim 29, wherein G2 is -L/-S(0)2R\ wherein IT is optionally substituted -CH2-.

31. The method of claim 30, wherein R7 is optionally substituted Ci 6 aliphatic.

32. The method of claim 30, wherein R’ is t-butyl.

33. The method of claim 30, wherein R’ is optionally substituted phenyl.

34. The method of claim 30, wherein R" is phenyl.

35. The method of claim 29, comprising one or more cycles, each of which independently comprises or consisting of:

1) deblocking;

2) coupling;

3) optionally a first capping;

4) modifying; and

5) optionally a second capping.

36. An oligonucleotide, comprising an intemucleotidic linkage having the structure of fonnula III:

Q is an anion;

e each of R1 and R5 is independently 1 1. -L-R’, halogen, -CN, NO-. -L-Si(R’)3, OR . SR or N( in ,

each of Y and Z is independently -0-, -S-, -N(-L-R:’)-, or L;

each L is independently a covalent bond, or a bivalent, optionally substituted, linear or branched group selected from a Ci.30 aliphatic group and a Ci.30 heteroaliphatic group having 1-10 heteroatoms, wherein one or more methylene units are optionally and independently replaced with Cj-6 alkylene, C1-6 alkenylene, CºC . a bivalent Cr-C6 heteroaliphatic group having 1-5 heteroatoms, -C(R’)2 , --Cy~-, 0 . S . S S . -N(R , i iO) . C(S) . ( C NR ) . -C(0)N(R’)- -N(R’)C(0)N(R’)-,

N{ - )C(0)0 . ~S(0)--, SiO)2-, -S(0)2N(R’)-, -C(0)S~, -C(0)0- -P(0)(OR’)- -P(0)(SR’)- -P(0)(R’)-, -P(0)(NR )-, -P(S)(OR’)- -P(S)(SR’)-, -P(S)(R’)-, -P(S)(NR’)-, -P(R’)-, -P(OR’)-, -P(SR’)-, PC NR ) . -P(OR’)[B(R’)3]-, -0P(0)(0R’)0- -0P(0)(SR’)0-, -0P(0)(R’)0-,

-0P(0)(NR’)0-, OFiOR K) . -0P(SR )0-, ()P(\R )() . -0P(R’)0-, or -OP(OR’)[B(R’)3JO-, and one or more CH or carbon atoms are optionally and independently replaced with Cyh

each -Cy- is independently an optionally substituted bivalent group selected from a C3-2o cycloaliphatic ring, a CV20 aryl ring, a 5-20 membered heteroaryl ring having 1 -10 heteroatoms, and a 3- 20 membered heterocydyl ring having 1-10 heteroatoms;

each CyL is independently an optionally substituted tri valent or tetravalent group selected from a C3.20 cycloaliphatic ring, a C6-20 aryl ring, a 5-20 membered heteroaryl ring having 1-10 heteroatoms, and a 3-20 membered heterocydyl ring having 1-10 heteroatoms;

each R is independently -R, -C(0)R, -C(0)OR, or -S(0)2R;

each R is independently I f. or an optionally substituted group selected from C-.-J0 aliphatic, (To heteroaliphatic having 1-10 heteroatoms, C6-30 aryl, C6-30 arylaliphatic, C6-30 arylheteroaliphatic having 1- 10 heteroatoms, 5-30 membered heteroaryl having 1-10 heteroatoms, and 3-30 membered heterocydyl having 1-10 heteroatoms, or

two R groups are optionally and independently taken together to form a covalent bond, or two or more R groups on tire same atom are optionally and independently taken together with the atom to form an optionally substituted, 3-30 membered, monocyclic, bicyelic or polycyclic ring having, in addition to the atom, 0-10 heteroatoms, or

two or more R groups on two or more atoms are optionally and independently taken together with their intervening atoms to form an optionally substituted, 3-30 membered, monocyclic, bicyelic or polycyclic ring having, in addition to the intervening atoms, 0-10 heteroatoms; and

wherein G comprises an electron - withdrawing group.

37 The oligonucleotide of claim 36, wherein G2 is -L’-S(0)2R\ wherein L’ is optionally substituted

-CH2-.

38. The oligonucleotide of claim 37, wherein R’ is optionally substituted C -s aliphatic.

39. The oligonucleotide of claim 38, wherein R’ is t-butyl.

40. The oligonucleotide of claim 37, wherein R’ is optionally substituted phenyl.

41 . The oligonucleotide of claim 40, wherein R’ is phenyl.

42. The oligonucleotide of any one of claims 36-41, wherein R1 is -C(0)R\

43. The oligonucleotide of claim 42, wherein R’ is -CI¾.

44. The oligonucleotide of any one of claims 36-41, wherein Q is F , Cl , Br , BF4 , PF6 , TfO , Tf2lSr, ASF6 , GOV, or SbF6 .

45. The oligonucleotide of any one of claims 36-44, wherein the oligonucleotide is atached to a solid support.

46. The oligonucleotide of claim 45, wherein the solid support is CPG.

47. A method for preparing an oligonucleotide, compri sing contacting an oligonucleotide of any one of claims 36-46 with a base.

48. The method of claim 47, wherein the contact is performed substantially absent of water.

49. The method of claim 47 or 48, wherein the contact is after the oligonucleotide length is achieved before deprotection and cleavage of oligonucleotide .

50. The method of any one of claims 47-49, wherein the base is an amine base having the structure of N R .

51. The method of claim 50, wherein the base is N. iV-diethylamine .

52. The oligonucleotide, compound or method of any one of Example Embodiments 1-420.

53. An oligonucleotide, wherein the oligonucleotide is, WV-20104, WV-20103, WV-20102, WV- 20101, WV-20100, WV-20099, WV-20098, WV-20097, WV-20096, WV-20095, WV-20094, WV- 20106, WV-20119, WV-20118, WV-13739, WV-13740, WV-9079, WV-9082, WV-9100, WV-9096, WV-9097, WV-9106, WV-9133, WV-9148, WV-9154, WV-9898, WV-9899, WV-9900, WV-9906, WV- 9907, WV-9908, WV-9909, WV-9756, WV-9757, WV-9517, WV-9714, WV-9715, WV-9519, WV- 9521 , WV-9747, WV-9748, WV-9749, WV-9897, WV-9898, WV-9900, WV-9899, WV-9906, WV- 9912, WV-9524, WV-9912, WV-9906, WV-9900, WV-9899, WV-9899, WV-9898, WV-9898, WV- 9898, WV-9898, WV-9898, WV-9897, WV-9897, WV-9897, WV-9897, WV-9897, WV-9747, WV- 9714, WV-9699, WV-9517, WV-9517, WV-13409, WV-13408, WV-12887, WV-12882, WV-12881 , WV-12880, WV-12880, WV-WV12880, WV-12878, WV-12877, WV-12877, WV-12876, WV-12873, WV-12872, WV-12559, WV-12559, WV-12558, WV-12558, WV-12557, WV-12556, WV-12556, WV-

12555, WV-12555, WV-12554, WV-12553, WV-12129, WV-12127, WV 15. WV-12123, WV·

11342, WV-11342, WV-11341 , WV-11341, WV-11340, WV-10672, WV-10671, WV-10670, WV-

10461, WV- 10455, WV-9897, WV-9898, WV-13826, WV-13827, WV-13835, WV-12880, WV-14344,

WV-13864, WV-13835, WV-14791, WV-14344, WV-13754, WV-13766,, WV-1 1086, WV-11089, WV- 17859, WV-17860, WV-20070, WV-20073, WV-20076, WV-20052, WV-20099, WV-20049, WV-

20085, WV -20087, WV-20034, WV -20046, WV-20052, WV-20061, WV-20064, WV-20067, WV-

20092, WV-20091 , WV-20093, WV -20084, WV-9738, WV-9739, WV-9740, WV-9741, WV-15860, WV-15862, WV-11084, WV-11086, WV-1 1088, WV-11089, WV-14522, WV-14523, WV-17861 , WV- 17862, WV-13815, WV-13816, WV-13817, WV-13780, WV-17862, WV-17863, WV-17864, WV- 17865, WV-17866, WV-20082, WV-20081, WV-20080, WV-20079, WV-20076, WV-20075, WV- 20074, WV -20073, WV-20072, WV-20071, WV -20064, WV-20059, WV-20058, WV-20057, WV- 20056, WV-20053, WV-20052, WV-20051, WV-20050, WV-20049, WV-20094, WV-20095, or a salt form thereof.

Description:
OLIGONUCLEOTIDE COMPOSITIONS AND METHODS OF USE THEREOF

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to United States Provisional Application Nos.

62/656,949, filed April 12, 2018, 62/670,709, filed May 11, 2018, 62/715,684, filed August 07, 2018, 62/723,375, filed August 27, 2018, and 62/776,432, filed December 06, 2018, the entirety of each of which is incorporated herein by reference.

BACKGROUND

[0002] Oligonucl eotides are useful in therapeutic, diagnostic, research and nanomaterials applications. The use of naturally occurring nucleic acids (e.g., unmodified DNA or RNA) for therapeutics can be limited, for example, because of their instability against extra- and intracellular nucleases and/or their poor cell penetration and distribution. There is a need for new and improved oligonucleotides and oligonucleotide compositions, such as, e.g., new oligonucleotides and oligonucleotide compositions capable of modulating exon skipping of Dystrophin for treatment of muscular dystrophy.

SUMMARY

[0003] Among other things, the present disclosure encompasses the recognition that structural elements of oligonucleotides, such as base sequence, chemical modifications (e.g., modifications of sugar, base, and/or internucleotidic linkages, and patterns thereof), and/or stereochemistry (e.g., stereochemistry of backbone chiral centers (chiral internucleotidic linkages), and/or patterns thereof), can have significant impact on oligonucleotide properties, e.g., activities, toxicities, e.g., as may be mediated by protein binding characteristics, stability, splicing-altering capabilities, etc. In some embodiments, the present disclosure demonstrates that oligonucleotide compositions comprising oligonucleotides with controlled structural elements, e.g., controlled chemical modification and/or controlled backbone stereochemistry patterns, provide unexpected properties, including but not limited to certain activities, toxicities, etc. In some embodiments, the present disclosure demonstrates that oligonucleotide properties, e.g., activities, toxicities, etc., can be modulated by chemical modifications (e.g., modifications of sugars, bases, internucleotidic linkages, etc.), chiral structures (e.g., stereochemistry' of chiral internucleotidic linkages and patterns thereof, etc), and/or combinations thereof.

[0004] In some embodiments, the present disclosure provides an oligonucleotide or an oligonucleotide composition. hi some embodiments, an oligonucleotide or an oligonucleotide composition is a DMD oligonucleotide or a DMD oligonucleotide composition. In some embodiments, a DMD oligonucleotide or a DMD oligonucleotide composition is an oligonucleotide or an oligonucleotide composition capable of modulating skipping of one or more exons of the target gene Dystrophin (DMD). In some embodiments, a DMD oligonucleotide or a DMD oligonucleotide composition is useful for treatment of muscular dystrophy. In some embodiments, an oligonucleotide or oligonucleotide composition is an oligonucleotide or oligonucleotide composition which comprises a non-negatively charged intemucleotidic linkage. In some embodiments, an oligonucleotide or oligonucleotide composition which comprises a non-negatively charged intemucleotidic linkage is capable of modulating the expression, level and/or activity of a gene target or a gene product thereof, including but not limited to, increasing or decreasing the expression, level and/or activity of a gene target or gene product thereof via any mechanism, including but not limited to: an RNase H-depemdent mechanism, steric hindrance, RNA interference, modulation of skipping of one or more exon, etc. In some embodiments, the present disclosure pertains to an oligonucleotide or oligonucleotide composition which comprises a non- negatively charged intemucleotidic linkage, in combination with any other structure or chemical moiety described herein. In some embodiments, the present disclosure pertains to a DMD oligonucleotide or DMD oligonucleotide composition which comprises a non-negatively charged intemucleotidic linkage.

[0005] In some embodiments, the present disclosure provides technologies related to an oligonucleotide or an oligonucleotide composition for reducing levels of a transcript and/or a protein encoded thereby. In some embodiments, as demonstrated by example data described herein, provided technologies are particularly useful for reducing levels of mRNA and/or proteins encoded thereby.

[0006] In some embodiments, the present disclosure provides technologies, e.g., oligonucleotides, compositions and methods, etc., for altering gene expression, levels and/or splicing of transcripts. In some embodiments, a transcript is Dystrophin (DMD). Splicing of a transcript, such as pre-mRNA, is an essential step for the transcript to perform its biological functions in many higher eukaryotes. In some embodiments, the present disclosure recognizes that targeting splicing, especially through compositions comprising oligonucleotides having base sequences and/or chemical modifications and/or stereochemistry' patterns (and/or patterns thereof) described in this disclosure, can effectively correct disease-associated mutations and/or aberrant splicing, and/or introduce and/or enhance beneficial splicing that lead to desired products, e.g., mRNA, proteins, etc. which can repair, restore, or add new desired biological functions e.g., one or more functions of Dystrophin.

[0007] In some embodiments, the present disclosure provides compositions and methods for altering splicing of DMD transcripts, wherein altered splicing deletes or compensates for an exon(s) comprising a disease-associated mutation.

]0008[ For example, in some embodiments, a Dystrophin gene can comprise an exon comprising one or more mutations associated with a disease, e.g., muscular dystrophy (including but not limited to Duchenne (Duchenme’s) muscular dystrophy (DMD) and Becker (Becker’s) muscular dystrophy (BMD)). In some embodiments, a disease-associated exon comprises a mutation (e.g., a missense mutation, a frame shift mutation, a nonsense mutation, a premature stop codon, etc.) in an exon. In some embodiments, the present disclosure provides compositions and methods for effectively skipping a disease-associated Dystrophin exon(s) and/or a different or an adjacent exon(s), while maintaining or restoring the reading frame so that a shorter (e.g., internally truncated) but partially functional dystrophin can be produced. A person having ordinary skill in the art appreciates that provided technologies (oligonucleotides, compositions, methods, etc.) can also be utilized for skipping of other exons, for example, those described in WO 2017/062862 and incorporated herein by reference, in accordance with the present disclosure to treat a disease and/or condition .

[0009] Among other things, the present disclosure demonstrates that chemical modifications and/or stereochemistry can be used to modulate transcript splicing by oligonucleotide compositions. In some embodiments, the present disclosure provides combinations of chemical modifications and stereochemistry to improve properties of oligonucleotides, e.g., their capabilities to alter splicing of transcripts. In some embodiments, the present disclosure provides chirally controlled oligonucleotide compositions that, when compared to a reference condition (e.g., absence of the composition, presence of a reference composition (e.g., a stereorandom composition of oligonucleotides having the same constitution (as understood by those skilled in the art, unless otherwise indicated constitution generally refers to the description of the identity and connectivity (and corresponding bond multiplicities) of the atoms in a molecular entity but omitting any distinction arising from their spatial arrangement), a different chirally controlled oligonucleotide composition, etc.), combinations thereof, etc.), provide altered splicing that can deliver one or more desired biological effects, for example, increase production of desired proteins, knockdown of a gene by producing mRNA with frameshift mutations and/or premature termination codons, knockdown of a gene expressing a mRNA with a frameshift mutation and/or premature termination codon, etc. In some embodiments, compared to a reference condition, provided chirally controlled oligonucleotide compositions are surprisingly effective. In some embodiments, desired biological effects (e.g., as measured by increased levels of desired mRNA, proteins, etc., decreased levels of undesired mRNA, proteins, etc. ) can be enhanced by more than 5, 10, 15, 20, 25, 30, 40, 50, or 100 fold.

[0010] The present disclosure recognizes challenges of providing low toxicity oligonucleotide compositions and methods of use thereof. In some embodiments, the present disclosure provides oligonucleotide compositions and methods with reduced toxicity. In some embodiments, the present disclosure provides oligonucleotide compositions and methods with reduced immune responses. In some embodiments, the present disclosure recognizes that various toxicities induced by oligonucleotides are related to cytokine and/or complement activation. In some embodiments, the present disclosure provides oligonucleotide compositions and methods with reduced cytokine and/or complement activation. In some embodiments, the present disclosure provides oligonucleotide compositions and methods with reduced complement activation via the alternative pathway. In some embodiments, the present disclosure provides oligonucleotide compositions and methods with reduced complement activation via the classical pathway. In some embodiments, the present disclosure provides oligonucleotide compositions and methods with reduced drug-induced vascular injur '. In some embodiments, the present disclosure provides oligonucleotide compositions and methods with reduced injection site inflammation. In some embodiments, reduced toxicity can be evaluated through one or more assays widely known to and practiced by a person having ordinary ' skill in the art, e.g. , evaluation of levels of complete activation product, protein binding, etc

100111 In some embodiments, the present disclosure provides oligonucleotides with enhanced antagonism of hTLR9 activity. In some embodiments, certain diseases, e.g., DMD, are associated with inflammation in, e.g , muscle tissues. In some embodiments, provided technologies (e.g., oligonucleotides, compositions, methods, etc.) provides both enhanced activities (e.g., exon-skipping activities) and hTLR9 antagonist activities which can be beneficial to one or more conditions and/or diseases associated with inflammation. In some embodiments, provided oligonucleotides and/or compositions thereof provides both exon-skipping capabilities and decreased levels of toxicity and/or inflammation. In some embodiments, the present disclosure provides an oligonucleotide which comprises one or more non-negatively charged intemucieotidic linkages, wherein the oligonucleotide agonizes TLR9 activity less than another oligonucleotide which does not comprise a non-negatively charged intemucieotidic linkage or which comprises fewer non-negatively charged intemucieotidic linkages and which is otherwise identical. In some embodiments, the present disclosure provides an oligonucleotide which comprises one or more non-negatively charged intemucieotidic linkages, wherein the oligonucleotide agonizes TLR9 activity less than an otherwise identical oligonucleotide which does not comprise a non-negatively charged intemucieotidic linkage or which comprises fewer non-negatively charged intemucieotidic linkages. In some embodiments, the present disclosure pertains to an oligonucleotide comprising at least one non-negatively charged intemucieotidic linkage. In some embodiments, the non-negatively charged intemucieotidic is selected from: nOOl, n002, n003, n004, n005, n006, n007, n008, n009, or nGlO, or a chirally controlled stereoisomer of nGOI, n002, n003, n004, n005, n006, n007, m008, n009, or nO!O. In some embodiments, the present disclosure pertains to an oligonucleotide which comprises at least two non-negatively charged intemucieotidic linkages, wherein the linkages are different from each other. In some embodiments, the present disclosure pertains to an oligonucleotide comprising a CpG motif, wherein at least one intemucleotidic linkage in the CpG (e.g., the p in CpG) or immediately upstream of the CpG (toward the 5’ end of the oligonucleotide) or immediately downstream of the CpG (toward the 3’ end of the oligonucleotide) is a non-negatively charged intemucleotidic linkage. In some embodiments, TLR9 is a human TLR9. In some embodiments, TLR9 is a mouse TLR9.

[0012] In some embodiments, the present disclosure demonstrates that oligonucleotide properties, e.g., activities, toxicities, etc., can be modulated through chemical modifications. In some embodiments, the present disclosure provides an oligonucleotide composition comprising a plurality of oligonucleotides which have a common base sequence, and comprise one or more modified intemucleotidic linkages (or‘non-natural intemucleotidic linkages”, linkages that are not but can be utilized in place of a natural phosphate intemucleotidic linkage (-OP(Q)(QH)0-, which may exist as a salt form (-0P(0)(0 )0-) at a physiological pH) found in natural DNA and RNA), one or more modified sugar moieties, and/or one or more natural phosphate linkages. In some embodiments, provided oligonucleotides may comprise two or more types of modified intemucleotidic linkages. In some embodiments, a provided oligonucleotide comprises a non-negatively charged intemucleotidic linkage. In some embodiments, a non-negatively charged intemucleotidic linkage is a neutral intemucleotidic linkage. In some embodiments, a neutral intemucleotidic linkage comprises a triazole, alkyne, or guanidine (e.g., cyclic guanidine) moiety. Such moieties are optionally substituted. In some embodiments, a provided oligonucleotide comprises a neutral intemucleotidic linkage and another intemucleotidic linkage which is not a neutral backbone. In some embodiments, a provided oligonucleotide comprises a neutral intemucleotidic linkage and a phosphorothioate intemucleotidic linkage. In some embodiments, provided oligonucleotide compositions comprising a plurality of oligonucleotides are chirally controlled and level of the plurality of oligonucleotides in the composition is controlled or pre-detemrined, and oligonucleotides of the plurality share a common stereochemistry configuration at one or more chiral intemucleotidic linkages. For example, in some embodiments, oligonucleotides of a plurality share a common stereochemistry configuration at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50 or more chiral intemucleotidic linkages, each of which is independently Rp or 5p; in some embodiments, oligonucleotides of a plurality share a common stereochemistry ' configuration at each chiral intemucleotidic linkages. In some embodiments, a chiral intemucleotidic linkage where a controlled level of oligonucleotides of a composition share a common stereochemistry' configuration (independently in the Rp or Ap configuration) is referred to as a chirally controlled intemucleotidic linkage.

[0013] In some embodiments, a modified intemucleotidic linkage is a non-negatively charged

(neutral or cationic) intemucleotidic linkage in that at a pH, (e.g., human physiological pH (~ 7.4), pH of a delivery site (e.g., an organelle, cell, tissue, organ, organism, etc.), etc.), it largely (e.g., at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, etc.; in some embodiments, at least 30%; in some embodiments, at least 40%; in some embodiments, at least 50%; in some embodiments, at least 60%; in some embodiments, at least 70%; in some embodiments, at least 80%; in some embodiments, at least 90%; in some embodiments, at least 99%; etc.;) exists as a neutral or cationic form (as compared to an anionic form (e.g., -0-P(0)(0 )-0- (the anionic form of natural phosphate linkage), -0-P(0)(S )-0- (the anionic torn: of phospfaorothioate linkage), etc.)), respectively in some embodiments, a modified intemucleotidic linkage is a neutral intemucleotidic linkage in that at a pH, it largely exists as a neutral form. In some embodiments, a modified intemucleotidic linkage is a cationic intemucleotidic linkage in that at a pH, it largely exists as a cationic form. In some embodiments, a pH is human physiological pH (~ 7.4). In some embodiments, a modified intemucleotidic linkage is a neutral intemucleotidic linkage in that at pH 7 4 in a water solution, at least 90% of the intemucleotidic linkage exists as its neutral form. In some embodiments, a modified intemucleotidic linkage is a neutral intemucleotidic linkage in that in a water solution of the oligonucleotide, at least 50%, 60%, 70%, 80%, 90%, 95%, or 99% of the intemucleotidic linkage exists in its neutral form. In some embodiments, the percentage is at least 90%. In some embodiments, the percentage is at least 95%. In some embodiments, the percentage is at least 99%. In some embodiments, a non-negative!y charged intemucleotidic linkage, e.g., a neutral intemucleotidic linkage, when in its neutral form has no moiety with a pKa that is less than 8, 9, 10, 11. 12, 13, or 14. In some embodiments, pKa of an intemucleotidic linkage in the present disclosure can be represented by pKa of CH 3- the intemucleotidic linkage ( ' i f (i.e., replacing the two nucleoside units connected by the intemucleotidic linkage with two CH 3 groups). Without wishing to be bound by any particular theory, in at least some cases, a neutral intemucleotidic linkage in an oligonucleotide can provide improved properties and/or activities, e.g., improved delivery ' , improved resistance to exonucleases and endonucleases, improved cellular uptake, improved endosomal escape and/or improved nuclear uptake, etc , compared to a comparable nucleic acid which does not comprises a neutral intemucleotidic linkage.

[0014] In some embodiments, a non-negatively charged intemucleotidic linkage has the structure of e.g., of formula I-n-1, I-n-2, 1-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, O-c-2, II-d-1, Il-d- 2, etc. In some embodiments, a non-negatively charged intemucleotidic linkage comprises a triazole or alkyne moiety. In some embodiments, a non-negatively charged intemucleotidic linkage comprises a guanidine moiety. In some embodiments, a non-negatively charged intemucleotidic linkage comprises a cyclic guanidine moiety. In some embodiments, a modified intemucleotidic linkage comprising a cyclic guanidine moiety has die structure of: . In some embodiments, a neutral intemucleotidic linkage comprising a cyclic guanidine moiety is chirally controlled. In some embodiments, the present disclosure pertains to a composition comprising an oligonucleotide comprising at least one neutral intemucleotidic linkage and at least one phosphorothioate intemucleotidic linkage.

[0015] In some embodiments, a non-negatively charged intemucleotidic linkage is nOOl, n002, n003, n004, n005, hqqό, n007, or n008. In some embodiments, a non-negatively charged intemucleotidic linkage is chirally controlled, e.g., nOOIR, n002R, n0G3R, n004R, n005R, n006R, n007R, n008R, n009R, nOOlS, n002S, n003S, n004S, n005S, n006S, n007S, n008S, n009S, etc.

[0016] In some embodiments, the present disclosure pertains to a composition comprising an oligonucleotide comprising at least one neutral intemucleotidic linkage and at least one phosphorothioate intemucleotidic linkage, wherein the phosphorothioate intemucleotidic linkage is a chirally controlled intemucleotidic linkage in the Sp configuration.

[0017] In some embodiments, the present disclosure pertains to a composition comprising an oligonucleotide comprising at least one neutral intemucleotidic linkage and at least one phosphorothioate intemucleotidic linkage, wherein the phosphorothioate intemucleotidic linkage is a chirally controlled intemucleotidic linkage in the Rp configuration.

In some embodiments, the present disclosure pertains to a composition comprising an oligonucleotide comprising at least one neutral intemucleotidic linkage selected from a neutral intemucleotidic linkage comprising an optionally substituted triazo!yl group, a neutral intemucleotidic linkage comprising an optionally substituted alkynyl group, and a neutral intemucleotidic linkage

comprising a moiety least one phosphorothioate intemucleotidic linkage. In some embodiments, the present disclosure pertains to a composition comprising an oligonucleotide comprising at least one neutral intemucleotidic linkage selected from a neutral intemucleotidic linkage comprising an optionally substituted triazolyl group, a neutral intemucleotidic linkage comprising an optionally

substituted alkynyl group, and a neutral intemucleotidic linkage comprising a Tmg group

and at least one phosphorothioate intemucleotidic linkage. In some embodiments, an oligonucleotide comprises at least one non-negatively charged intemucleotidic linkage and at least one phosphorothioate intemucieotidic linkage. In some embodiments, the non-negatively charged intemucieotidic linkage is nOOi . In some embodiments, the non-negatively charged intemucieotidic linkage and the phosphorothioate intemucieotidic linkage are independently chiraliy controlled. In some embodiments, each of the non-negatively charged intemucieotidic linkage and the phosphorothioate intemucieotidic linkages are independently chiraliy controlled.

[0019] In some embodiments, the present disclosure pertains to a composition comprising an oligonucleotide comprising at least one neutral intemucieotidic linkage selected from a neutral intemucieotidic linkage comprising an optionally substituted triazoly! group, a neutral intemucieotidic linkage comprising an optionally substituted aikynyl group, and a neutral intemucieotidic linkage comprising a Ting group, and at least one phosphorothioate, wherein the phosphorothioate is a chiraliy controlled intemucieotidic linkage in the Sp configuration.

[0020] In some embodiments, the present disclosure pertains to a composition comprising an oligonucleotide comprising at least one neutral internucleotidic linkage selected from a neutral intemucieotidic linkage comprising an optionally substituted triazoly! group, a neutral intemucieotidic linkage comprising an optionally substituted aikynyl group, and a neutral intemucieotidic linkage comprising a Tmg group, and at least one phosphorothioate, wherein the phosphorothioate is a chiraliy controlled intemucieotidic linkage in the Rp configuration .

[0021] Various types of internucleotidic linkages differ in properties. Without wishing to be bound by any theory, the present disclosure notes that a natural phosphate linkage (phosphodiester intemucieotidic linkage) is anionic and may be unstable when used by itself without other chemical modifications in vivo; a phosphorothioate intemucieotidic linkage is anionic, generally more stable in vivo than a natural phosphate linkage, and generally more hydrophobic; a neutral intemucieotidic linkage such as one exemplified in the present disclosure comprising a cyclic guanidine moiety is neutral at physiological pH, can be more stable in vivo than a natural phosphate linkage, and more hydrophobic.

100221 In some embodiments, an intemucieotidic linkage (e.g., a non-negatively charged internucleotidic linkage, a chiraliy controlled non-negatively charged internucleotidic linkage, etc.) is neutral at physiological pH, chiraliy controlled, stable in vivo, hydrophobic, and may increase endosomal escape.

|0023| In some embodiments, an oligonucleotide or oligonucleotide composition is: a DMD oligonucleotide or oligonucleotide composition; an oligonucleotide or oligonucleotide composition comprising a non-negatively charged intemucieotidic linkage; or a DMD oligonucleotide comprising a non-negatively charged intemucieotidic linkage.

100241 In some embodiments, an oligonucleotide has, as non-limiting examples, a wing -core wing, wing-core, core-wing, wing-wing-core-wing-wing, wing-wing -core -wing, or wing-core-wing-wing structure (in some embodiments, a wing-wing comprises or consists of a first wing and a second wing, wherein the first wing is different than the second wing, and the first and second wings are different than the core). A wing or core can be defined by any structural elements and/or patterns and/or combinations thereof. In some embodiments, a wing and core is defined by nucleoside modifications, sugar modifications, and/or intemucleotidic linkages, wherein a wing comprises a nucleoside modification, sugar modification and/or intemucleotidic linkage and/or pattern and/or combination thereof, that the core region does not have, or vice versa. In some embodiments, oligonucleotides of the present disclosure comprise or consist of a 5’-end region, a middle region, and a 3’-end region. In some embodiments, a 5’- end region is a 5’-wing region. In some embodiments, a 5 -wing region is a 5’ -end region. In some embodiments, a 3’-end region is a 3’ -wing region. In some embodiments, a 3’-wing region is a 3 -end region. In some embodiments, a core region is a middle region.

[0025] In some embodiments, each wing region (or each of the 5’-end and 3’-end regions) independently comprises one or more modified phosphate linkages and no natural phosphate linkages, and the core region (the middle region) comprises one or more modified intemucleotidic linkages and one or more natural phosphate linkages. In some embodiments, each wing region (or each of the 5’-end and 3’-end regions) independently comprises one or more natural phosphate linkages and optionally one or more modified intemucleotidic linkages, and the core (or the middle region) comprises one or more modified intemucleotidic linkages and optionally one or more natural phosphate linkages. In some embodiments, a wing (or a 5’-end or 3’-end region) comprises modified sugar moieties. In some embodiments, a modified intemucleotidic linkage is a phosphorothioate intemucleotidic linkage.

[0026] Among other things, the present disclosure encompasses the recognition that stereorandom oligonucleotide preparations contain a plurality of distinct chemical entities that differ from one another, e.g , in the stereochemical structure of individual backbone chiral centers within the oligonucleotide chain. Without control of stereochemistry' of backbone chiral centers, stereorandom oligonucleotide preparations provide uncontrolled (or stereorandom) compositions comprising undetermined levels of oligonucleotide stereoisomers. Even though these stereoisomers may have the same base sequence and/or chemical modifications, they are different chemical entities at least due to their different backbone stereochemistry, and they can have, as demonstrated herein, different properties, e.g., activities, toxicides, distribution etc. Among other things, the present disclosure provides chi rally controlled compositions that are or contain particular stereoisomers of oligonucleotides of interest; in contrast to chirally uncontrolled compositions, chirally controlled compositions comprise controlled levels of particular stereoisomers of oligonucleotides. In some embodiments, a particular stereoisomer may be defined, for example, by its base sequence, its pattern of backbone linkages, its pattern of backbone chiral centers, and pattern of backbone phosphorus modifications, etc. As is understood in the art, in some embodiments, base sequence may refer solely to the sequence of bases and/or to the identity and/or modification status of nucleoside residues (e.g., of sugar and/or base components, relative to standard naturally occurring nucleotides such as adenine, cytosine, guanosine, thymine, and uracil) in an oligonucleotide and/or to the hybridization character (i.e., the ability to hybridize with particular complementary residues) of such residues. In some embodiments, the present disclosure demonstrates that property improvements (e.g. , improved activities, lower toxicities, etc.) achieved through inclusion and/or location of particular chiral structures within an oligonucleotide can be comparable to, or even better than those achieved through use of chemical modifications, e.g., particular backbone linkages, residue modifications, etc. (e.g., through use of certain types of modified phosphates [e.g., phosphorothioate, substituted phosphorothioate, etc. ], sugar modifications [e.g., 2 - modifications, etc.], and/or base modifications [e.g., inethylation, etc.\). in some embodiments, the present disclosure demonstrates that chirally controlled oligonucleotide compositions of oligonucleotides comprising certain chemical modifications (e.g., 2’-F, 2’-OMe, phosphorothioate intemucleotidic linkages, lipid conjugation, etc.) demonstrate unexpectedly high exon-skipping efficiency.

[0027] in some embodiments, provided oligonucleotides are blockmers. in some embodiments, a blockmer is an oligonucleotide comprising one or more blocks.

100281 In some embodiments, a block is a portion of an oligonucleotide. In some embodiments, a block is a wing or a core. In some embodiments, a blockmer comprises one or more blocks. In some embodiments, a 5’ -block is a 5’-end region or 5’-wing. In some embodiments, a 3’-block is a 3’-end region or 3’ -wing.

|0029| In some embodiments, provided oligonucleotide are altmers. In some embodiments, provided oligonucleotides are altmers comprising alternating blocks. In some embodiments, a blockmer or an altmer can be defined by chemical modifications (including presence or absence), e.g., base modifications, sugar modification, intemucleotidic linkage modifications, stereochemistry ' , etc.

100301 In some embodiments, provided oligonucleotides comprise blocks comprising different intemucleotidic linkages. In some embodiments, provided oligonucleotides comprise blocks comprising modified intemucleotidic linkages and/or natural phosphate linkages.

[0031] In some embodiments, provided oligonucleotides comprise blocks comprising sugar modifications. In some embodiments, provided oligonucleotides comprise one or more blocks comprising one or more 2’-F modifications (2’-F blocks). In some embodiments, provided oligonucleotides comprise blocks comprising consecutive 2’-F modifications. In some embodiments, a block comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, 14, 15, 16, 17, 18, 19, 20 or more consecutive 2’-F modifications.

In some embodiments, provided oligonucleotides comprises one or more blocks comprising one or more 2’OR 1 modifications (2 , -()R 1 blocks), wherein R 1 is independently as defined and described herein and below. In some embodiments, provided oligonucleotides comprise both 2’-F and 2’~OR 1 blocks. In some embodiments, provided oligonucleotides comprise alternating 2’~F and 2’- OR 5 blocks. In some embodiments, provided oligonucleotides comprise a first 2’~F block at the 5’-end, and a second 2’-F block at the 3’ -end, each of which independently comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more consecutive 2’ -F modifications.

[0033] In some embodiments, provided oligonucleotides comprise a 5’ -block wherein each sugar moiety of the 5’-block comprises a 2’-F modification. In some embodiments, provided oligonucleotides comprise a S’-block wherein each sugar moiety of the 3’-block comprises a 2’-F modification. In some embodiments, such provided oligonucleotides comprise one or more 2 -O 5 blocks, and optionally one or more 2’-F blocks, between the 5’ and 3’ 2’~F blocks. In some embodiments, such provided oligonucleotides comprise one or more 2’~OR i blocks, and one or more 2’-F blocks, between the 5’ and 3’ 2 -F blocks (e.g., WV-3047, WV-3048, etc).

[0034] In some embodiments, a block is a stereochemistry block. In some embodiments, a block is an Rp block in that each intemucleotidic linkage of the block is Rp. In some embodiments, a 5’-block is an Rp block. In some embodiments, a 3’-hlock is an Rp block. In some embodiments, a block is an Sp block in that each intemucleotidic linkage of the block is Sp. In some embodiments, a 5’-block is an Sp block. In some embodiments, a 3’-block is an 5p block. In some embodiments, provided oligonucleotides comprise both Rp and 5p blocks. In some embodiments, provided oligonucleotides comprise one or more Rp but no Sp blocks. In some embodiments, provided oligonucleotides comprise one or more Sp but no Rp blocks.

[0035] In some embodiments, provided oligonucleotides comprise one or more PO blocks wherein each intemucleotidic linkage in a natural phosphate linkage.

[0036] In some embodiments, a 5’-block is an Sp block wherein each sugar moiety comprises a

2’-F modification. In some embodiments, a 5’-block is an Sp block wherein each intemucleotidic linkage is a modified intemucleotidic linkage and each sugar moiety comprises a 2’-F modification. In some embodiments, a 5’-block is an 5'p block wherein each intemucleotidic linkage is a phosphorothioate linkage and each sugar moiety comprises a 2’-F modification. In some embodiments, a 5’-block comprises 4 or more nucleoside units.

[0037] In some embodiments, a 3’-block is an Sp block wherein each sugar moiety comprises a

2’-F modification. In some embodiments, a 3’-block is an Sp block wherein each intemucleotidic linkage is a modified intemucleotidic linkage and each sugar moiety comprises a 2’~F modification. In some embodiments, a 3’-block is an Sp block wherein each intemucleotidic linkage is a phosphorothioate linkage and each sugar moiety comprises a 2’-F modification. In some embodiments, a 3’-block comprises 4 or more nucleoside units.

[0038] In some embodiments, provided oligonucleotides comprise alternating blocks comprising different modified sugar moieties and/or unmodified sugar moieties. In some embodiments, provided oligonucleotides comprise alternating blocks comprising different modified sugar moieties and unmodified sugar moieties. In some embodiments, provided oligonucleotides comprise alternating blocks comprising different modified sugar moieties. In some embodiments, provided oligonucleotides comprise alternating blocks comprising different modified sugar moieties, wherein the modified sugar moieties comprise different 2 '-modifications. For example, in some embodiments, provided oligonucleotide comprises alternating blocks comprising 2’-OMe and 2’-F, respectively.

[0039] In some embodiments, the present disclosure provides an oligonucleotide composition comprising a plurality of oligonucleotides which:

1 ) have a common base sequence complementary to a target sequence in a transcript; and

2) comprise one or more modified sugar moieties and modified intemucleotidic linkages.

[0040] In some embodiments, a provided oligonucleotide composition is characterized in that, when it is contacted with the transcript in a transcript splicing system, splicing of the transcript is altered relative to that observed under a reference condition selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof.

[0041] In some embodiments, a reference condition is absence of the composition. In some embodiments, a reference condition is presence of a reference composition. Example reference compositions comprising a reference plurality of oligonucleotides are extensively described in this disclosure. In some embodiments, oligonucleotides of the reference plurality have a different structural elements (chemical modifications, stereochemistry, etc.) compared with oligonucleotides of the plurality in a provided composition. In some embodiments, a reference composition is a stereorandom preparation of oligonucleotides having the same chemical modifications. In some embodiments, a reference composition is a mixture of stereoisomers while a provided composition is a chi rally controlled oligonucleotide composition of one stereoisomer. In some embodiments, oligonucleotides of the reference plurality have the same base sequence, same sugar modifications, same base modifications, same intemucleotidic linkage modifications, and/or same stereochemistry' as oligonucleotide of the plurality in a provided composition but different chemical modifications, e.g., base modification, sugar modification, intemucleotidic linkage modifications, etc.

[0042] Example splicing systems are widely known in the art. In some embodiments, a splicing system is an in vivo or in vitro system including components sufficient to achieve splicing of a relevant target transcript. In some embodiments, a splicing system is or comprises a spliceosome (e.g., protein and/or RNA components thereof). In some embodiments, a splicing system is or comprises an organellar membrane (e.g., a nuclear membrane) and/or an organelle (e.g., a nucleus). In some embodiments, a splicing system is or comprises a cell or population thereof. In some embodiments, a splicing system is or comprises a tissue. In some embodiments, a splicing system is or comprises an organism, e.g., an animal, e.g., a mammal such as a mouse, rat, monkey, dog, human, etc.

[0043] In some embodiments, the present disclosure provides an oligonucleotide composition comprising a plurality of oligonucleotides which:

1 ) have a common base sequence complementary ' to a target sequence in a transcript; and

2) comprise one or more modified sugar moieties and modified intemucleotidic linkages, the oligonucleotide composition being characterized in that, when it is contacted with the transcript in a transcript splicing system, spticmg of the transcript is altered relative to that observed under reference conditions selected from the group consi sting of absence of the composition, presence of a reference composition, and combinations thereof.

[0044] In some embodiments, the present disclosure provides an oligonucleotide composition comprising a plurality of oligonucleotides of a particular oligonucleotide type defined by:

1) base sequence;

2) pattern of backbone linkages;

3) pattern of backbone chiral centers; and

4) pattern of backbone phosphorus modifications.

[0045] In some embodiments, the present disclosure provides an oligonucleotide composition comprising a plurality of oligonucleotides of a particular oligonucleotide type defined by:

1) base sequence;

2) pattern of backbone linkages;

3) pattern of backbone chiral centers; and

4) pattern of backbone phosphorus modifications,

which composition is chirally controlled and it is enriched, relative to a substantially racemic preparation of oligonucleotides having tire same base sequence, for oligonucleotides of the particular oligonucleotide type,

the oligonucleotide composition being characterized in that, when it is contacted with the transcript in a transcript splicing system, splicing of the transcript is altered relative to that observed under reference conditions selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof.

[0046] In some embodiments, the present disclosure provides a chirally controlled oligonucleotide composition comprising oligonucleotides of a particular oligonucleotide type characterized by: 1) base sequence;

2) pattern of backbone linkages;

3 ) pattern of backbone chiral centers; and

4) pattern of backbone phosphorus modifications,

which composition is a substantially pure preparation of a single oligonucleotide in that at least about 10% of the oligonucleotides in the composition have the common base sequence and length, the common pattern of backbone linkages, and the common pattern of backbone chiral centers

[0047] In some embodiments, each region (e.g., a block, wing, core, 5’ -end, 3’-end, or middle region, etc.) of an oligonucleotide independently comprises 3, 4, 5, 6, 7, 8, 9, 10 or more bases. In some embodiments, each region independently comprises 3 or more bases. In some embodiments, each region independently comprises 4 or more bases. In some embodiments, each region independently comprises 5 or more bases. In some embodiments, each region independently comprises 6 or more bases. In some embodiments, each sugar moiety in a region is modified. In some embodiments, a modification is a 2’- modification. in some embodiments, each modification is a 2’-modification. In some embodiments, a modification is 2’-F. In some embodiments, each modification is 2’-F. In some embodiments, a modification is 2 , ~OR i . In some embodiments, each modification is 2’-OR 1 . In some embodiments, a modification is 2’-OR 1 . In some embodiments, each modification is 2’-OMe. In some embodiments, each modification is 2’-OMe. In some embodiments, each modification is 2’-MOE. in some embodiments, each modification is 2’-MOE In some embodiments, a modification is an LNA sugar modification. In some embodiments, each modification is an LNA sugar modification. In some embodiments, each intemucleotidic linkage in a region is a chiral intemucleotidic linkage. In some embodiments, each intemucleotidic linkage a wing, or 5’-end or 3’-end region, is an Ap chiral intemucleotidic linkage. In some embodiments, a chiral intemucleotidic linkage is a phosphorothioate linkage. In some embodiments, a core or middle region comprises one or more natural phosphate linkages and one or more modified internucleotidic linkages. In some embodiments, a core or middle region comprises one or more natural phosphate linkages and one or more chiral internucleotidic linkages. In some embodiments, a core region comprises one or more natural phosphate linkages and one or more Ap chiral internucleotidic linkages. In some embodiments, a core or middle region comprises one or more natural phosphate linkages and one or more Ap phosphorothioate linkages.

[0048] In some embodiments, a region (e.g., a block, wing, core, 5’-end, 3’-end, middle region, etc.) of an oligonucleotide comprises a non-negatively charged internucleotidic linkage, e.g., of formula I- n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, Il-fo-2, II-c-1, II-c-2, II-d-1, II-d-2, etc. In some embodiments, a region comprises a neutral intemucleotidic linkage. In some embodiments, a region comprises an intemucleotidic linkage which comprises a triazole or alkyne moiety. In some embodiments, a region comprises an intemucleotidic linkage which comprises a cyclic guanidine guanidine. In some embodiments, a region comprises an intemucleotidic linkage which comprises a cyclic guanidine moiety. In some embodiments, a region comprises an intemucleotidic linkage having the structure of

In some embodiments, such intemucleotidic linkages are ehiraily controlled.

[0049] In some embodiments, the base sequence of an oligonucleotide, e.g , the base sequence of a plurality of oligonucleotides of a particular oligonucleotide type, is or comprises a base sequence disclosed herein (e.g., a base sequence of an example oligonucleotide (e.g., those listed in the tables, examples, etc.), a target sequence, etc.) (or a portion thereof which is at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 bases long). In some embodiments, a provided oligonucleotide has a base sequence comprising the base sequence of any example oligonucleotides or another base sequence disclosed herein, and a length of up to 30 bases. In some embodiments, a provided oligonucleotide has a base sequence comprising the base sequence of any example oligonucleotides or another base sequence disclosed herein, and a length of up to 40 bases. In some embodiments, a provided oligonucleotide has a base sequence comprising the base sequence of any example oligonucleotides or another base sequence disclosed herein, and a length of up to 50 bases. In some embodiments, a provided oligonucleotide has a base sequence comprising at least 15 contiguous bases of the base sequence of an oligonucleotide example or another sequence disclosed herein, and a length of up to 30 bases. In some embodiments, a provided oligonucleotide has a base sequence comprising at least 15 contiguous bases of the base sequence of an oligonucleotide example or another sequence disclosed herein, and a length of up to 40 bases. In some embodiments, a provided oligonucleotide has a base sequence comprising at least 15 contiguous bases of the base sequence of an oligonucleotide example or another sequence disclosed herein, and a length of up to 50 bases. In some embodiments, a provided oligonucleotide has a base sequence comprising a sequence having no more than 5 mismatches from the base sequence of an example oligonucleotide or another sequence disclosed herein, and a length of up to 30 bases. In some embodiments, a provided oligonucleotide has a base sequence comprising a sequence having no more than 5 mismatches from the base sequence of an example oligonucleotide or another sequence disclosed herein, and a length of up to 40 bases. In some embodiments, a provided oligonucleotide has a base sequence comprising a sequence having no more than 5 mismatches from the base sequence of an example oligonucleotide or another sequence disclosed herein, and a length of up to 50 bases.

[0050] In some embodiments, the base sequence of a provided oligonucleotide is the base sequence of an example oligonucleotide or another sequence disclosed herein, and a pattern of backbone chiral centers comprises at least one chirally controlled center which is a rip linkage phosphorus of a phosphorothioate linkage. In some embodiments, the base sequence of a provided oligonucleotide is the base sequence of an example oligonucleotide or another sequence disclosed herein, the oligonucleotide has a length of up to 30 bases, and a pattern of backbone chiral centers comprises at least one chirally controlled center which is a rip linkage phosphorus of a phosphorothioate linkage. In some embodiments, the base sequence of a provided oligonucleotide is the base sequence of an example oligonucleotide or another sequence di sclosed herein, the oligonucleotide has a length of up to 40 bases, and a pattern of backbone chiral centers comprises at least one chirally controlled center which is a rip linkage phosphorus of a phosphorothioate linkage. In some embodiments, the base sequence of a provided oligonucleotide comprises at least 15 contiguous bases of any example oligonucleotides or another sequence disclosed herein, the oligonucleotide has a length of up to 30, 40, or 50 bases, and a pattern of backbone chiral centers comprises at least one chirally controlled center which is a rip linkage phosphorus of a phosphorothioate linkage .

[0051] In some embodiments, a mismatch is a difference between the base sequence or length when two sequences are maximally aligned and compared. As a non-limiting example, a mismatch is counted if a difference exists between the base at a particular location in one sequence and the base at the corresponding position in another sequence. Thus, a mismatch is counted, for example, if a position in one sequence has a particular base (e.g., A), and the corresponding position on the other sequence has a different base (e.g., G, C or U). A mismatch is also counted, e.g., if a position in one sequence has a base (e.g., A), and the corresponding position on the other sequence has no base (e.g., that position is an abasic nucleotide which comprises a phosphate-sugar backbone but no base) or that position is skipped. A single-stranded nick in either sequence (or in the sense or antisense strand) may not be counted as mismatch, for example, no mismatch would be counted if one sequence comprises the sequence 5’-AG S’, but the other sequence comprises the sequence 5’ -AG-3’ with a single-stranded nick between the A and the G. A base modification is generally not considered a mismatch, for example, if one sequence comprises a C, and the other sequence comprises a modified C (e.g., with a ^-modification) at the same position, no mismatch may be counted.

[0052] In some embodiments, oligonucleotides of a particular type are chemically identical in that they have the same base sequence (including length), the same pattern of chemical modifications to sugar and base moieties, the same pattern of backbone linkages (e.g., pattern of natural phosphate linkages, phosphorothioate linkages, phosphorothioate triester linkages, non-negative ly charged linkages, and combinations thereof), the same pattern of backbone chiral centers (e.g., pattern of stereochemistry ' (i?p/rip) of chiral intemucleotidic linkages), and the same pattern of backbone phosphorus modifications (e.g., pattern of modifications on the intemucleotidic phosphorus atom, such as -S , and -L-R 1 of formula I).

[0053] In some embodiments, the present disclosure provides chirally controlled oligonucleotide compositions of oligonucleotides comprising multiple (e.g., more than 5, 6, 7, 8, 9, or 10) intemucleotidic linkages, and particularly for oligonucleotides comprising multiple (e.g., more than 5, 6, 7, 8, 9, or 10) chiral intemucleotidic linkages, wherein the oligonucleotides comprise at least one, and in some embodiments, more than 5, 6, 7, 8, 9, or 10 chirally controlled intemucleotidic linkages. In some embodiments, in a chirally controlled composition of oligonucleotides each chiral intemucleotidic linkage of the oligonucleotides is independently a chirally controlled intemucleotidic linkage. In some embodiments, in a stereorandom or racemic composition of oligonucleotides, each chiral intemucleotidic linkage is formed with less than 90: 10, 95:5, 96:4, 97:3, or 98:2 diastereoselectivity. In some embodiments, in a stereoselective or chirally controlled composition of oligonucleotides, each chirally controlled intemucleotidic linkage of the oligonucleotides independently has a diastereopurity of at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% at its chiral linkage phosphorus (either Rp orS'p). Among other things, the present disclosure pro vides technologies to prepare oligonucleotides of high diastereopurity. In some embodiments, diastereopurity of a chiral intemucleotidic linkage in an oligonucleotide may be measured through a model reaction, e.g. formation of a dimer under essentially the same or comparable conditions wherein the dimer has the same intemucleotidic linkage as the chiral intemucleotidic linkage, the 5’-nucleoside of the dimer is the same as the nucleoside to the 5’-end of the chiral intemucleotidic linkage, and the 3’-nucleoside of the dimer is the same as the nucleoside to the 3’- end of the chiral intemucleotidic linkage.

[0054] As described herein, provided compositions and methods are capable of altering splicing of transcripts. In some embodiments, provided compositions and methods provide improved splicing patterns of transcripts compared to reference conditions selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof. An improvement can be an improvement of any desired biological functions. In some embodiments, for example, in DMD, an improvement is production of an mRNA from winch a dystrophin protein with improved biological activities is produced.

[0055] In some embodiments, the present disclosure provides a method for altering splicing of a target transcript, comprising administering a provided composition, wherein the splicing of the target transcript is altered relative to reference conditions selected from the group consisting of absence of tire composition, presence of a reference composition, and combinations thereof.

[0056] In some embodiments, the present disclosure provides a method of generating a set of spliced products from a target transcript, the method comprising steps of:

contacting a splicing system containing the target transcript with an oligonucleotide composition comprising a plurality of oligonucleotides (e.g., a provided chirally controlled oligonucleotide composition), in an amount, for a time, and under conditions sufficient for a set of spliced products to be generated that is different from a set generated under reference conditions selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof.

[0057] In some embodiments, the present disclosure provides a method for treating or preventing a disease, comprising administering to a subject an oligonucleotide composition described herein.

[0058] In some embodiments, the present disclosure provides a method for treating or preventing a disease, comprising administering to a subject an oligonucleotide composition comprising a plurality of oligonucleotides, which:

1) have a common base sequence complementary to a target sequence a transcript: and

2) comprise one or more modified sugar moieties and modified internucleotidic linkages, the oligonucleotide composition being characterized in that, when it is contacted with the transcript in a transcript splicing system, splicing of the transcript is altered relative to that observed under reference conditions selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof.

[0059] In some embodiments, the present disclosure provides a method for treating or preventing a disease, comprising administering to a subject a chirally controlled oligonucleotide composition comprising a plurality of oligonucleotides of a particular oligonucleotide type defined by:

1) base sequence;

2) pattern of backbone linkages;

3) pattern of backbone chiral centers; and

4) pattern of backbone phosphorus modifications,

which composition is chirally controlled and it is enriched, relative to a substantially racemic preparation of oligonucleotides having the same base sequence, for oligonucleotides of the particular oligonucleotide type, wherein:

the oligonucleotide composition being characterized in that, when it is contacted with the transcript in a transcript splicing system, splicing of the transcript is altered relative to that observed under reference conditions selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof.

[0060] In some embodiments, a disease is one in which, after administering a provided composition, one or more spliced transcripts repair, restore or introduce a new beneficial function. For example, in DMD, after skipping one or more exons, fimctions of dystrophin can be restored, or partially restored, through a truncated but (at least partially) active version. In some embodiments, a disease is one in which, after administering a provided composition, one or more spliced transcripts repair, a gene is effectively knockdown by altering splicing of the gene transcript.

[0061] In some embodiments, a disease is muscular dystrophy, including but not limited to

Duchenne (Duchenne’s) muscular dystrophy (DMD) and Becker (Becker's) muscular dystrophy (BMD).

[0062] In some embodiments, a transcript is of Dystrophin gene or a variant thereof.

[0063] In some embodiments, the present disclosure provides a method of treating a disease by administering a composition comprising a plurality of oligonucleotides sharing a common base sequence comprising a nucleotide sequence, which nucleotide sequence is complementary ' to a target sequence in the target transcript,

the improvement that comprises using as the oligonucleotide composition a chirally controlled oligonucleotide composition characterized in that, when it is contacted with the transcript in a transcript splicing system, splicing of the transcript is altered relative to that observed under reference conditions selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof.

[0064] In some embodiments, a common sequence comprises a sequence (or at least 15 base long portion thereof) of any oligonucleotide in Table At.

[0065] In some embodiments, the present disclosure provides a method of administering an oligonucleotide composition comprising a plurality of oligonucleotides having a common nucleotide sequence, the improvement that comprises:

administering an oligonucleotide composition comprising the plurality of oligonucleotides each of which independently comprises one or more negatively charged intemucleotidic linkages and one or more non-negatively charged intemucleotidic linkages, wherein the oligonucleotide composition is optionally chirally controlled.

[0066] In some embodiments, the present disclosure provides a method of administering an oligonucleotide composition comprising a plurality of oligonucleotides having a common nucleotide sequence, the improvement that comprises:

administering an oligonucleotide composition comprising the plurality of oligonucleotides that is chirally controlled and that is characterized by reduced toxicity ' relative to a reference oligonucleotide composition of the same common nucleotide sequence.

100671 In some embodiments, the present disclosure provides a method of administering an oligonucleotide composition comprising a plurality of oligonucleotides having a common nucleotide sequence, the improvement that comprises:

administering an oligonucleotide composition in which each oligonucleotide in the plurality includes one or more natural phosphate linkages and one or more modified phosphate linkages;

wherein tire oligonucleotide composition is characterized by reduced toxicity when tested in at least one assay that is observed with an otherwise comparable reference composition whose oligonucleotides do not comprise natural phosphate linkages.

[0068] In some embodiments, oligonucleotides can elicit proinflammatory responses. In some embodiments, the present disclosure provides compositions and methods for reducing inflammation. In some embodiments, the present disclosure provides compositions and methods for reducing proinflammatory responses. In some embodiments, the present disclosure provides methods for reducing injection site inflammation using provided compositions. In some embodiments, the present disclosure provides methods for reducing drug-induced vascular injur' using provided compositions.

100691 In some embodiments, the present disclosure provides a method, comprising administering a composition comprising a plurality of oligonucleotides of a common base sequence, which composition displays reduced injection site inflammation as compared with a reference composition comprising a plurality of oligonucleotides, each of which also has the common base sequence , but which differs structurally from the oligonucleotides of the plurality in that:

individual oligonucleotides within the reference plurality differ from one another in

stereochemical structure; and/or

at least some oligonucleotides within the reference plurality have a structure different from a structure represented by the plurality of oligonucleotides of the composition; and/or

at least some oligonucleotides within tire reference plurality do not comprise a wing region and a core region.

[0070] In some embodiments, the present disclosure provides a method, comprising administering a composition comprising a plurality of oligonucleotides of a common base sequence, which composition displays altered protein binding as compared with a reference composition comprising a plurality of oligonucleotides, each of which also has the common base sequence but which differs structurally from the oligonucleotides of the plurality in that:

individual oligonucleotides within the reference plurality differ from one another in

stereochemical structure; and/or

at least some oligonucleotides within the reference plurality have a structure different from a structure represented by the plurality of oligonucleotides of the composition; and/or

at least some oligonucleotides within the reference plurality do not comprise a wing region and a core region.

[0071] In some embodiments, the present disclosure provides a method of administering an oligonucleotide composition comprising a plurality of oligonucleotides having a common nucleotide sequence, the improvement that comprises:

administering an oligonucleotide composition comprising a plurality of oligonucleotides that is characterized by altered protein binding relative to a reference oligonucleotide composition of the same common nucleotide sequence.

[0072] In some embodiments, the present disclosure provides a method comprising administering a composition comprising a plurality of oligonucleotides of a common base sequence, which composition displays improved delivery as compared with a reference composition comprising a reference plurality of oligonucleotides, each of which also has the common base sequence but which differs structurally from the oligonucleotides of the plurality in that:

individual oligonucleotides within the reference plurality differ from one another in

stereochemical structure; and/or

at least some oligonucleotides within the reference plurality have a structure different from a structure represented by the plurality of oligonucleotides of the composition; and/or

at least some oligonucleotides within the reference plurality do not comprise a wing region and a core region.

[0073] hi some embodiments, the present disclosure provides a method of administering an oligonucleotide composition comprising a plurality of oligonucleotides having a common nucleotide sequence, the improvement that comprises:

administering an oligonucleotide comprising a plurality of oligonucleotides that is characterized by improved delivery relati ve to a reference oligonucleotide composition of the same common nucleotide sequence.

[0074] In some embodiments, the present disclosure provides a composition comprising any oligonucleotide disclosed herein. In some embodiments, the present disclosure provides a composition comprising any chiraliy controlled oligonucleotide disclosed herein.

[0075] In some embodiments, the present disclosure provides a composition comprising an oligonucleotide disclosed herein winch is capable of mediating skipping of Dystrophin exon 45 In some embodiments, the present disclosure provides a composition comprising an oligonucleotide disclosed herein which is capable of mediating skipping of Dystrophin exon 51. In some embodiments, the present disclosure provides a composition comprising an oligonucleotide disclosed herein which is capable of mediating skipping of Dystrophin exon 53 In some embodiments, the present disclosure provides a composition comprising an oligonucleotide(s) disclosed herein which is capable of mediating skipping of multiple Dystrophin exons. In some embodiments, such a composition is a chiraliy controlled oligonucleotide composition.

[0076] In some embodiments, the present disclosure pertains to an oligonucleotide or an oligonucleotide composition capable of mediating skipping of a DMD exon or multiple DMD exons. In some embodiments, a DMD exon is exon 51. In some embodiments, a DMD exon is exon 53. In some embodiments, a DMD exon is exon 45. In some embodiments, the present disclosure pertains to an oligonucleotide composition capable of mediating skipping of a DMD exon 53, wherein the oligonucleotide composition comprises at least one chirally controlled intemucleotidic linkage.

100771 In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of DMD exon 45. In some embodiments, the present disclosure pertains to an oligonucleotide composition capable of mediating skipping of DMD exon 45, wherein the oligonucleotide composition comprises at least one chirally controlled intemucleotidic linkage and comprises at least one non-negatively charged intemucleotidic linkage. In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of DMD exon 45 and comprises at least one non-negatively charged intemucleotidic linkage.

[0078] In some embodiments, the present disclosure pertains to an oligonucleotide composition capable of mediating skipping of DMD exon 45, wherein the oligonucleotide composition comprises at least one non-negatively charged intemucleotidic linkage. In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein tire oligonucleotide is capable of mediating skipping of DMD exon 45 and comprises at least one non-negatively charged intemucleotidic linkage.

[0079] In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of DMD exon 51. In some embodiments, the present disclosure pertains to an oligonucleotide composition capable of mediating skipping of DMD exon 51, wherein the oligonucleotide composition comprises at least one chirally controlled intemucleotidic linkage and comprises at least one non-negatively charged intemucleotidic linkage. In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of DMD exon 51 and comprises at least one non-negatively charged intemucleotidic linkage.

[0080] In some embodiments, the present disclosure pertains to an oligonucleotide composition capable of mediating skipping of DMD exon 51, wherein the oligonucleotide composition comprises at least one non-negatively charged intemucleotidic linkage. In some embodiments, the present disclosure perta s to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of DMD exon 51 and comprises at least one non-negatively charged intemucleotidic linkage. [0081] In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of DMD exon 53 In some embodiments, the present disclosure pertains to an oligonucleotide composition capable of mediating skipping of DMD exon 53, wherein the oligonucleotide composition comprises at least one chirally controlled mtemucleotidic linkage and comprises at least one non-negatively charged intemucleotidic linkage. In some embodim nts, the present disclosure pertains to a chirally controlled oligonucleotide composition, wiierein the oligonucleotide is capable of mediating skipping of DMD exon 53 and comprises at least one non-negatively charged intemucleotidic linkage.

[0082] In some embodiments, the present disclosure pertains to an oligonucleotide composition capable of mediating skipping of DMD exon 53, wherein the oligonucleotide composition comprises at least one non-negatively charged intemucleotidic linkage. In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of DMD exon 53 and comprises at least one non-negatively charged intemucleotidic linkage.

100831 In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of multiple DMD exons. In some embodiments, the present disclosure pertains to an oligonucleotide composition capable of mediating skipping of multiple DMD exons, wherein the oligonucleotide composition comprises at least one chirally controlled intemucleotidic linkage and comprises at least one non- negatively charged mtemucleotidic linkage hr some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of multiple DMD exons and comprises at least one non-negatively charged intemucleotidic linkage.

[0084] In some embodiments, the present disclosure pertains to an oligonucleotide composition capable of mediating skipping of a DMD exon, wiierein the oligonucleotide composition comprises at least one non-negatively charged intemucleotidic linkage. In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of a DMD exon and comprises at least one non-negatively charged intemucleotidic linkage. In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of multiple DMD exons. In some embodiments, the present disclosure pertains to an oligonucleotide composition capable of mediating skipping of multiple DMD exons, wherein the oligonucleotide composition comprises at least one chirally controlled intemucleotidic linkage and comprises at least one non-negatively charged internucleotidic linkage. In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of multiple DMD exons and comprises at least one non-negatively charged internucleotidic linkage. In some embodiments, a DMD exon is any DMD exon disclosed herein, including but not limited to exon 45, exon 51, exon 52, exon 53, exon 55, exon 56, and exon 57.

100851 In some embodiments, the present disclosure pertains to an oligonucleotide composition capable of mediating skipping of multiple DMD exons, wherein the oligonucleotide composition comprises at least one non-negatively charged internucleotidic linkage. In some embodiments, the present disclosure pertains to a chirally controlled oligonucleotide composition, wherein the oligonucleotide is capable of mediating skipping of multiple DMD exons and comprises at least one non- negatively charged internucleotidic linkage.

[0086] In some embodiments, the present disclosure provides a chirally controlled composition of an oligonucleotide capable of mediating skipping of Dystrophin exon 51. In some embodiments, the present disclosure provides a chirally controlled composition of an oligonucleotide capable of mediating skipping of Dystrophin exon 51 and disclosed herein.

[0087] In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which is, compri ses, or comprises a 15-base portion of the base sequence of UCAAGGAAGAUGGCAUUUCU, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally chirally controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which is UCAAGGAAGAUGGCAUUUCU, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally chirally controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which comprises UCAAGGAAGAUGGCAUUUCU, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally chirally controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which comprises a 15- base portion of the base sequence of UCAAGGAAGAUGGCAUUUCU, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally chirally controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which is, comprises, or comprises a 15-base portion of any of: UCAAGGAAGAUGGCAUUUCU, UCAAGGAAGAUGGCAUUUC, UCAAGGAAGAUGGCAIJUU, UCAAGGAAGAUGGCAUU, UCAAGGAAGAUGGCAU, UCAAGGAAGAUGGCA,

CAAGGAAGAUGGCAUUUCU, AAGGAAGAUGGCAUUUCU, AGGAAGAUGGCAUUUCU, GGAAGAUGGCAUUUCU, GAAGAUGGCAUUUCU, CAAGGAAGAUGGCAUUUC,

C AAGGAAGA U GGC AUUU , AAGGAAGAUGGCAU U UC, AAGGAAGAUGGCAU U U,

AGGAAGAUGGCAUUU, or AAGGAAGAUGGCAUU, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally chiraliy controlled.

[0088] In some embodiments, the present disclosure provides a chiraliy controlled composition of an oligonucleotide capable of mediating skipping of Dystrophin exon 53. In some embodiments, the present disclosure provides a chiraliy controlled composition of an oligonucleotide capable of mediating skipping of Dystrophin exon 53 and disclosed herein

100891 In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9517. in some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9519. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9521. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9524. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV- 9714. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9715. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9747. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9748. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9749. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV- 9897. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9898. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9899. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9900. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-9906. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV- 9912. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV- 10670. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV- 10671. In some embodiments, the present disclosure provides a chiraliy controlled composition of oligonucleotide WV-10672.

[0090] In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which is, compri ses, or comprises a 15-base portion of the base sequence of CUCCGGUUCUGAAGGUGUUC, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally chiraliy controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which is CUCCGGUUCUGAAGGUGUUC, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally ehirally controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which comprises CUCCGGUUCUGAAGGUGUUC, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally ehirally controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which is, comprises, or comprises a 15-base portion of CUCCGGUUCUGAAGGUGUUC, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally ehirally controlled. In some embodiments, the present disclosure pro vides a composition of an oligonucleotide having a base sequence which is or comprises CUCCGGUUCUGAAGGUGUUCC, UCCGGUUCUGAAGGUGUUC, U CC GGUU CUGA AGGU GIJIJ C, CCGGUUCUGAAGGUGUUC, CGGUUCUGAAGGUGUUC,

GGUUCUGAAGGUGUUC, GUUCUGAAGGUGUUC, CUCCGGUUCUGAAGGUGUU,

CUCCGGUU CU GAAGGU GU CUCCGGUUCUGAAGGUG, CU CCGGUUCUGAAGGU , CUCCGGUU CUGAAGG, UCCGGUUCUGAAGGUGUU, CCGGUUCUGAAGGUGUU,

U CCGGUU CUG A AGGU GU, CCGGUUCUGAAGGUGU, U CCGGUU CU G A AGGUG,

CGGUUCUGAAGGUGU, UCCGGUUCUGAAGGU, CCGGUUCUGAAGGUG,

CGGUUCUGAAGGUGUU,

UCCGGUUCUGAAGGUGUUC,UCCGGUUCUGAAGGUG,UCCGGUUCUGAAGGU

CGGUUCUGAAGGUGUU, GGUUCUGAAGGUGUU, or GGUUCUGAAGGUGUU, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally ehirally controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which is, comprises, or comprises a 15-base portion of the base sequence of UUCUGAAGGUGUUCUUGUAC, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally ehirally controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which is UUCUGAAGGUGUUCUUGUAC, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally ehirally controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which comprises UUCUGAAGGUGUUCUUGUAC, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally ehirally controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which comprises a 15- base portion of the base sequence of UUCUGAAGGUGUUCUUGUAC, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally ehirally controlled. In some embodiments, the present disclosure provides a composition of an oligonucleotide having a base sequence which is or comprises UUCUGAAGGUGUUCUUGUAC, UCUGAAGGUGUUCUUGUAC, CUGAAGGUGUUCUUGUAC, UGAAGGUGUUCUUGUAC, GAAGGUGUUCUUGUAC, AAGGUGUUCUUGUAC, UUCUGAAGGUGUUCUUGUA, UUCUGAAGGUGUUCUUGU, UUCUGAAGGUGUUCUUG, UUCUGAAGGUGUUCUU, U U CU GAAGGU GU UCU, UCUGAAGGUGUUCUUGUA, UCUGAAGGUGUUCUUGU,

UCUGAAGGUGUUCUUG, UCUGAAGGUGUUCUU, CUGAAGGUGUUCUUGUA,

CUGAAGGUGUUCUUGU, CUGAAGGUGUUCUUG, UGAAGGUGUUCUUGU, or UGAAGGUGUUCUUGUA, wherein each U can be optionally and independently replaced by T, and wherein the composition is optionally clnraily controlled.

[0091] In some embodiments, the present disclosure provides a chiraliy controlled oligonucleotide composition of an oligonucleotide selected from any of the Tables. In some embodiments, the present disclosure provides a chiraliy controlled oligonucleotide composition of an oligonucleotide selected from any of the Tables, wherein the oligonucleotide is conjugated to a lipid or a targeting moiety.

[0092] In some embodiments, an oligonucleotide is at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,

20 bases long, and optionally no more than 25, 30, 35, 40, 45, 50, 55, or 60 bases long. In some embodiments, an oligonucleotide is no more than 25 bases long. In some embodiments, an oligonucleotide is no more than 30 bases long. In some embodiments, an oligonucleotide is no more than 35 bases long. In some embodiments, an oligonucleotide is no more than 40 bases long. In some embodiments, an oligonucleotide is no more than 45 bases long. In some embodiments, an oligonucleotide is no more than 50 bases long. In some embodiments, an oligonucleotide is no more than 55 bases long. In some embodiments, an oligonucleotide is no more than 60 bases long. In some embodiments, each base is independently optionally substituted A, T, C, G, or U, or an optionally substituted tautomer of A, T, C, G, or U

[0093] In some embodiments, provided oligonucleotides comprise additional chemical moieties besides their oligonucleotide chains (oligonucleotide backbones and bases), e.g., lipid moieties, targeting moieties, etc. In some embodiments, a lipid is a fatty add. In some embodiments, an oligonucleotide is conjugated to a fatty acid. In some embodiments, a fatty acid comprises 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more carbon atoms.

[0094] In some embodiments, a lipid is stearic acid or turbinaric acid. In some embodiments, a lipid is stearic acid acid. In some embodiments, a lipid is turbinaric acid.

[0095] In some embodiments, a lipid comprises an optionally substituted, Cio-Cgo, Cio~C o, or

C -C saturated or partially unsaturated aliphatic group, wherein one or more methylene units are optionally and independently replaced by Ci-Cg alkylene, Cr-C 6 alkenylene, , a Ci-C 6 heteroaliphatic moiety, -C(R') 2 -, -Cy-, -0-, -S-, -S---S---, -N(R')-, -C(O)-, -C(S)-, --C(NR')-, - C(0)N(R') , -N(R')C(0)N(R')-, N(R ' )( ((> . -N(R')C(0)0-, -OC(0)N(R')-, -S(O)-, -S(0) 2- , -S(0) 2 N(R')-, -N(R')S(0) 2 -, -SC(0)-, -C(0)S-, -0C(0)-, and—C(0)0— , wherein each variable is independently as defined and described herein.

[0096] In some embodiments, a lipid is selected from the group consisting of: lauric acid, myristic acid, palmitic acid, stearic acid, oleic acid, linoleic acid, alpha-1 inolenic acid, gamma-linolemc acid, docosahexaenoic acid (DHA or cis-DHA), turbinaric acid and dilinoleyl.

100971 In some embodiments, a lipid is conjugated to an oligonucleotide chain, optionally through one or more linker moieties. In some embodiments, a lipid is not conjugated to an ol igonucleotide chain .

In some embodiments, a provided oligonucleotide is conjugated, optionally through a linker, to a chemical moiety, e.g., a lipid moiety, a peptide moiety, a targeting moiety, a carbohydrate moiety, a sulfonamide moiety, an antibody or a fragment thereof. In some embodiments, a provided compound, e.g., an oligonucleotide, has the structure of:

A c -[-L l D -(R LD ) a ] b , . | i . t R’X ,. [<AVL M ] b- R D , {A%-1, M -(A%, or (A c ) a --L M --(R D ) b , or a slat thereof, wherein:

A c is an oligonucleotide chain (e.g., H-A c , [H] a -A c or [H] b -A c is an oligonucleotide);

a is 1 -1000;

b is 1-1000;

each of IA D and L M is independently a linker moiety;

R LD is a lipid moiety; and

each R D is independently a tipid moiety or a targeting moiety.

In some embodiments, a provided compound, e.g., an oligonucleotide, has the structure of:

or a salt thereof, wherein:

A c is an oligonucleotide chain (e.g., 1 1 A . is an oligonucleotide);

a is 1-1000;

b is 1-1000;

each R D is independently R l :i , R CD or R [D :

R CD is an optionally substituted, linear or branched group selected from a C MOO aliphatic group and a C MOO heteroaliphatic group having 1-30 heteroatoms, wherein one or more methylene units are optionally and independently replaced with Ci -6 alkylene, C 3-6 alkenylene, cº c 5 a bivalent C -C 6 heteroaliphatic group having 1 -5 heteroatoms, -C(R’) 2 -, -Cy-, 0 . -S-, -S-S-, -N(R’)-, -C(O)-, C(S) . -C(NR’)- -C(0)N(R’)- -N(R’)C(0)N(R’)-, N( R )( (())() . S(O) . S(0) 2 .

-S(0) 2 N(R’)- HOjS . -C(0)0- -P(0)(0R’)-, -P(0)(SR’)- -P(0)(R’)- -P(0)(NR’)- -P(S)(OR’)-, -P(S)(SR’) , -P(S)(R )-, -P(S)(NR’)-, -P(R’)-, Pi OR ) . Pi SR ) . -P(NR’)- -P(OR’)[B(R’) 3 ]-, OPiOKOR ) . -0P(0)(SR’)0- -0P(0)(R’)0-, -0P(0)(NR’)0-, OPi OR K) . -0P(SR’)0- 0P( NR )0 - -GP(R’)Q-, or 0P(0R )| B( R ) , |0 : and one or more CH or carbon atoms are optionally and independently replaced with Cy L ;

R LD is an optionally substituted, linear or branched C H oe aliphatic group wherein one or more methylene units are optionally and independently replaced with C s 6 alkylene, Ci_ 6 alkenylene,

, Ci R ) - . -Cy-, -0-, S . -S-S-, -N(R’)-, UO) . ( (S) . C( N R ) . ( (O)N( R ) .

-N(R’)C(0)N(R’)-, N(R ) (0)0 . S(O) . -S(0) 2 - S(O) · N ( R ) . CiO sS . ( (OK) .

P(OKOR ' ) . PiOKSin . ihonm . -P<O)(NR’)-, P(S KOR ) . PC SMS K ) .. P(SK R ' ) .

-P(S)(NR’)-, -P(R’)-, -P(OR’)-, -P(SR’)-, -P(NR’)-, -P(OR’)[B(R’) 3 ]-, -0P(0)(0R’)0-

-0P(0)(SR’)0-, -0P(0)(R )0-, -0P(0)(NR’)0-, -0P(0R’)0- C)P( SR )0 . -0P(NR’)0- -OP(R’)0-, or -OP(OR )[B(R’) 3 ]{)-; and one or more CH or carbon atoms are optionally and independently replaced with Cy L ;

R* 15 is a targeting moiety;

each of L LD and L M is independently a covalent bond, or a bivalent or multivalent, optionally substituted, linear or branched group selected from a C MOO aliphatic group and a Cnoo heteroaliphatic group having 1-30 heteroatoms, wherein one or more methylene units are optionally and independently replaced with C-,_ 6 alkylene, Ci- 6 alkenylene, cºc , a bivalent C --C 6 heteroaliphatic group having 1- 5 heteroatoms, -C(R , ) 2 -, -Cy-, -0-, -S-, -S-S-, -N(R’)-, -C(O)-, -C(S)-, -C(NR’)-,

-C(0)N(R’)-, -N(R’)C(0)N(R’)- -N(R’)C(0)0- S(O) . -S(0) 2 -, -S(0) 2 N(R )-, ( (O)S .

C (0)0 . -P(0)(0R’)- -P(0)(SR’)-, P(O)i R ) . -P(0)(NR’)- P( S)(OR ) . -P(S)(SR’)- -P(S)(R’)- -P(S)(NR’)- -P(R’)-, -P(OR’)- Pi SR i . P( N R ) . P( R )| B(R ) i .

-0P(0)(0R’)0- 0R(0)(SR )0 . -0P(0)(R’)0-, -0P(0)(NR’)0- -0P(0R’)0-, -0P(SR’)0- -0P(NR’)0-, -0P(R’)0 , or -OP OR’jfBi ^^JO-; and one or more CH or carbon atoms are optionally and independently replaced with Cv ^ ;

each -Cy- is independently an optionally substituted bivalent group selected from a C 3-2 o cycloaliphatic ring, a C 6-2 o aryl ring, a 5-2.0 membered heteroaryl ring having 1 -10 heteroatoms, and a 3- 20 membered heterocyclyl ring having 1-10 heteroatoms;

each Cy L is independently an optionally substituted tri valent or tetravalent group selected from a C 3- 2o cycloaliphatic ring, a C 6-2 o aiyl ring, a 5-20 membered heteroaryl ring having 1-10 heteroatoms, and a 3-20 membered heterocyclyl ring having 1-10 heteroatoms; each R’ is independently ---R, -C(0)R, -C(0)OR, or -S(0) 2 R; and

each R is independently -H, or an optionally substituted group selected from C ]-30 aliphatic, Ci- 30 heteroaliphatic having 1-10 heteroatoms, C 6.30 aryl, C 6-3 o arylaliphatic, C 6~3 o arylheteroaliphatic having 1 - 10 heteroatoms, 5-30 membered heteroaryl having 1-10 heteroatoms, and 3-30 membered heterocyclyl having 1-10 heteroatoms, or

two R groups are optionally and independently taken together to form a covalent bond, or two or more R groups on the same atom are optionally and independently taken together with the atom to form an optionally substituted, 3-30 membered monocyclic, bicyc!ic or polycyclic ring having, in addition to the atom, 0-10 heteroatoms, or

two or more R groups on two or more atoms are optionally and independently taken together with their intervening atoms to form an optionally substituted, 3-30 membered monocyclic, bicyclic or polycyclic ring having, in addition to the intervening atoms, 0-10 heteroatoms.

j 00100! In some embodiments, the present disclosure provides an oligonucleotide composition comprising a plurality of oligonucleotides each having the structure of:

A c -[-L l D -(R LD ) 3 ] b , A c -[-L M -(R D ) a ] b , [<AVL M ] b -R D , (A T 1." <A or (A c ) a -L M -(R D ) b , or a salt thereof.

100101 In some embodiments, [H] b -Ac (wherein b is 1-1000) is an oligonucleotide of any one of the Tables. In some embodiments, [H] b -Ac is an oligonucleotide of Table AI .

[00102] In some embodiments, a is 1 -100. In some embodiments, a is 1-50. In some embodiments, a is 1-40. In some embodiments, a is 1-30. In some embodiments, a is 1-20. In some embodiments, a is 1 -15. In some embodiments, a is 1 -10. In some embodiments, a is 1 -9. In some embodiments, a is 1-8. In some embodiments, a is 1-7. In some embodiments, a is 1-6. In some embodiments, a is 1-5. In some embodiments, a is 1-4. In some embodiments, a is 1-3. In some embodiments, a is 1 -2. In some embodiments, a is 1. In some embodiments, a is 2. In some embodiments, a is 3. In some embodiments, a is 4. In some embodiments, a is 5. In some embodiments, a is 6. hi some embodiments, a is 7. In some embodiments, a is 8. hi some embodiments, a is 9. In some embodiments, a is 10. In some embodiments, a is more than 10. In some embodiments, b is 1-100. In some embodiments, b is 1 -50. In some embodiments, b is 1-40. In some embodiments, b is 1-30. In some embodiments, b is 1-20. In some embodiments, b is 1-15. In some embodiments, b is 1-10. In some embodiments, b is 1-9. In some embodiments, b is 1-8. In some embodiments, b is 1-7. In some embodiments, b is 1-6. In some embodiments, b is 1-5. In some embodiments, b is 1-4. In some embodiments, b is 1-3. In some embodiments, b is 1-2. In some embodiments, b is 1. In some embodiments, b is 2. In some embodiments, b is 3. In some embodiments, b is 4. In some embodiments, b is 5. In some embodiments, b is 6. In some embodiments, b is 7. In some embodiments, b is 8. In some embodiments, b is 9. In some embodiments, b is 10. In some embodiments, b is more than 10. In some embodiments, an oligonucleotide has the structure of A'-L^-R 10 . In some embodiments, A c is conjugated through one or more of its sugar, base and/or intemucleotidic linkage moieties. In some embodiments, A c is conjugated through its 5’ -OH (5’-0-). In some embodiments, A c is conjugated through its 3’-QH (3 -Q-). In some embodiments, before conjugation, A C -(H)«, (b is an integer of 1-1000 depending on valency of A c ) is an oligonucleotide as described herein, for example, one of those described in any one of the Tables. In some embodiments, L M is -L-. In some embodiments, L M comprises a phosphorothioate group. In some embodiments, L M is -C(0)NH-(CH 2 ) 6 _ 0P(=0)(S-)-0-. In some embodiments, the -C(0)NH end is connected to R lD , and the O end is connected to the oligonucleotide, e.g , through 5’- or 3’-end. In some embodiments, R LD is optionally substituted C [0 , C 15 , C- 6 , C 7 , Cis, C 9 , C 2 o, C 2 ·, C 22 , C 23 , C 2 4, or C 25 to C 20 , C 21 , C 22 , C 23 , C 24 , C 25 , C 26 , C 27 , C 28 , C 29 , C 30 , C 35 , C 40 , C 45 , C 50 , C 60 , C 70 , or Cgo aliphatic. In some embodiments, R lD is optionally substituted Cio-so aliphatic. In some embodiments, R LD is optionally substituted C 20-g o aliphatic. In some embodiments, R LD is optionally substituted CV70 aliphatic. In some embodiments, R Ll> is optionally substituted C 20-7 o aliphatic. In some embodiments, R LD is optionally substituted C10-60 aliphatic. In some embodiments, R LD is optionally substituted C 20 6 o aliphatic. In some embodiments, R LD is optionally substituted C 10-50 aliphatic. In some embodiments, R LD is optionally substituted C 20 -5o aliphatic. In some embodiments, R LD is optionally substituted Ci 0- o aliphatic. In some embodiments, R L J is optionally substituted C 2 o -4 o aliphatic. In some embodiments, R LD is optionally substituted C 10-30 aliphatic. In some embodiments, R LD is optionally substituted C 20-3 o aliphatic. In some embodiments, R lD is unsubstituted C10, C i5 , Ci 6 , Cn, C i8 , C 19 , C 20 , C 21 , C 22 , C 23 , C 24 , or C 25 to C 20 , C 21 , C 22 , C 23 , C 24 , C 25 , C 25 , C 27 , C 28 , C 29 , C 30 , C 35 , C 40 , C 45 , C 50 , Coo, C 7 o, or C 80 aliphatic, In some embodiments, R LD is unsubstituted C JO-SO aliphatic. In some embodiments, R LD is unsubstituted C 20-8 o aliphatic. In some embodiments, R LD is unsubstituted C. 0-70 aliphatic. In some embodiments, R LD is unsubstituted C 20-7 o aliphatic. In some embodim nts, R LD is unsubstituted Cio 6o aliphatic. In some embodiments, R lJ3 is unsubstituted C 20- 6o aliphatic. In some embodiments, R LD is unsubstituted C 10-50 aliphatic. In some embodiments, R lD is unsubstituted C 20- so aliphatic. In some embodiments, R LD is unsubstituted C KMO aliphatic. In some embodiments, R LD is unsubstituted C 20.4 o aliphatic. In some embodiments, R lD is unsubstituted C 10- 3o aliphatic. In some embodiments, R LD is unsubstituted C 20.3 o aliphatic,

j00103j In some embodiments, incorporation of a lipid moiety into an oligonucleotide improves at least one property of the oligonucleotide compared to an otherwise identical oligonucleotide without the lipid moiety. In some embodiments, improved properties include increased activity (e.g., increased ability to induce desirable skipping of a deleterious exon), decreased toxicity, and/or improved distribution to a tissue. In some embodiments, a tissue is muscle tissue. In some embodiments, a tissue is skeletal muscle, gastrocnemius, triceps, heart or diaphragm. In some embodiments, improved properties include reduced hTLR9 agonist activity. In some embodiments, improved properties include hTLR9 antagonist activity. In some embodiments, improved properties include increased hTLR9 antagonist activity.

[00104] In some embodiments, an oligonucleotide or oligonucleotide composition is: a DMD oligonucleotide or oligonucleotide composition; an oligonucleotide or oligonucleotide composition comprising a non-negatively charged intemucieotidic linkage; or a DMD oligonucleotide comprising a non-negatively charged intemucieotidic linkage.

jOO!OSj In some embodiments, the present disclosure pertains to a composition comprising an a

DMD oligonucleotide comprising at least one chirally controlled phosphorothioate intemucieotidic linkage in the Rp or Sp configuration, at least one natural phosphate intemucieotidic linkage, and at least one non-negatively charged intemucieotidic linkage. In some embodiments, the present disclosure pertains to a composition comprising an a DMD oligonucleotide comprising at least one phosphorothioate intemucieotidic linkage, at least one natural phosphate intemucieotidic linkage, and at least one non- negatively charged intemucieotidic linkage. In some embodiments, the present disclosure pertains to a composition comprising an a DMD oligonucleotide comprising at least one phosphorothioate intemucieotidic linkage, at least one natural phosphate intemucieotidic linkage, and at least one chirally controlled non-negatively charged intemucieotidic linkage. In some embodiments, the present disclosure pertains to a composition comprising an a DMD oligonucleotide comprising at least one chirally controlled phosphorothioate intemucieotidic linkage in the Rp or Sp configuration, at least one natural phosphate intemucieotidic linkage, and at least one chirally controlled non-negatively charged intemucieotidic linkage .

[00106] In some embodiments, a DMD oligonucleotide (e.g., an oligonucleotide whose base sequence contains no more than 5, 4, 3, 2, or I mismatches when hybridizing to a portion of a DMD transcript or a DMD genetic sequence having the same length) is capable of mediating skipping of one or more exons of the Dy strophin transcript.

[00107] In some embodiments, a DMD oligonucleotide has a base sequence which consists of the base sequence of an example oligonucleotide disclosed herein (e.g., an oligonucleotide listed in a Table), or a base sequence which comprises a 15-base portion of an example oligonucleotide nucleotide described herein. In some embodiments, a DMD oligonucleotide has a length of 15 to 50 bases.

[00108] In some embodiments, an oligonucleotide comprises a nucleobase modification, a sugar modification, and/or an intemucieotidic linkage. In some embodiments, a DMD oligonucleotide has a patern of nucleobase modifications, sugar modifications, and/or intemucieotidic linkages of an example oligonucleotide described herein (or any portion thereof having a length of at least 5 bases). hr some embodiments, an oligonucleotide comprises a nucleobase modification which is

BrlJ.

[00110] In some embodiments, an oligonucleotide comprises a sugar modification which is 2’-

OMe, 2 -F, 2’-MOE, or LNA.

[00111] In some embodiments, an oligonucleotide comprises an internucleotidic linkage which is a natural phosphate linkage or a phosphorothioate internucleotidic linkage. In some embodiments, a phosphorothioate internucleotidic linkage is not chirally controlled. In some embodiments, a phosphorothioate internucleotidic linkage is a chirally controlled internucleotidic linkage (e.g., Sp or Rp).

[00112] In some embodiments, an oligonucleotide comprises a non-negatively charged internucleotidic linkage. in some embodiments, a DMD oligonucleotide comprises a neutral internucleotidic linkage. In some embodiments, a neutral internucleotidic linkage is or comprises a triazole, alkyne, or cyclic guanidine moiety.

[00113] In some embodiments, an internucleotidic linkage comprising a tnazole moiety (e.g., an optionally substituted triazolyl group) in a provided oligonucleotide, e.g., a DMD oligonucleotide, has the

structure of: hr some embodiments, an internucleotidic linkage comprising a triazole

moiety has the formula In some embodiments, an internucleotidic linkage comprising an alkyne moiety (e.g., an optionally substituted alkynyl group) has

the formula of: , wherein W is O or S. In some embodiments, an internucleotidic linkage comprises a guanidine moiety. In some embodiments, an internucleotidic linkage comprises a cyclic guanidine moiety. In some embodiments, an internucleotidic linkage comprising a cyclic guanidine

moiety has the structure of: . In some embodiments, a neutral internucleotidic linkage or internucleotidic linkage comprising a cyclic guanidine moiety is stereochemically controlled .

In some embodiments, a DMD oligonucleotide comprises a lipid moiety In some embodiments, an intemucleotidic linkage comprises a Trrig group In some embodiments,

an intemucleotidic linkage comprises a Tmg group and has the structure (the lmg intemucleotidic linkage”). In some embodiments, neutral intemucleotidic linkages include intemucleotidic linkages of PNA and PMO, and an Tmg intemucleotidic linkage.

[00115] In general, properties of oligonucleotide compositions as described herein can be assessed using any appropriate assay. Relative toxicity and/or protein binding properties for different compositions (e.g., stereocontrol led vs non-stereocontro!led, and/or different stereocontrolled compositions) are typically desirably determined in the same assay, in some embodiments substantially simultaneously and in some embodiments with reference to historical results.

[00116] Those of skill the art will be aware of and/or will readily be able to develop appropriate assays for particular oligonucleotide compositions. The present disclosure provides descriptions of certain particular assays, for example that may be useful in assessing one or more features of oligonucleotide composition behavior e.g., complement activation, injection site inflammation, protein biding, etc.

[00117] For example, certain assays that may be useful in the assessment of toxicity and/or protein binding properties of oligonucleotide compositions may include any assay described and/or exemplified herein.

[00118] Among other things, in some embodiments, the present disclosure provides an oligonucleotide composition, comprising a plurality of oligonucleotides of a particular oligonucleotide type defined by:

1 ) base sequence;

2) pattern of backbone linkages;

3) pattern of backbone chiral centers; and

4) pattern of backbone phosphorus modifications,

wherein:

oligonucleotides of the plurality comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 chi rally controlled intemucleotidic linkages; and

the oligonucleotide composition being characterized in that, when it is contacted with a transcript in a transcript splicing system, splicing of the transcript is altered relative to that observed under a reference condition selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof

[00119] In some embodiments, the present disclosure provides a composition comprising a plurality of oligonucleotides of a particular oligonucleotide type defined by:

1) base sequence;

2) pattern of backbone linkages:

3) pattern of backbone chiral centers; and

4) pattern of backbone phosphorus modifications,

which composition is chi rally controlled and it is enriched, relative to a substantially racemic preparation of oligonucleotides having the same base sequence, pattern of backbone linkages and pattern of backbone phosphorus modifications, for oligonucleotides of the particular oligonucl eotide type, wherein:

the oligonucleotide composition is characterized in that, when it is contacted with a transcript in a transcript splicing system, splicing of the transcript is altered in that level of skipping of an exon is increased relative to that observed under a reference condition selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof

j 00120] In some embodiments, the present disclosure provides a composition comprising a plurality of oligonucleotides of a particular oligonucleotide type defined by:

1) base sequence;

2) pattern of backbone linkages; and

3 ) pattern of backbone phosphorus modifications,

wherein:

oligonucleotides of the plurality comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 non-negative!y charged intemucleotidic linkages;

the oligonucleotide composition is characterized in that, when it is contacted with a transcript in a transcript splicing system, splicing of the transcript is altered in that level of skipping of an exon is increased relative to that observed under a reference condition selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof

[00121] In some embodiments, the present disclosure provides a composition comprising a plurality of oligonucleotides of a particular oligonucleotide type defined by:

1) base sequence;

2) pattern of backbone linkages; and

3 ) pattern of backbone phosphorus modifications,

wherein: oligonucleotides of the plurality comprise:

1) a 5’-end region comprising 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleoside units comprising a 2’~ F modified sugar moiety;

2) a 3’-end region comprising 1. 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleoside units comprising a 2’- F modified sugar moiety: and

3) a middle region between the 5’-end region and the 3’-region comprising 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nue!eotidie units comprising a phosphodiester linkage.

[00122] In some embodiments, the present disclosure provides a composition comprising a plurality of oligonucleotides of a particular oligonucleotide type defined by:

1) base sequence:

2) patern of backbone linkages;

3) pattern of backbone chiral centers; and

4) pattern of backbone phosphorus modifications,

wherein:

oligonucleotides of the plurality comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 chi rally controlled intemucleotidic linkages; and

oligonucleotides of the plurality comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 non-negatively charged intemucleotidic linkages.

[00123] In some embodiments, the present disclosure provides a composition comprising a plurality of oligonucleotides of a particular oligonucleotide type defined by:

1) base sequence;

2) patern of backbone linkages;

3) patern of backbone chiral centers; and

4) pattern of backbone phosphorus modifications,

wherein:

the oligonucleotides of the plurality comprise cholesterol; L-camitine (amide and carbamate bond); Folic acid; Cleavable lipid (1,2-dilaurin and ester bond); Insulin receptor ligand; Gambogic acid; CPP; Glucose (tri- and hex-antennary); or Mannose (tri- and hex-antennary, alpha and beta).

[00124] In some embodiments, the present disclosure provides a pharmaceutical composition comprising an oligonucleotide or an oligonucleotide composition of the present disclosure and a pharmaceutically acceptable earner.

[00125] In some embodiments, the present disclosure provides a method for altering splicing of a target transcript, comprising administering an oligonucleotide composition of the present disclosure. In some embodiments, the present disclosure provides a method for reducing level of a transcript or a product thereof, comprising administering an oligonucleotide composition of the present disclosure. In some embodiments, the present disclosure provides a method for increase level of a transcript or a product thereof, comprising administering an oligonucleotide composition of the present disclosure. A method for treating muscular dystrophy, Duchenne (Duchenne’s) muscular dystrophy (DMD), or Becker (Becker’s) muscular dystrophy (BMD), comprising administering to a sub j ect susceptible thereto or suffering therefrom a composition described in the present disclosure.

[00126] In some embodiments, the present disclosure provides a method for treating muscular dystrophy, Duchenne (Duchenne’s) muscular dystrophy (DMD), or Becker (Becker’s) muscular dystrophy (BMD), comprising administering to a subject susceptible thereto or suffering therefrom a composition comprising any DMD oligonucleotide disclosed herein.

[00127] In some embodiments, the present disclosure provides a method for treating muscular dystrophy, Duchenne (Duchenne’s) muscular dystrophy (DMD), or Becker (Becker’s) muscular dystrophy (BMD), comprising (a) administering to a subject susceptible thereto or suffering therefrom a composition comprising any oligonucleotide disclosed herein, and (b) administering to the subject additional treatment which is capable of preventing, treating, ameliorating or slowing the progress of muscular dystrophy, Duchenne (Duchenne’s) muscular dystrophy (DMD), or Becker (Becker’s) muscular dystrophy (BMD).

BRIEF DESCRIPTION OF THE DRAWINGS

[00128] Figure 1. Figure 1 shows an example of multiple exon skipping

[00129] Figure 2. Figure 2 shows a cartoon of a method for detecting multiple exon skipping.

[00130] Figure 3. Figure 3 illustrates various strategies for multiple exon slapping.

DEFINITIONS

1001311 As used herein, the following definitions shall apply unless otherwise indicated. For purposes of this disclosure, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed. Additionally, general principles of organic chemistry are described in "Organic Chemistr'", Thomas Sorrell, Universi ty Science Books, Sausalito: 1999, and "March's Advanced Organic Chemistry", 5th Ed., Ed.: Smith, M.B. and March, J., John Wiley & Sons, New York: 2001.

[00132] Aliphatic. The term“aliphatic” or“aliphatic group”, as used herein, means a straight- chain (i.e., unbranched) or branched, substituted or unsubstituted hydrocarbon chain that is completely saturated or that contains one or more units of unsaturation, or a monocyclic hydrocarbon or bicyclic or polycyclic hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic (also referred to herein as "carbocycle" “cycloaliphatic” or“cycloalkyl”), or combinations thereof. In some embodiments, aliphatic groups contain 1-100 aliphatic carbon atoms. In some embodiments, aliphatic groups contain 1-20 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-10 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-9 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-8 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-7 aliphatic carbon atoms hi other embodiments, aliphatic groups contain 1-6 aliphatic carbon atoms. In still other embodiments, aliphatic groups contain 1-5 aliphatic carbon atoms, and in yet other embodiments, aliphatic groups contain 1, 2, 3, or 4 aliphatic carbon atoms. In some embodiments,“cycloaliphatic” (or“carbocycle” or“cycloalkyl”) refers to a monocyclic or bicyclic or polycyclic hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic. In some embodiments,“cycloaliphatic” (or “carbocycle” or“cycloalkyl’) refers to a monocyclic C 3- C 6 hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic. Suitable aliphatic groups include, but are not limited to, linear or branched, substituted or unsubstituted alkyl, alkenyl, alkynyl groups and hybrids thereof such as (cyeloalkyl)alkyi, (cyeloalkenyi)alkyl or (cycloalkyi)alkenyl.

[00133] Alkenyl. As used herein, the term“alkenyl” refers to an aliphatic group, as defined herein, having one or more double bonds.

[00134] Alkyl : As used herein, the term“alkyl” is given its ordinary meaning in the art and may include saturated aliphatic groups, including straight-chain alkyl groups, branched-chain alkyl groups, cycloalkyl (ahcyclic) groups, alkyl substituted cycloalkyl groups, and cycloalkyl substituted alkyl groups. In some embodiments, an alkyl has 1-100 carbon atoms. In certain embodiments, a straight chain or branched chain alkyl has about 1-20 carbon atoms in its backbone (e.g., C ] -C 20 for straight chain, C 2 -C 20 for branched chain), and alternatively, about 1-10. In some embodiments, cycloalkyl rings have from about 3-10 carbon atoms in their ring structure where such rings are monocyclic, bicyclic, or polycyclic, and alternatively about 5, 6 or 7 carbons in the ring structure. In some embodiments, an alkyl group may be a lower alkyl group, wherein a lower alkyl group comprises 1-4 carbon atoms (e.g., C r C 4 for straight chain lower alkyls).

[00135] Alkynyl: As used herein, the term“alkynyl” refers to an aliphatic group, as defined herein, having one or more triple bonds.

[00136] Animal: As used herein, the term“animal” refers to any member of the animal kingdom.

In some embodiments,“animal” refers to humans, at any stage of development. In some embodiments, “animal” refers to non-human animals, at any stage of development in certain embodiments, the non human animal is a mammal (e.g.. a rodent, a mouse, a rat, a rabbit, a monkey, a dog, a cat, a sheep, cattle, a primate, and/or a pig). In some embodiments, animals include, but are not limited to, mammals, birds, reptiles, amphibians, fish, and/or worms. In some embodiments, an animal may be a transgenic animal, a genetically-engineered animal, and/or a clone.

[00137] Approximately: As used herein, the terms“approximately or“about” in reference to a number are generally taken to include numbers that fall within a range of 5%, 10%, 15%, or 20% in either direction (greater than or less than) of the number unless otherwise stated or otherwise evident from the context (except where such number would be less than 0% or exceed 100% of a possible value). In some embodiments, use of the term“about” in reference to dosages means ± 5 mg/kg/day.

[00138] Aryl: The term“aryl", as used herein, used alone or as part of a larger moiety as in

“aralkyl,”“aralkoxy,” or“aryloxyalkyl,” refers to monocyclic, bicyclic or polycyclic ring systems having a total of, e.g., five to thirty ring members, wherein at least one ring in the system is aromatic. In some embodiments, an aryl group is a monocyclic, bicyclic or polycyclic ring system having a total of five to fourteen ring members, wherein at least one ring in the system is aromatic, and wherein each ring in the system contains 3 to 7 ring members. In some embodiments, an aryl group is a biaryl group. The term “aryl” may be used interchangeably with the term“aryl ring.” In certain embodiments of the present disclosure,“aryl” refers to an aromatic ring system which includes, but not limited to, phenyl, biphenyl, naphthyl, binaphthyl, anthracyl and the like, which may bear one or more substituents. Also included within the scope of the term“aryl,” as it is used herein, is an aromatic ring fused to one or more non- aromatic rings, such as indanyl, phthalimidyl, naphthimidyl, phenanthridinyl, or tetrahydronaphthyl, and the like.

[00139] Characteristic sequence : A“characteristic sequence” is a sequence that is found in all members of a family of polypeptides or nucleic acids, and therefore can be used by those of ordinary skill in the art to define members of the family.

[00140] Comparable : The term“comparable” is used herein to describe two (or more) sets of conditions or circumstances that are sufficiently similar to one another to permit comparison of results obtained or phenomena observed. In some embodiments, comparable sets of conditions or circumstances are characterized by a plurality of substantially identical features and one or a small number of varied features. Those of ordinary skill in the art will appreciate that sets of conditions are comparable to one another when characterized by a sufficient number and type of substantially identical features to warrant a reasonable conclusion that differences in results obtained or phenomena observed under the different sets of conditions or circumstances are caused by or indicative of the variation in those features that are varied.

[00141] Cycloaliphatic·. The term “cycloaliphatic,” “carbocycie,” “carbocycly!,” “carbocyclic radical,” and“carbocyclic ring,” are used interchangeably, and as used herein, refer to saturated or partially unsaturated, but non-aromatic, cyclic aliphatic monocyclic, bicyclic, or polycyclic ring systems, as described herein, having, unless otherwise specified, from 3 to 30 ring members. Cycloaliphatic groups include, without limitation, cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyi, cycloheptenyl, cyclooctyl, cyclooctenyl, norbomyl, adamantyl, and cyclooetadienyl . In some embodiments, a cycloaliphatic group has 3-6 carbons. In some embodiments, a cycloaliphatic group is saturated and is cycloalkyl. The term ‘cycloaliphatic” may also include aliphatic rings that are fused to one or more aromatic or nonaromatic rings, such as decahydronaphthyl or 1, 2,3,4- tetrahydronaphth-l-yl. In some embodiments, a cycloaliphatic group is bicyclic. in some embodiments, a cycloaliphatic group is tricyclic. In some embodiments, a cycloaliphatic group is polycyclic. In some embodiments,“cycloaliphatic” refers to C 3 -C 6 monocyclic hydrocarbon, or C 8 -Ci 0 bicyclic or polycyclic hydrocarbon, that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic, or a C 9~ C !6 polycyclic hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic

100142 Dosing regimen: As used herein, a“dosing regimen” or“therapeutic regimen” refers to a set of unit doses (typically more than one) that are administered individually to a subject, typically separated by periods of time. In some embodiments, a given therapeutic agent has a recommended dosing regimen, which may involve one or more doses. In some embodiments, a dosing regimen comprises a plurality of doses each of which are separated from one another by a time period of the same length; in some embodiments, a dosing regime comprises a plurality of doses and at least two different time periods separating individual doses. In some embodiments, all doses within a dosing regimen are of the same unit dose amount. In some embodiments, different doses within a dosing regimen are of different amounts. In some embodiments, a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount different from the first dose amount. In some embodiments, a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount same as the first dose amount.

|00143| Heteroaliphatic : The term“heteroaliphatic” refers to an aliphatic group wherein one or more units selected from C, CH, CH 2 , and CH < are independently replaced by one or more heteroatoms. In some embodiments, a heteroaliphatic group is heteroalkyl. In some embodiments, a heteroaliphatic group is heteroalkenyl .

[00144] Heteroaryl : The terms“heteroaiyl” and“heteroar-”, as used herein, used alone or as part of a larger moiety, e.g.,“heteroaralkyl,” or“heteroaralkoxy,” refer to monocyclic, bicyclic or polycyclic ring systems having a total of, e.g., five to thirty ring members, wherein at least one ring in the system is aromatic and at least one aromatic ring atom is a heteroatom. In some embodiments, a heteroaryl group is a group having 5 to 10 ring atoms (i.e , monocyclic, bicyclic or polycyclic), in some embodiments 5, 6, 9, or 10 ring atoms. In some embodiments, a heteroaiyl group has 6, 10, or 14 p electrons shared in a cyclic array; and having, in addition to carbon atoms, from one to five heteroatoms. Heteroaryl groups include, without limitation, thienyl, furanyl, pyrrolyl, imidazo!yl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyi, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidiny], pyraziny], indolizinyl, purinyl, naphthyridinyl, and pteridinyl. In some embodiments, a heteroaryl is a heterobiaryl group, such as bipyridyl and the like. The terms“heteroaryl” and“heteroar-”, as used herein, also include groups in which a heteroaromatic ring is fused to one or more aryl, cycloaliphatic, or heterocyclyl rings, where the radical or point of atachment is on the heteroaromatic ring. Non-limiting examples include indoiyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzthiazolyl, quinolyl, isoquinolyl, cinnolinyl, phthalazinyl, qninazolinyl, quinoxalinyl, 4H- quinohzinyl, carbazolyl, acndinyl, phenazinyl, phenothiazinyl, phenoxazinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and pyrido[2,3 b]-! ,4-oxazin-3(4H)-one. A heteroaiyl group may be monocyclic, bicyclic or polycyclic. The term“heteroaryl” may be used interchangeably with the terms “heteroaryl ring/’“heteroaryl group,” or“heteroaromatic,” any of which terms include rings that are optionally substituted. The term“heteroaralkyl” refers to an alkyl group substituted by a heteroaryl group, wherein the alkyl and heteroaryl portions independently are optionally substituted.

[00145] Heteroatom: The term“heteroatom” means an atom that is not carbon or hydrogen. In some embodiments, a heteroatom is oxygen, sulfur, nitrogen, phosphorus, boron or silicon (including any oxidized form of nitrogen, sulfur, phosphorus, or silicon; the quatermzed form of any basic nitrogen or a substitutable nitrogen of a heterocyclic ring (for example, N as in 3,4~dihydro~2/7~pyrrolyl), NH (as in pyrrolidinyl) or NR + (as in N-substituted pyrrolidinyl); etc.). In some embodiments, a heteroatom is boron, nitrogen, oxygen, silicon, sulfur, or phosphorus. In some embodiments, a heteroatom is nitrogen, oxygen, silicon, sulfur, or phosphorus. In some embodiments, a heteroatom is nitrogen, oxygen, sulfur, or phosphorus. In some embodiments, a heteroatom is nitrogen, oxygen or sulfur.

[00146] Heterocycle: As used herein, the terms“heterocycle,”“heterocyclyl,”“heterocyclic radical,” and“heterocyclic ring", as used herein, are used interchangeably and refer to a monocyclic, bicyclic or polycyclic ring moiety (e.g., 3-30 membered) that is saturated or partially unsaturated and has one or more heteroatom ring atoms. In some embodiments, a heterocyclyl group is a stable 5- to 7- membered monocyclic or 7- to 10-membered bicyclic heterocyclic moiety that is either saturated or partially unsaturated, and having, in addition to carbon atoms, one or more, preferably one to four, heteroatoms, as defined above. When used in reference to a ring atom of a heterocycle, the term "nitrogen" includes substituted nitrogen. As an example, in a saturated or partially unsaturated ring having 0-3 heteroatoms selected from oxygen, sulfur and nitrogen, the nitrogen may be N (as in 3,4-dihydro- 2H-pyrrolyl), NH (as in pyrrolidinyl), or T\ T R (as in N-substituted pyrrolidinyl). A heterocyclic ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure and any of the ring atoms can be optionally substituted. Examples of such saturated or partially unsaturated heterocyclic radicals include, without limitation, tetrahydroiuramy!, tetrahydrothienyl, pyrrolidinyl, piperidinyl, pyrrolinyl, tetrahydroquinolinyl, tetrahydroisoquinoliny], decahydroquinolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyi, moipholinyl, and quinuclidinyl . The terms “heterocycle,” “heterocyclyl,” “heterocyclyl ring,” “heterocyclic group,” “heterocyclic moiety,” and“heterocyclic radical,” are used interchangeably herein, and also include heterocyclyl rings fused to one or more aryl, heteroaryl, or cycloaliphatic rings, such as indolinyl, 3H-indolyl, chromany!, phenanthridinyl, or tetrahydroquinolinyl. A heterocyclyl group may be monocyclic, bi cyclic or polycyclic. The term“heterocyclylalkyl” refers to an alkyl group substituted by a heterocyclyl, wherein the alkyl and heterocyclyl portions independently are optionally substituted.

[00147] Intraperitonea l : The phrases “intraperitonea! administration” and “administered intraperitonea!y” as used herein have their art-understood meaning referring to administration of a compound or composition into the peritoneum of a subject.

[00148] In vitro·. As used herein, the term‘In vitro’' refers to events that occur in an artificial environment, e.g., in a test tube or reaction vessel, in cell culture, etc. , rather than within an organism (e.g., animal, plant, and/or microbe)

[00149] In vivo: As used herein, the term“in vivo’ refers to events that occur within an organism

(e.g., animal, plant, and/or microbe).

[00150] Lower alkyl: The term“lower alkyl” refers to a C M straight or branched alky! group.

Example lower alkyl groups are methyl, ethyl, propyl, isopropyl, butyl, isobutyl, and tert-buty!.

100151 Lower haloalkyl: The term“lower haloalkyl” refers to a C M straight or branched alkyl group that is substituted with one or more halogen atoms.

[00152] Optionally substituted : As described herein, compounds of the disclosure, e.g., oligonucleotides, lipids, carbohydrates, etc., may contain“optionally substituted” moieties. In general, the term“substituted,” whether preceded by the term“optionally” or not, means that one or more hydrogens of the designated moiety are replaced with a suitable substituent. Unless otherwise indicated, an“optionally substituted” group may have a suitable substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted wtth more than one substituent selected from a specified group, the substituent may be either the same or different at every position. Combinations of substituents envisioned by this disclosure are preferably those that result in the formation of stable or chemically feasible compounds. The term“stable,” as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and, in certain embodiments, their recovery, purification, and use for one or more of the purposes disclosed herein. [00153] Suitable monovalent substituents are halogen; -(CH 2 ) 0 ^R°; -(CH 2 )o^OR°; -0(CH 2 )o- 4 RX

-0-(CH 2 ) O-4 C(0)OR°; -(CH 2 ) O-4 CH(OR°) 2 ; ·( ( P ·) :: Ph. which may be substituted with R°; -(CH 2 ) 0 _ 4 0(CH 2 )o-iPh which may be substituted with R°; -CH=CHPh, which may be substituted with R°; - (CH 2 )o- 4 0(CH 2 )o-i-pyridyl which may be substituted with R°; -N0 2 ; -CN: -N 3 ; -(CH 2 ) 0 ^N(R°) 2 ; - {( ' 1 ! }:, X( R )( ' {0}R°. -N(R°)C(S)R°; -(CH 2 ), M N(R O )C(0)N(R o ) 2 ; -N(R°)C(S)N(R°) 2 ; -(CH 2 ) 0 4 N(R°)C(0)0R o ; -N(R°)N(R°)C(0)R°; -N(R°)N(R O )C(0)N(R o ) 2 ; -N(R°)N(R°)C(0)0R°; { ( I I },.

4 C(0)R°; -C(S)R°; « l b), .( i ( )) ( )R : -(CH 2 ) 0.4 C(O)SR ; -(CH 2 ) 0 4 C(O)OSs(R c ) 3 ; (Cl I },. ()( ' {( ) )R :

-SC(S)SR°, -(CH 2 ) O.4 OC(0)N(R 0 ) 2 ; -C(0)N(0R°)R°; -C(0)C(0)R°; -C(0)CH 2 C(0)R o ;

-C(NOR°)R°; -(CH 2 ) O-4 SSR°; -(CH 2 ) 0-4 S(O) 2 R o ; { ( I hh S(O) C)R°; -(CH 2 ) 0-4 OS(O) 2 R c ;

-S(0) 2 N(R°) 2 ; -(CH 2 ) O-4 S(0)R°; -N(R°)S(0) 2 N(R°) 2 ; -N(R°)S(0) 2 R o ; -N(OR°)R°; -C(NH)N(R°) 2 ; - Si(R°) 3 ; -OSi(R°) 3 ; -P(R 0 ) 2 ; -P(OR°) 2 ; -P(R°)(OR°); -OP(R°) 2 ; -OP(OR°) 2 ; -OP(R°)(OR°); -P[N(R°) 2 ] 2 -P(R°)[N(R°) 2 ]; -P(OR°)[N(R°) 2 ] ; -OP[N(R°) 2 ] 2 ; -OP(R°)[N(R°) 2 ]; -OP(OR°)[N(R°) 2 ]; -N(R°)P(R°) 2 ; -N(R°)P(OR°) 2 ; -N(R°)P(R o )(0R°); -N(R°)P[N(R°) 2 ] 2 ; -N(R°)P(R°)[N(R°) 2 ];

-P(0)(R°) 2 ; -P(0)(R°)(0R°); -P(0)(R°)(SR°); -P(0)(R°)[N(R o ) 2 ]; -P(0)(0R o ) 2 ; -P(0)(SR°) 2 ; -P(0)(0R°)[N(R o ) 2 ]; -P(0)(SR°)[N(R o ) 2 ]; -P(0)(0R°)(SR°); -P(0)[N(R o ) 2 ] 2 ; -0P(0)(R o ) 2 ;

-0P(0)(R°)(0R o ); -0P(0)(R°)(SR°); -0P(0)(R°)[N(R o ) 2 ]; -0P(0)(0R°) 2 ; -0P(0)(SR°) 2 ;

-0P(0)(0R°) [NCR 0 ),] ; -0P(0)(SR°)[N(R°) 2 ]; -0P(0)(0R°)(SR°); 0P(0)[ N(R ) | -SP(0)(R°) 2 ;

-SP(0)(R°)(0R°); -SP(0)(R°)(SR°); -SP(0)(R o )[N(R o ) 2 ]; -SP(0)(0R°) 2 ; -SP(0)(SR°) 2 ;

-SP(0)(0R°) [N(R°) 2 ] ; -SP(0)(SR°) i X( R ) . | ; -SP(0)(0R°)(SR°) ; - SP(O) [N(R°) 2 ] 2 ; -N(R°)P(0)(R°) 2 ; -N(R°)P(0)(R°)(0R o ); -N(R°)P(0)(R°)(SR o ); -N(R°)P(0)(R°)[N(R°) 2 ] : -N(R°)P(0)(0R°) 2 ;

-N(R°)P(0)(SR°) 2 ; -N (R°)P (O )(0 R° ) [N( R° ) 2 ] ; -N(R°)P(0)(SR°)[N(R°) 2 ]; -N(R°)P(0)(OR°)(SR°); -N(R°)P(0)[N(R o ) 2 ] 2 ; -P(R 0 ) 2 [B(R°) 3 ]; -P(0R°) 2 [B(R o ) 3 ]; -P(NR°) 2 [B(R 0 ) 3 ]; -P(R°)(0R O )[B(R o ) 3 ]; -P(R°)[ (R°) 2 ][B(R°) 3 ]; -P(OR°) [N(R°) 2 ] [B(R°) 3 ] ; -()P(R 0 ) 2 [B(R 0 ) 3 ]; OPi OR ) - j B( R ) : :

-OP(NR°) 2 [B(R°) 3 ]; -OP(R°)(OR°)[B(R°) 3 ] ; -0P(R°)[N(R O ) 2 ] [B(R°) 3 ]; -0P(0R°)[N(R O ) 2 ] [B(R°) 3 ]; -N(R°)P(R°) 2 [B(R°) 3 ]; -N(R°)P(OR°) 2 [B(R°) 3 ]; -N(R°)P(NR C ) 2 [B(R 0 ) 3 ] ; -N(R°)P(R O )(0R O )[B(R o ) 3 ]; -N(R°)P(R°) [N(R°) 2 ] [B(R°) 3 ] ; -N(R°)P(0R O )[N(R O ) 2 ][B(R°) 3 ]; -P(OR’)[B(R’) 3 ]-; -(C^ straight or branched alkylene)0-N(R°) 2 ; or— (Ci__ 4 straight or branched alkylene)C(0)0-N(R°) 2 , wherein each R° may be substituted as defined below and is independently hydrogen, Ci 2 o aliphatic, Ci 20 heteroaliphatic having 1-5 heteroatoms independently selected from nitrogen, oxygen, sulfur, silicon and phosphorus, - CH 2 -(C 6-20 aryl), -0(CH 2 ) O-L (C 6-2O ar l), -CH 2 -(5-20 membered heteroaryl ring having 1-5 heteroatoms independently selected from nitrogen, oxygen, sulfur, silicon and phosphorus), a 5-20 membered, monocyclic, bicyclic, or polycyclic, saturated, partially unsaturated or aryl ring having 0-5 heteroatoms independently selected from nitrogen, oxygen, sulfur, silicon and phosphorus, or, notwithstanding the definition above, two independent occurrences of R°, taken together with their intervening atom(s), form a 3-20 membered, monocyclic, bicyclic, or polycyclic, saturated, partially unsaturated or aryl ring having 0-5 heteroatoms independently selected from nitrogen, oxygen, sulfur, silicon and phosphorus, which may be substituted as defined below.

[00154] Suitable monovalent substituents on R° (or the ring formed by taking two independent occurrences of R° together with their intervening atoms), are independently halogen, -(CH 2 ) 0-2 R ® , -

{CH 2 ) O 2 C(G)QH, -(CH 2 ) O-2 C(G)GR ® , -(CH 2 ) O-2 SR ® , -(CH 2 ) O-2 SH, -(CH 2 ) O-2 NH 2 , -(CH 2 ) O-2 NHR·, - (CH 2 ) 0-2 NR ® 2 , N0 2 , -SiR* 3 , -OSiR ® 3, -C(0)SR· , - (C^ straight or branched alky!ene)C(0)OR ® , or - SSR· wherein each R ® is unsubstituted or where preceded by '‘halo” is substituted only with one or more halogens, and is independently selected from C1-4 aliphatic, -ClRPh, -0(CH 2 )o-iPh, and a 5-6-membered saturated, partially unsaturated, or ary l ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. Suitable divalent substituents on a saturated carbon atom of R° include =0 and =S

j00155j Suitable divalent substituents, e.g., on a suitable carbon atom, nitrogen atom, are independently the following: O. S. =CR * 2 , =NNR * 2 , =NNHC(0)R * , =NNHC(0)OR * , =NNHS(0) 2 R * , =NR * , -NOR " , -0(C(R 2 )) 2-3 0-, or -S(C(R\)) 2-3 S-, wherein each R may be substituted as defined below and is independently hydrogen, C t-20 aliphatic, C ] -20 heteroaliphatic having 1-5 heteroatoms independently selected from nitrogen, oxygen, sulfur, silicon and phosphorus, -CH 2- (C 6-20 aryl), - 0(CH 2 ) O-I (C 6.2O aryl), -CH 2 -(5-20 membered heteroaryl ring having 1-5 heteroatoms independently selected from nitrogen, oxygen, sulfur, silicon and phosphorus), a 5-20 membered, monocyclic, bicyclic, or polycyclic, saturated, partially unsaturated or aryl ring having 0-5 heteroatoms independently selected from nitrogen, oxygen, sulfur, silicon and phosphorus, or, notwithstanding the definition above, two independent occurrences of R * , taken together with their intervening atorn(s), form a 3-20 membered, monocyclic, bicyclic, or polycyclic, saturated, partially unsaturated or aryl ring having 0-5 heteroatoms independently selected from nitrogen, oxygen, sulfur, silicon and phosphorus, which may be substituted as defined below. Suitable divalent substituents that are bound to vicinal substitutable atoms of an “optionally substituted” group include: -0(CR * 2 ) 2-3 0-.

[00156] Suitable monovalent substituents on R (or the ring formed by taking two independent occurrences of R " together with their intervening atoms), are independently halogen, -(CH 2 ) 0-2 R ® , - (haloR ® ), (CH R -01 1. -(CH 2 ) 0..2 OR ® , -<CH 2 V 2 CH(OR * ) 2 ; -0(haloR e ), -CN, -N 3 , -(CH 2 ) 0..2 C(O)R ® , - {<·! !;}„ ( ' {0)01 !. ·(( ! ! ): : ; C(0)0 * . (P ί .),: SR * . -(CH 2 ) O-2 SH, -(CH 2 ) O-2 NH 2 , -<CH 2 ) O-2 NHR ® , -

(CH 2 ) O-2 NK ® 2, -N0 2 , -SiR* 3 , ---OSiR ® 3, -C(0)SR· , - (C1-4 straight or branched alkylene)C(0)0R ® , or - SSR ® wherein each R ® is unsubstituted or where preceded by“halo” is substituted only with one or more halogens, and is independently selected from C s .4 aliphatic, -CH 2 Ph, -O(CH 2 ) 0 _iPh, and a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. Suitable divalent substituents on a saturated carbon atom of include =0 and =S.

[00157] In some embodiments, suitable substituents on a substitutable nitrogen of an“optionally substituted" group include -R , NR\. -C(0)R , -C(0)OR , -C(0)C(0)R , -C(0)CH 2 C(0)R , S(O) R . -S(0) 2 NR 2 , -C(S)NR t 2 , -C(NH)NR 2 , or -N(R )S(0) 2 R ; wherein each R is independently hydrogen, C._ 6 aliphatic which may be substituted as defined below, unsubstituted -OPh, or an unsubstituted 5-6 membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R * . taken together with their intervening atom(s) form an unsubstituted 3-12 membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

j00158j In some embodiments, suitable substituents on the aliphatic group of R' are independently halogen, -R ® , -(haloR ® ), -OH, -OR ® , Of baioR*}. -CN, (0)01 1. -C(0)OR ® , M ! , -NHR ® , -NR ® 2, or -NQ 2 , wherein each R ® is unsubstituted or where preceded by“halo” is substituted only with one or more halogens, and is independently Ci_ 4 aliphatic, -CH 2 Ph, -O(CH 2 ) 0 _iPh, or a 5-6 membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[00159] Oral: The phrases“oral administration” and“administered orally” as used herein have their art-understood meaning referring to administration by mouth of a compound or composition.

|00160| Parenteral·. The phrases“parenteral administration” and“administered parenterally” as used herein have their art-understood meaning referring to modes of administration other than enteral and topical administration, usually by injection, and include, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitonea!, transtracheal, subcutaneous, subcuticular, intraarticulare, subcapsular, subarachnoid, intraspinal, and intrastemal injection and infusion.

[00161] Partially unsaturated: As used herein, the term“partially unsaturated” refers to a ring moiety that includes at least one double or triple bond. The term“partially unsaturated” is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aryl or heteroaryl moieties, as herein defined. [00162] Pharmaceutical composition: As used herein, the term“pharmaceutical composition’ refers to an active agent, formulated together with one or more pharmaceutically acceptable carriers. In some embodiments, active agent is present in unit dose amount appropriate for administration in a therapeutic regimen that shows a statistically significant probability of achieving a controlled therapeutic effect when administered to a relevant population in some embodiments, pharmaceutical compositions may be specially formulated for administration in solid or liquid form, including those adapted for the following: oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; topical application, for example, as a cream, ointment, or a eontrolled- release patch or spray applied to the skin, lungs, or oral cavity; intravaginal!y or intrarectally, for example, as a pessary, cream, or foam; sublingually; ocularly; transderrnally; or nasally, pulmonary', and to other mucosal surfaces.

[00163] Pharmaceutically acceptable: As used herein, the phrase“pharmaceutically acceptable” refers to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

[00164] Pharmaceutically acceptable carrier: As used herein, the term “pharmaceutically acceptable carrier” means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body. Each earner must be“acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient. Some examples of materials which can serve as pharmaceutically-acceptable carriers include: sugars, such as lactose, glucose and sucrose; starches, such as com starch and potato starch; cellulose, and its derivatives, such as sodium earboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, com oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer’s solution; ethyl alcohol; pH buffered solutions; polyesters, polycarbonates and/or polyanhydrides; and other non-toxic compatible substances employed in pharmaceutical formulations. [00165] Pharmaceutically acceptable salt: The term“pharmaceutically acceptable salt”, as used herein, refers to salts of such compounds that are appropriate for use in pharmaceutical contexts, i.e., salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge, et al. describes pharmaceutically acceptable salts in detail in j. Pharmaceutical Sciences, 66: 1-19 (1977). In some embodiments, pharmaceutically acceptable salts include, but are not limited to, nontoxic acid addition salts, which are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange in some embodiments, pharmaceutically acceptable salts include, but are not limited to, adipate, alginate, ascorbate, aspartate, benzene sulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphors ulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethane sulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy- ethanesulfonate, lactobionate, lactate, !aurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3- phenylpropionate, phosphate, picrate, pfva!ate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. In some embodiments, pharmaceutically acceptable salts include, wlien appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, alkyl having from 1 to 6 carbon atoms, sulfonate and aryl sulfonate. In some embodiments, a provided compound comprises one or more acidic groups, e.g., an oligonucleotide, and a pharmaceutically acceptable salt is an alkali, alkaline earth metal, or ammonium (e.g., an ammonium salt of N(R) 3 , wherein each R is independently as defined and described in the present disclosure) salt. Representative alkali or alkaline earth metal salts include salts of sodium, lithium, potassium, calcium, magnesium, and the like. In some embodiments, a pharmaceutically acceptable salt is a sodium salt. In some embodiments, a pharmaceutically acceptable salt is a potassium salt. In some embodiments, a pharmaceutically acceptable salt is a calcium salt. In some embodiments, pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, alkyl having from 1 to 6 carbon atoms, sulfonate and aryl sulfonate. In some embodiments, a provided compound comprises more than one acid groups, for example, a provided oligonucleotide rnay comprise two or more acidic groups (e.g., in natural phosphate linkages and/or modified intemucleotidic linkages). In some embodiments, a pharmaceutically acceptable salt, or generally a salt, of such a compound comprises two or more cations, which can be the same or different. In some embodiments, in a pharmaceutically acceptable salt (or generally, a salt), each acidic group having sufficient acidity independently exists as its salt form (e.g., in an oligonucleotide comprising natural phosphate linkages and phosphorothioate intemucleotidic linkages, each of the natural phosphate linkages and phosphorothioate intemucleotidic linkages independently exists as its salt form). In some embodiments, a pharmaceutically acceptable salt of an oligonucleotide is a sodium salt of a provided oligonucleotide. In some embodiments, a pharmaceutically acceptable salt of an oligonucleotide is a sodium salt of a provided oligonucleotide, wherein each acidic linkage, e.g., each natural phosphate linkage and phosphorothioate intemucleotidic linkage, exists as a sodium salt form (all sodium salt).

[00166] Protecting group: The term '‘protecting group,” as used herein, is well known in the art and includes those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3 rn edition, J ohn Wiley & Sons, 1999, the entirety of which is incorporated herein by reference. Also included are those protecting groups specially adapted for nucleoside and nucleotide chemistry, e.g., those described in Current Protocols in Nucleic Acid Chemistry, edited by Serge L. Beaucage et al. 06/2012, the entirety of Chapter 2 is incorporated herein by reference. Suitable amino-protecting groups include methyl carbamate, ethyl carbamante, 9-fiuorenylmethyl carbamate (Fmoc), 9-(2- sulfo)fluorenyim ethyl carbamate, 9-(2,7-dibromo)fIuoroeny!niethyi carbamate, 2,7-di-/-butyl-[9- ( 10, 10-dioxo- 10, 10, 10, 10-tetrahvdrothioxanthyl)]methyl carbamate (DBD-Tmoc), 4-methoxyphenacy! carbamate (Phenoc), 2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate (Teoc), 2- phenyiethyl carbamate (hZ), l-(l-adamantyl)-l-methyiethyl carbamate (Adpoc), 1,1-dimethyl- 2- haloethyl carbamate, Ll-dimethyl-2,2-dibromoethyi carbamate (DB-/-BOC), Ll-dimethy -2,2,2- trichloroethy! carbamate (TCBOC), 1 -me thyl-1 -(4-biphenyl yljethyl carbamate (Bpoc), 1— (3,5— di— r— butylphenyl)-l-methylethyl carbamate (r-Bumeoc), 2-(2’- and ’-pyridy ethyl carbamate (Pyoc), 2- (AyW-dicyclohexylcarboxamido)ethyl carbamate, /-butyl carbamate (BOC), 1-adamantyl carbamate (Adoc), vinyl carbamate (Voc), ally! carbamate (Alloc), 1-isopropylallyl carbamate (Ipaoc), c namyl carbamate (Coe), 4-nitrocinnamyl carbamate (Noe), 8-quinolyl carbamate, A'-hydroxypiperidinyl carbamate, alky!dithio carbamate, benzyl carbamate (Cbz), tnethoxybenzyl carbamate (Moz), p- nitobenzyl carbamate, ?-bromobenzyl carbamate, />--chlorobenzyl carbamate, 2,4-dichlorobenzyl carbamate, 4-methyisulfmyibenzyl carbamate (Msz), 9-anthryimethyl carbamate, diphenylmethyl carbamate, 2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate, 2-(p-toluenesulfonyl)ethyI carbamate, [2-(l,3-ditbianyl)]methy] carbamate (Dmoc), 4-methyithiophenyl carbamate (Mtpc), 2,4- dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate (Peoc), 2- triphenylphosphonioisopropyl carbamate (Ppoc), 1,1-- dimethyl-2 --cyanoethyl carbamate, hi-άύoΐo-r- acyloxybenzyl carbamate, /?-(dihydroxyhoryl)benzyl carbamate, 5-benzisoxazolylmethyi carbamate, 2- (trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), /w-nitrophenyl carbamate, 3,5- dimethoxybenzyl carbamate, o-nitrobenzyl carbamate, 3,4-dimethoxy-6-nitrobenzyl carbamate, phenyi(o-mtrophenyl)metliyl carbamate, phenothiazinyl-(10)-carbonyl derivative, N ' -p - toluenesuifonyiaminocarbonyi derivative, A r ’-phenylaminothiocarbonyl derivative, t- amyl carbamate, S- benzyl thiocarbamate, p -cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl carbamate, -decyloxybenzyl carbamate, 2,2- dimethoxy carbonyl vinyl carbamate, o---(A¥¥-dimethylcarboxamido)benzyl carbamate, 1 , l-dimethyl-3- (A¥¥-dimethyicarboxamido)propyl carbamate, 1, l-dimethylpropynyl carbamate, di(2-pyridyl)methyl carbamate, 2-fi.iranylmethyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p (p’-methoxyphenylazo)benzyl carbamate, 1 -methyl cyclobutyl carbamate, 1- methylcyclohexyl carbamate, 1 -methyl- 1 -cyclopropylmethyl carbamate, l-methyl-l-(3,5- dimethoxyphenyi)ethyl carbamate, 1 -methyl- l- o-phenylazophenyl)ethyl carbamate, 1 -methyl- 1- phenylethyl carbamate, l-methyl-l-(4-pyridyl)ethyl carbamate, phenyl carbamate, y>-(phenylazo)benzyl carbamate, 2,4,6-tri-f-butylphenyl carbamate, 4-(trimethylammonium)benzyl carbamate, 2,4,6- trimethylbenzyl carbamate, fomiamide, acetamide, chloroacetamide, trichloroacetamide, tnfluoroacetamide, phenyiacetamide, 3-phenylpropanamide, picolinamide, 3-pyridylcarboxamide, N~ benzoylphenyialanyi derivative, benzamide, ?-phenylbenzamide, o-nitrophenylacetamide, o - nitrophenoxyacetamide, acetoacetamide, (.¥’-dithiobenzyloxycarbonylammo)acetamide, 3 (p hydroxyphenyi)propanamide, 3-(o-nitrophenyl)propanamide, 2-methyl-2-(o- nitrophenoxy)propanamide, 2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide, 3- methyl-3-nitrobutanamide, o-nitrocinnamide, L-acetylmethionine derivative, o-nitrobenzamide, o- (benzoyloxymethyl)benzamide, 4,5-diphenyl-3-oxazolin-2-one, ¥-phthalimide, A-dithiasuccinimide (Dts), ¥-2,3-diphenylmaleimide, A-2,5-dimethylpyrrole, /V-l,l ,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5-substituted 1 ,3-dimethyl- 1 ,3 ,5-triazacyclohexan-2~one, 5-substituted 1,3- dibenzyl- 1 ,3 ,5-tiiazacyciohexan-2-one, 1 -substituted 3 ,5-dinitiO-4-pyndone, A-methylamine, L- allylamine, A/-[2-(trimethylsilyl)ethoxy]methylamine (SEM), A-3-acetoxypropylamine, A-(l- isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternar' ammonium salts, A-benzylamine, A-di(4- methoxyphenyl)methylamine, A-5-dibenzosuberylamine, A-triphenylmethylamine (Tr), A-[(4- methoxyphenyl)diphenylmethyl]amine (AIMTr), A-9-phenylfliiorenylamine (PhF), A-2,7-dicliloro-9- fluorenylmethyleneamine, L-ferrocenylmethylamino (Fcm), A-2-picolylamino ¥’-oxide, L-1,1- dimethylthiomethyleneamine, A-benzylideneamine, A-y-methoxybenzylideneamine, N- diphenyimethyleneamine, A-[(2-pyridyl)mesityT|methyleneamine, N~(N’,N’ dimethylaminomethylene)amine, N,N ---isopropylidenediamine, A^-p-nitrobenzylidenearnine, A- sa!ieyiideneamine, jV-5-ch!orosa!icylideneamme, A-(5-chloro-2- hydroxyphenylipheny!methyleneamine, A-cyclohexylideneamine, A-(5 ,5-dimethyl-3-oxo- 1 - cyclohexenyl)amine, A-borane derivative, A-diphenylborinic acid derivative, A- [phenyi(pentacarbonylchromium- or tungsten)carbonyl]amine, A-copper chelate, A-zinc chelate, A- nitroamine, A-nitrosoamine, amine A -oxide, diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt), diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzyl phosphoramidate, diphenyl phosphoramidate, benzenesulfenamide, o-nitrobenzenesulfenamide (Nps), 2,4- dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide, triphenylmethylsulfenamide, 3-nitropyridinesulfenamide (Npys), /’-toluene sulfonamide (Ts), benzenesulfonamide, 2,3,6,-trimethyl-4-methoxybenzenesulfonamide (Mtr), 2,4,6- trimethoxybenzenesulfonamide (Mtb), 2,6-dimethyl-4—methoxybenzenesulfonamide (Pme) 2, 3,5,6- tetramethyl-4-methoxybenzenesulfonamide (Mte), 4-methoxybenzenesulfonamide (Mbs), 2,4,6- trimethylbenzenesulfonamide (Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds), 2,2,5 ,7, 8- pentamethylchroman-6-sulfonamide (Pme), methanesulfonamide (Ms), b- trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide, 4-(4’,8 , ~ dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS), benzylsulfonamide, tnfluoromethylsulfonamide, and phenacylsulfonamide .

[00167] Suitably protected carboxylic acids further include, but are not limited to, silyl-, alkyl-, alkenyl-, aryl-, and aryla!kyl-protected carboxylic acids. Examples of suitable silyl groups include trimcthylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triisopropyl silyl, and the like. Examples of suitable alkyl groups include methyl, benzyl, p-methoxybenzyl, 3,4-dimethoxybenzyl, trityl, t-butyl, tetrahydropyran-2-yl. Examples of suitable alkenyl groups include ally!. Examples of suitable aryl groups include optionally substituted phenyl, biphenyl, or naphthyl. Examples of suitable arylalkyl groups include optionally substituted benzyl (e.g., p-methoxybenzyl (MPM), 3,4- dimethoxybenzyl, O-nitrobenzyl, p-nitrobenzyl, p-halobenzyi, 2,6-dichlorobenzyl, p-cyanobenz } 4), and 2- and 4-picolyl.

[00168] Suitable hydroxyl protecting groups include methyl, methoxylmethyl (MOM), methyithiomethyl (MTM), r-butylthiomethyl (phenyldimethylsilyl)methox \T nethyl (SMOM) benzyl oxymethyl (BOM), /i-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl ( v-AOM), guaiacolmethyl (GUM), /-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2- methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl, bis(2-chloroethoxy)methyl, 2- (trimethylsilyl)ethox\nnethyl (SEMOR), tetrahydropyranyi (THP), 3-bromotetrahydropyranyl, tetrahydrothiopyranyl, l-methoxycyclohexyl, 4-methoxytetrahydropyranyl (MTHP), 4- methoxytetrahydrothiopyranyl, 4-methoxytetrahydrothiopyranyl S,S-dioxide, l-[(2-chloro-4- methyl)phenyl]-4-methoxypiperidin-4-yl (CTMP), 1 ,4-dioxan-2-yl, tetrahydrofuranyl, tetra ydrothiofuranyl, 2,3,3a,4,5,6,7,7a-octahydro-7,8,8-triraethyl-4,7-methanobenz ofuraxi-2-yl, 1- ethoxyethyl, 1 -(2-chloroethoxy)ethyl, 1 -methyl- 1-methoxyethyl, 1 -methyl- 1 -benzyl oxyethyl, 1- methyl- l-benzyloxy-2-fluoroethyl, 2,2,2-trichloroethyl, 2-trimethylsilyiethyl, 2-(phenylselenyl)ethyl, /-butyl, ally!, p-chlorophenyL /y-methoxyphenyl, 2,4-dinitrophenyl, benzyl, p-methoxy benzyl, 3,4- dimethoxyhenzyl, o-nitro benzyl, -nitrobenzyl, />-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl, p phenylbenzy], 2-picolyl, 4-picolyl, 3-methyl-2-picolyl Ά-oxido, diphenylmethyl, p,p’ dinitrobenzhydryl, 5-dibenzosuberyl, triphenylmethyl, a-naphthyldiphenylmethyl, p- methoxyphenyldiphenylmethyl, di(p-methoxyphenyl)phenylmeth}4, tri(p-methoxyphenyl)methyl, 4-(4’- bromophenacyloxyphenyl)diphenylmethyl, 4,4 , ,4 , , -tris(4,5-dichlorophthalimidophenyl)methyl, 4,4’,4”- tris(levulinoyloxyphenyi)methyl, ^y ^ -trisibenzoyloxyphenyllmethy], 3-(imidazol-l-yl)bis(4 , ,4 , , - dimethoxyphenyl)methyl, 1 , l-bis(4-methoxyphenyl)- 1’-pyrenylrnethyi, 9-anthryi, 9-(9- phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryi, l,3-benzodithiolan-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyi (TIPS), dimethylisopropylsilyl (iPDMS), diethylisopropylsilyl (DEIPS), dimethylthexylsilyl, /-butyldimetbylsilyl (TBDMS), /-butyl diphenylsilyl (TBDPS), tribenzyl silyl, tri-p-xylylsilyl, triphenylsilyl, diphenylmethylsilyl (DPMS), /- butylmethoxyphenyisilyl (TBMPS), formate, benzoylformate, acetate, chioroacetate, dichloroacetate, trichloroacetate, trif!uoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p- chlorophenoxyacetate, 3-phenylpropionate, 4-oxopentanoate (levulinate), 4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4-methoxycrotonate, benzoate, p- phenyibenzoate, 2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate, 9-fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl 2,2,2-trichloroethyl carbonate (Troc), 2- (trimethyisi!yl)ethyl carbonate (TMSEC), 2-(phenylsulfonyl) ethyl carbonate (Psec), 2- (triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutyl carbonate, alkyl vinyl carbonate alkyl ally! carbonate, alkyl p-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p-methoxybenzyl carbonate, alkyl 3,4-dimethoxybenzyl carbonate, alkyl o- nitrobenzyl carbonate, alkyl p-nitrobenzyl carbonate, alkyl S- benzyl thiocarbonate, 4-ethoxy- 1-napththyl carbonate, methyl dithiocarbonate, 2-iodobenzoate, 4- azidobutyrate, 4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate, 2-formylbenzenesulfonate, 2- (methylthiomethoxy)ethyi, 4-(methylthiomethoxy)biityrate, 2-(methylthiomethoxymethyT)benzoate, 2,6- dichloro-4-niethylphenoxyacetate, 2,6-dichloro-4-(l ,l,3,3-tetramethyibutyl)phenoxyacetate, 2,4- bis(l,l-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, isobutyrate, monosuccinoate, ( E} 2 - methyl -2-butenoate, o-(methoxycarbonyl)benzoate, a-naphthoate, nitrate, alkyl N.JS T ,N’,N’- tetrarnethyiphosphorodiamidate, alkyl A -phenylcarbarnate, borate, dimethylphosphinothioyl, alkyl 2,4- dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts). For protecting 1,2- or 1,3-diols, the protecting groups include methylene acetal, ethylidene acetal, 1-f- butylethylidene ketal, 1-phenylethylidene ketal, (4-methoxyphenyl)ethylidene acetal, 2,2,2- trichloroethylidene acetal, acetonide, cyclopentylidene ketal, cyclohexylidene ketal, cycloheptylidene ketal, benzylidene acetal, /?-methoxybenzylidene acetal, 2,4-dimethoxybenzylidene ketal, 3,4- dimethoxybenzylidene acetal, 2-nitrobenzylidene acetal, methoxymethylene acetal, ethoxymethylene acetal, dimethoxymethylene ortho ester, l-methoxy ethylidene ortho ester, 1-ethoxyethylidine ortho ester, 1 ,2-dimethoxyethylidene ortho ester, a-methoxybenzylidene ortho ester, \-(NN- dimethylamino)ethylidene derivative, a-(iV,Ar-dimethylamino)benzylidene derivative, 2- oxacyclopentyiidene ortho ester, di-t-butylsilyiene group (DTBS), 1,3— (1, 1,3,3— tetraisopropyldisiloxanylidene) derivative (TIPDS), tetra-/-butoxydisiloxane- 1 ,3-diylidene derivative (TBDS), cyclic carbonates, cyclic boronates, ethyl boronate, and phenyl boronate.

1001691 In some embodiments, a hydroxyl protecting group is acetyl, t-butyl, tbutoxymethyl, methoxymethyl, tetrahydropyranyl, 1 -ethoxyethyl, 1 -(2-chloroethoxy)ethyl, 2- trimethylsilylethyl, p- chlorophenyl, 2,4-dinitrophenyl, benzyl, benzoyl, p-phenylbenzoyl, 2,6- dichlorobenzyl, diphenylmethyl, p-nitrobenzyl, triphenyimethyl (trityl), 4,4'-dimethoxytrityl, tri methyl silyl, triethyl sily 1 , t- butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, triisopropylsilyl, benzoylformate, chloroacetyl, trichloroacetyl, trifiuoroacetyl, pivalovl, 9- fluorenylmethyl carbonate, mesylate, tosylate, triflate, trityl, mono ethoxytrityi (MM Tr), 4,4'-dimethoxytrityl, (DMTr) and 4,4',4"-trimethoxytrityl (TM ' Tr), 2- cyanoethyi (CE or Cne), 2-(trimethylsilyl)ethyl (TSE), 2-(2-nitrophenyl)ethyl, 2-(4-cyanophenyl)ethyl 2- (4-nitrophenyl)ethyl (NPE), 2-(4-nitrophenylsulfonyl)ethyl, 3,5-dichlorophenyl, 2,4-dimethylphenyl, 2- nitrophenyl, 4-nitrophenyl, 2,4,6-trimethylphenyi, 2-(2-nitrophenyl)ethyl, butylthiocarbonyl, 4,4', 4"- tris(benzoyloxy)trityl, diphenylcarbamoyl, levulinyl, 2-(dibromomethyl)benzoyl (Dbmb), 2- (isopropylthiomethoxymethy])benzoyl (Print), 9-phenylxanthen-9-yl (pixyl) or 9-(p- methoxyphenyl)xanthine-9-yl (MOX). In some embodiments, each of the hydroxyl protecting groups is, independently selected from acetyl, benzyl, t- butyldimethylsilyl, t-butyldiphenylsilyl and 4,4'- dimethoxytntyl. In some embodiments, the hydroxyl protecting group is selected from the group consisting of trityl, monomethoxytrityi and 4,4'~dimethoxytrity! group

[00170] In some embodiments, a phosphorous protecting group is a group attached to the intemucleotide phosphorous linkage throughout oligonucleotide synthesis. In some embodiments, the phosphorous protecting group is attached to the sulfur atom of the intemucleotide phosphorothioate linkage. In some embodiments, the phosphorous protecting group is attached to the oxygen atom of the intemucleotide phosphorothioate linkage. In some embodiments, the phosphorous protecting group is attached to the oxygen atom of the intemucleotide phosphate linkage. In some embodiments the phosphorous protecting group is 2-cyanoethyl (CE or Cne), 2-trimethylsilylethyl, 2-nitroethyl, 2- sulfonylethyl, methyl, benzyl, o-nitrobenzyl, 2-(p-nitrophenyl)ethyl (NPE or Npe), 2-phenylethyl, 3-(N- /crr~butylcarboxamido)-i-propyl, 4-oxopentyl, 4-methylthio-l-butyl, 2-cyano-l ,1-dimethylethyl, 4 ~N~ methylaminobutyl, 3 -(2-pyridyl)- 1 -propyl , 2- jA-methyl -iV-(2 -pyridyl) j aminoethyl, 2-(A 7 -formyl,A r - methyDaminoethyi, 4-[A methyl-A , -(2,2,2-tnfluoiOacetyl)amino]butyl.

[00171] Protein: As used herein, the term ‘protein” refers to a polypeptide (i.e., a string of at least two amino acids linked to one another by peptide bonds). In some embodiments, proteins include only naturally-occurring amino acids. In some embodiments, proteins include one or more non-naturally- occurring amino acids (e.g., moieties that form one or more peptide bonds with adjacent amino acids). In some embodiments, one or more residues in a protein chain contain a non-amino-acid moiety (e.g., a giycan, etc). In some embodiments, a protein includes more than one polypeptide chain, for example linked by one or more disulfide bonds or associated by other means. In some embodiments, proteins contain L-amino acids, D-amino acids, or both; in some embodiments, proteins contain one or more amino acid modifications or analogs known in the art. Useful modifications include, e.g., terminal acetylation, amidation, methylation, etc. The term“peptide” is generally used to refer to a polypeptide having a length of less than about 100 amino acids, less than about 50 amino acids, less than 20 amino acids, or less than 10 amino acids.

[00172] Subject: As used herein, the term“subject” or“test subject” refers to any organism to which a provided compound or composition is administered in accordance with the present disclosure e.g., for experimental, diagnostic, prophylactic, and/or therapeutic purposes. Typical subjects include animals (e.g., mammals such as mice, rats, rabbits, non-human primates, and humans; insects; worms; etc.) and plants. In some embodiments, a subject may be suffering from, and/or susceptible to a disease, disorder, and/or condition.

[00173] Substantially: As used herein, the term“substantially” refers to the qualitative condition of exhibiting total or near-to tal extent or degree of a characteristic or property of interest. One of ordinary skill in the biological arts will understand that biological and chemical phenomena rarely, if ever, go to completion and/or proceed to completeness or achieve or avoid an absolute result. The term “substantially” is therefore used herein to capture the potential lack of completeness inherent in many biological and/or chemical phenomena.

[00174] Suffering from..· An individual who is “suffering from” a disease, disorder, and/or condition has been diagnosed with and/or displays one or more symptoms of a disease, disorder, and/or condition.

[00175] Susceptible to: An individual who is“susceptible to” a disease, disorder, and/or condition is one who has a higher risk of developing the disease, disorder, and/or condition than does a member of the general public in some embodiments, an individual who is susceptible to a disease, disorder and/or condition may not have been diagnosed with the disease, disorder, and/or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and/or condition may exhibit symptoms of the disease, disorder, and/or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and/or condition may not exhibit symptoms of the disease, disorder, and/or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and/or condition will develop the disease, disorder, and/or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and/or condition will not develop the disease, disorder, and/or condition.

[00176] Systemic: The phrases ‘"systemic administration,” “administered systemically,”

“peripheral administration,” and“administered peripherally” as used herein have their art-understood meaning referring to administration of a compound or composition such that it enters the recipient’s system.

[00177] Tautomeric forms: The phrase “tautomeric forms,” as used herein and generally understood in the art, is used to describe different isomeric forms of organic compounds that are capable of facile interconversion. Tautomers may be characterized by the formal migration of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond. In some embodiments, tautomers may result from prototropic tautomerism (i.e , the relocation of a proton). In some embodiments, tautomers may result from valence tautomerism (i.e., the rapid reorganization of bonding electrons). .411 such tautomeric forms are intended to be included within the scope of the present disclosure. In some embodiments, tautomeric forms of a compound exist in mobile equilibrium with each other, so that attempts to prepare the separate substances results in the formation of a mixture hi some embodiments, tautomeric forms of a compound are separable and isolatable compounds. In some embodiments of the disclosure, chemical compositions may be provided that are or include pure preparations of a single tautomeric form of a compound in some embodiments of the disclosure, chemical compositions may be provided as mixtures of two or more tautomeric forms of a compound. In certain embodiments, such mixtures contain equal amounts of different tautomeric forms; in certain embodiments, such mixtures contain different amounts of at least two different tautomeric forms of a compound . In some embodiments of the disclosure, chemical compositions may contain all tautomeric forms of a compound. In some embodiments of the disclosure, chemical compositions may contain less than all tautomeric forms of a compound. In some embodiments of the disclosure, chemical compositions may contain one or more tautomeric forms of a compound in amounts that vary' over time as a result of interconversion. In some embodiments of the disclosure, the tautomerism is keto-enol tautomerism. One of skill in the chemical arts would recognize that a keto-enol tautomer can be“trapped” (i.e., chemically modified such that it remains in the“enol” form) using any suitable reagent known in the chemical arts in to provide an enol derivative that may subsequently be isolated using one or more suitable techniques known in the art. Unless otherwise indicated, the present disclosure encompasses all tautomeric fonns of relevant compounds, whether in pure form or in admixture with one another.

[00178] Therapeutic agent: As used herein, the phrase“therapeutic agent” refers to any agent that, when administered to a subject, has a therapeutic effect and/or elicits a desired biological and/or pharmacological effect. In some embodiments, a therapeutic agent is any substance that can be used to alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of, and/or reduce incidence of one or more symptoms or features of a disease, disorder, and/or condition.

[00179] Therapeutically effective amount: As used herein, the term“therapeutically effective amount” means an amount of a substance (e.g., a therapeutic agent, composition, and/or formulation) that elicits a desired biological response when administered as part of a therapeutic regimen. In some embodiments, a therapeutically effective amount of a substance is an amount that is sufficient, when administered to a subject suffering from or susceptible to a disease, disorder, and/or condition, to treat, diagnose, prevent, and/or delay the onset of the disease, disorder, and/or condition. As will be appreciated by those of ordinary skill in this art, the effective amount of a substance may vary ' depending on such factors as the desired biological endpoint, the substance to be delivered, the target cell or tissue, etc. For example, the effective amount of compound in a formulation to treat a disease, disorder, and/or condition is the amount that alleviates, ameliorates, relieves, inhibits, prevents, delays onset of, reduces severity of and/or reduces incidence of one or more symptoms or features of the disease, disorder, and/or condition. In some embodiments, a therapeutically effective amount is administered in a single dose; in some embodiments, multiple unit doses are required to deliver a therapeutically effective amount.

[00180] Treat: As used herein, the term“treat,”“treatment,” or“treating” refers to any method used to partially or completely alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of, and/or reduce incidence of one or more symptoms or features of a disease, disorder, and/or condition. Treatment may be administered to a subject who does not exhibit signs of a disease, disorder, and/or condition in some embodiments, treatment may be administered to a subject who exhibits only early signs of the disease, disorder, and/or condition, for example for the purpose of decreasing the risk of developing pathology associated with the disease, disorder, and/or condition.

[00181] Unit dose: The expression“unit dose” as used herein refers to an amount administered as a single dose and/or in a physically discrete unit of a pharmaceutical composition. In many embodiments, a unit dose contains a predetermined quantity of an active agent. In some embodiments, a unit dose contains an entire single dose of the agent. In some embodiments, more than one unit dose is administered to achieve a total single dose. In some embodiments, administration of multiple unit doses is required, or expected to be required, in order to achieve an intended effect. A unit dose may be, for example, a volume of liquid (e.g., an acceptable carrier) containing a predetermined quantity of one or more therapeutic agents, a predetermined amount of one or more therapeutic agents in solid form, a sustained release formulation or drug delivery device containing a predetermined amount of one or more therapeutic agents, etc. It will be appreciated that a unit dose may be present in a formulation that includes any of a variety of components in addition to the therapeutic agent(s). For example, acceptable carriers (e.g., pharmaceutically acceptable carriers), diluents, stabilizers, buffers, preservatives, etc., may be included as described infra. It will be appreciated by those skilled in the art, in many embodiments, a total appropriate daily dosage of a particular therapeutic agent may comprise a portion, or a plurality, of unit doses, and may be decided, for example, by the attending physician within the scope of sound medical judgment in some embodiments, the specific effective dose level for any particular subject or organism may depend upon a variety of factors including the disorder being treated and the severity of the disorder; activity of specific active compound employed; specific composition employed; age, body weight, general health, sex and diet of the subject; time of administration, and rate of excretion of the specific active compound employed; duration of the treatment; drugs and/or additional therapies used in combination or coincidental with specific compound(s) employed, and like factors well known in the medical arts.

[00182] Unsaturated: The term "unsaturated," as used herein, means that a moiety has one or more units of unsaturation.

[00183] Wild-type: As used herein, the term“wild-type” has its art-understood meaning that refers to an entity having a structure and/or activity as found in nature in a“normal” (as contrasted with mutant, diseased, altered, etc) state or context. Those of ordinary skill in the art will appreciate that wild type genes and polypeptides often exist in multiple different forms (e.g., alleles).

[00184] Nucleic acid. The term“nucleic acid” includes any nucleotides, analogs thereof, and polymers thereof. The term“polynucleotide” as used herein refer to a polymeric form of nucleotides of any length, either ribonucleotides (RNA) or deoxyribonucleotides (DNA) or analogs thereof. These terms refer to the primary structure of the molecules and include double- and single-stranded DNA, and double- and single-stranded RNA. These terms include, as equivalents, analogs of either RNA or DNA made from nucleotide analogs and modified polynucleotides such as, though not limited to, methylated, protected and/or capped nucleotides or polynucleotides. The terms encompass poly- or oligo- ribonucleotides (RNA) and poly- or oligo-deoxyribonucleotides (DNA); RNA or DNA derived from N- glycosides or C-glycosides of nucleobases and/or modified nucleobases; nucleic acids derived from sugars and/or modified sugars; and nucleic acids derived from phosphate bridges and/or modified phosphorus-atom bridges (also referred to herein as“intern ucleotidic linkages”). The term encompasses nucleic acids containing any combinations of nucleobases, modified nucleobases, sugars, modified sugars, natural natural phosphate intemucleotidic linkages or non-natural imtemucleotidic linkages. Examples include, and are not limited to, nucleic acids containing ribose moieties, nucleic acids containing deoxy-ribose moieties, nucleic acids containing both ribose and deoxyribose moieties, nucleic acids containing ribose and modified ribose moieties. Unless otherwise specified, the prefix poly- refers to a nucleic acid containing 2 to about 10,000 nucleotide monomer units and wherein the prefix oligo- refers to a nucleic acid containing 2 to about 200 nucleotide monomer units.

[00185] Nucleotide: The term '‘nucleotide” as used herein refers to a monomeric unit of a polynucleotide that consists of a heterocyclic base, a sugar, and one or more phosphate groups or phosphorus-containing intemucleotidic linkages. Naturally occurring bases, (guanine, (G), adenine, (A), cytosine, (C), thymine, (T), and uracil (U)) are derivatives of purine or pyrimidine, though it should be understood that naturally and non-naturally occurring base analogs are also included. Naturally occurring sugars include the pentose (five-carbon sugar) deoxyribose (which is found in natural DNA) or ribose (which is found in natural RNA), though it should be understood that naturally and non-naturally occurring sugar analogs are also included, such as sugars with Z’-modificatioms, sugars in locked nucleic acid (LNA) and phosphorodiamidate morpho!ino oligomer (PMO) Nucleotides are linked via intemucleotidic linkages to form nucleic acids, or polynucleotides. Many intemucleotidic linkages are known in the art (such as, though not limited to, natural phosphate linkage, phosphorothioate linkages, boranophosphate linkages and the like). Artificial nucleic acids include PNAs (peptide nucleic acids), phosphotriesters, phosphorothionates, /7-phosphonates, phosphoramidates, boranophosphates, methylphosphonates, phosphonoacetates, thiophosphonoacetates and other variants of the phosphate backbone of native nucleic acids, etc. hi some embodiments, a nucleotide is a natural nucleotide comprising a naturally occurring nucleobase, a natural occurring sugar and the natural phosphate linkage. In some embodiments, a nucleotide is a modified nucleotide or a nucleotide analog, which is a structural analog that can be used in lieu of a natural nucleotide.

|00186| Modified nucleotide: The term‘ modified nucleotide” includes any chemical moiety which differs structurally from a natural nucleotide but is capable of performing at least one function of a natural nucleotide. In some embodiments, a modified nucleotide comprises a modification at a sugar, base and/or intemucleotidic linkage. In some embodiments, a modified nucleotide comprises a modified sugar, modified nucleobase and/or modified intemucleotidic linkage. In some embodiments, a modified nucleotide is capable of at least one function of a nucleotide, e.g., forming a subunit in a polymer capable of base-pairing to a nucleic acid compri sing an at least complementary sequence of bases.

[00187] Analog : The term“analog” includes any chemical moiety which differs structurally from a reference chemical moiety or class of moieties, but which is capable of performing at least one function of such a reference chemical rnoiety or class of moieties. As non-limiting examples, a nucleotide analog differs structurally from a nucleotide hut performs at least one function of a nucleotide; a nucleobase analog differs structurally from a nucleobase but performs at least one function of a nucleobase; a sugar analog differs structurally from a nucleobase but performs at least one function of a sugar, etc.

[00188] Nucleoside: The term ‘nucleoside” refers to a moiety wherein a nucleobase or a modified nucleobase is covalently bound to a sugar or modified sugar.

[00189] Modified nucleoside : Tire term "modified nucleoside" refers to a chemical moiety which is chemically distinct from a natural nucleoside, but which is capable of performing at least one function of a nucleoside. In some embodiments, a modified nucleoside is derived from or chemically similar to a natural nucleoside, but which comprises a chemical modification which differentiates it from a natural nucleoside. Non-limiting examples of modified nucleosides include those which comprise a modification at the base and/or the sugar. Non-limiting examples of modified nucleosides include those with a 2’~ modification at a sugar. Non-limiting examples of modified nucleosides also include abasic nucleosides (which lack a nucleobase). In some embodiments, a modified nucleoside is capable of at least one function of a nucleoside, e.g., forming a moiety in a polymer capable of base-pairing to a nucleic acid comprising an at least complementary ' sequence of bases.

[00190] Nucleoside analog: The term "nucleoside analog" refers to a chemical moiety which is chemically distinct from a natural nucleoside, but which is capable of performing at least one function of a nucleoside. In some embodiments, a nucleoside analog comprises an analog of a sugar and/or an analog of a nucleobase. In some embodiments, a modified nucleoside is capable of at least one function of a nucleoside, e.g., forming a moiety in a polymer capable of base-pairing to a nucleic acid comprising a complementary sequence of bases.

[00191] Sugar: The term“sugar” refers to a monosaccharide or polysaccharide in closed and/or open form. In some embodiments, sugars are monosaccharides. In some embodiments, sugars are polysaccharides. Sugars include, but are not limited to, ribose, deoxyribose, pentofuranose, pentopyranose, and hexopyranose moieties. As used herein, the term“sugar” also encompasses structural analogs used in lieu of conventional sugar molecules, such as glycol, polymer of which forms the backbone of the nucleic acid analog, glycol nucleic acid (“GNA”), etc. As used herein, the term“sugar” also encompasses structural analogs used in lieu of natural or naturally-occurring nucleotides, such as modified sugars and nucleotide sugars. In some embodiments, a sugar is D-2-deoxyribose. In some embodiments, a sugar is beta-D-deoxyribofuranose. In some embodiments, a sugar moiety' is a beta-D- deoxyribofuranose moiety. In some embodiments, a sugar is D-ribose. In some embodiments, a sugar is beta-D-ribofuranose. In some embodiments, a sugar moiety is a beta-D-ribofuranose moiety. In some embodiments, a sugar is optionally substituted beta-D-deoxyribofuranose or beta-D-ribofuranose. In some embodiments, a sugar moiety is an optionally substituted beta-D-deoxyribofuranose or beta-D- ribofuranose moiety in some embodiments, a sugar moiety/unit in an oligonucleotide, nucleic acid, etc. is a sugar which comprises one or more carbon atoms each independently connected to an intemucleotidic linkage, e.g., optionally substituted beta-D-deoxyribofuranose or beta-D-ribofuranose whose 5’-C and/or 3’-C are each independently connected to an intemucleotidic linkage (e.g., a natural phosphate linkage, a modified intemucleotidic linkage, a chirally controlled intemucleotidic linkage, etc.).

[00192] Modified sugar: The term‘"modified sugar” refers to a moiety that can replace a sugar.

A modified sugar mimics the spatial arrangement, electronic properties, or some other physicochemical property of a sugar. In some embodiments, a modified sugar is substituted beta-D-deoxyribofuranose or beta-D-ribofuranose. In some embodiments, a modified sugar comprises a 2’-modification hi some embodiments, a modified sugar comprises a linker (e.g., optionally substituted bivalent heteroaiiphatie) connecting two sugar carbon atoms (e.g , C2 and C4), e.g., as found in LNA. In some embodiments, a linker is -O-CH(R)-, wherein R is as described in the present disclosure. In some embodiments, a linker is -O-CH(R)-, wherein O is connected to C2, and -CH(R)- is connected to C4 of a sugar, and R is as described in the present disclosure. In some embodiments, R is methyl. In some embodiments, R is -H. In some embodiments, -CH(R)- is of S configuration. In some embodiments, -CH(R)- is of R configuration.

[00193] Nucleobase : The term“nucleobase” refers to the parts of nucleic acids that are invol ved in the hydrogen-bonding that binds one nucleic acid strand to another complementary strand in a sequence specific manner. The most common naturally-occurring nucleobases are adenine (A), guanine (G), uracil (U), cytosine (C), and thymine (T). In some embodiments, a modified nucleobase is a substituted nucleobase which nucleobase is selected from A, T, C, G, U, and tautomers thereof. In some embodiments, the naturally-occurring nucleobases are modified adenine, guanine, uracil, cytosine, or thymine. In some embodiments, the naturally -occurring nucleobases are methylated adenine, guanine, uracil, cytosine, or thymine. In some embodiments, a nucleobase is a“modified nucleobase,” e.g., a nucleobase other than adenine (A), guanine (G), uracil (U), cytosine (C), and thymine (T). In some embodiments, the modified nucleobases are methylated adenine, guanine, uracil, cytosine, or thymine. In some embodiments, the modified nucleobase mimics the spatial arrangement, electronic properties, or some other physicochemical property of the nucleobase and retains the property of hydrogen-bonding that binds one nucleic acid strand to another in a sequence specific manner. In some embodiments, a modified nucleobase can pair with all of the five naturally occurring bases (uracil, thymine, adenine, cytosine, or guanine) without substantially affecting the melting behavior, recognition by intracellular enzymes or activity of the oligonucleotide duplex. As used herein, the term“nucleobase” also encompasses structural analogs used in lieu of natural or naturally-occurring nucleotides, such as modified nucleobases and nucleobase analogs. In some embodiments, a nucleobase is an optionally substituted A, T, C, G, or U, or a substituted nucleobase which nucleobase is selected from A, T, C, G, U, and tautomers thereof.

[00194] Modified nucleobase: The terms "modified nucleobase", "modified base" and the like refer to a chemical moiety which is chemically distinct from a nucleobase, but which is capable of performing at least one function of a nucleobase. In some embodiments, a modified nucleobase is a nucleobase which comprises a modification. In some embodiments, a modified nucleobase is capable of at least one function of a nucleobase, e.g., forming a moiety in a polymer capable of base-pairing to a nucleic acid comprising an at least complementar ' sequence of bases. In some embodiments, a modified nucleobase is a substituted nucleobase which nucleobase is selected from A, T, C, G, U, and tautomers thereof.

[00195] Chiral ligand: The term“chiral ligand” or chiral auxiliary” refers to a moiety that is chiral and can be incorporated into a reaction so that the reaction can be carried out with certain stereoselectivity. In some embodiments, the term may also refer to a compound that comprises such a moiety.

[00196] Blocking group: The term“blocking group” refers to a group that masks the reactivity of a functional group. The functional group can be subsequently unmasked by removal of the blocking group. In some embodiments, a blocking group is a protecting group.

[00197] Moiety: The term“moiety” refers to a specific segment or functional group of a molecule. Chemical moieties are often recognized chemical entities embedded in or appended to a molecule. In some embodiments, a moiety of a compound is a monovalent, bivalent, or polyvalent group formed from the compound by removing one or more H and/or equivalents thereof from a compound. In some embodiments, depending on its context,“moiety” may also refer to a compound or entity from which the moiety is derived from.

[00198] Solid support: The term“solid support” when used in the context of preparation of nucleic acids, oligonucleotides, or other compounds refers to any support which enables synthesis of nucleic acids, oligonucleotides or other compounds. In some embodiments, the term refers to a glass or a polymer, that is insoluble in the media employed in the reaction steps performed to synthesize nucleic acids, and is derivatized to comprise reactive groups. In some embodiments, the solid support is Highly Cross-linked Polystyrene (HCP) or Controlled Pore Glass (CPG). In some embodiments, the solid support is Controlled Pore Glass (CPG). In some embodiments, the solid support is hybrid support of Controlled Pore Glass (CPG) and Highly Cross-linked Polystyrene (HCP).

[00199] Reading frame: The term“reading frame” refers to one of the six possible reading frames, three in each direction, of a double stranded DNA molecule. The reading frame that is used determines which codons are used to encode ammo acids within the coding sequence of a DNA molecule. [00200] Antisense : As used herein, an "antisense" nucleic acid molecule comprises a nucleotide sequence which is complementary to a "sense" nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule, complementary to an mRNA sequence or complementary to the coding strand of a gene. Accordingly, an antisense nucleic acid molecule can associate via hydrogen bonds to a sense nucleic acid molecule in some embodiments, transcripts may be generated from both strands. In some embodiments, transcripts may or may not encode protein products. In some embodiments, when directed or targeted to a particular nucleic acid sequence, a '‘antisense” sequence may refer to a sequence that is complementary' to the particular nucleic acid sequence.

100201 Oligonucleotide: the term "oligonucleotide" refers to a polymer or oligomer of nucleotide monomers, containing any combination of nucleobases, modified nucleobases, sugars, modified sugars, natural phosphate linkages, or non-natural intemucleotidic linkages.

[00202] Oligonucleotides can be single-stranded or double-stranded. As used herein, the term

oligonucleotide strand” encompasses a single-stranded oligonucleotide. A single-stranded oligonucleotide can have double-stranded regions and a double-stranded oligonucleotide can have single- stranded regions. Example oligonucleotides include, but are not limited to structural genes, genes including control and termination regions, self-replicating systems such as viral or plasmid DNA, single- stranded and double-stranded siRNAs and other RNA interference reagents (RNAi agents or iRNA agents), shRNA, antisense oligonucleotides, ribozymes, microRNAs, microRNA mimics, supermirs, aptamers, antimirs, antagomirs, U1 adaptors, triplex-forming oligonucleotides, G-quadrupiex oligonucleotides, RNA activators, immuno-stimulatory oligonucleotides, and decoy oligonucleotides.

[00203] Double -stranded and single-stranded oligonucleotides that are effective in inducing RNA interference may also be referred to as siRNA, RNAi agent, or iRNA agent. In some embodiments, these RNA interference inducing oligonucleotides associate with a cytoplasmic multi-protein complex known as RNAi-induced silencing complex (RISC) In many embodiments, single-stranded and double -stranded RNAi agents are sufficiently long that they can be cleaved by an endogenous molecule, e.g., by Dicer, to produce smaller oligonucleotides that can enter the RISC machinery and participate in RISC mediated cleavage of a target sequence, e.g. a target mRNA.

[00204] Oligonucleosides of the present disclosure can be of various lengths. In particular embodiments, oligonucleosides can range from about 2 to about 200 nucleosides in length. In various related embodiments, oligonucleosides, single-stranded, double -stranded, and triple-stranded, can range in length from about 4 to about 10 nucleosides, from about 10 to about 50 nucleosides, from about 20 to about 50 nucleosides, from about 15 to about 30 nucleosides, from about 20 to about 30 nucleosides in length. In some embodiments, the oligonudeoside is from about 9 to about 39 nucleosides in length. In some embodiments, the oligonudeoside is at least 15 nucleosides in length. In some embodiments, the oligonucleoside is at least 20 nucleosides in length. In some embodiments, the oligonucleoside is at least 25 nucleosides in length. In some embodiments, the oligonucleoside is at least 30 nucleosides in length. In some embodiments, the oligonucleoside is a duplex of complementary strands of at least 18 nucleosides in length. In some embodiments, the oligonucleoside is a duplex of complementary' strands of at least 21 nucleosides in length. In some embodiments, for the purpose of oligonucleotide lengths, each nucleoside counted independently comprises an optionally substituted nucleobase selected from A, T, C, G, U and their tautomers.

[00205] Internude otidic linkage: As used herein, the phrase“intemucleotidic linkage” refers generally to a linkage, typically a phosphorus-containing linkage, between nucleotide units of a nucleic acid or an oligonucleotide, and is interchangeable with“inter-sugar linkage”,“internucleosidic linkage,” and“phosphorus atom bridge,” as used above and herein. As appreciated by those skilled in the art, natural DNA and RNA contain natural phosphate linkages. In some embodiments, an intemucleotidic linkage is a natural phosphate linkage (-0P(0)(0H)0-, typically existing as its anionic form -0P(0)(0 )0- at pH e.g., ~7.4), as found in naturally occurring DNA and RNA molecules. In some embodiments, an intemucleotidic linkage is a modified intemucleotidic linkage (or non-natural intemucleotidic linkage), which is structurally different from a natural phosphate linkage but may be utilized in place of a natural phosphate linkage, e.g., phosphorothioate intemucleotidic linkage, PMC) linkages, etc. In some embodiments, an intemucleotidic linkage is a modified intemucleotidic linkage wherein one or more oxygen atoms of a natural phosphodiester linkage are independently replaced by one or more organic or inorganic moieties. In some embodiments, such an organic or inorganic moiety is selected from but not limited to =S, -Se, =NR’, -SR’, -SeR’, -N(R’) 2 , B(R’) 3 - S-, -Se-, and -N(R’)-, wherein each R’ is independently as defined and described below. In some embodiments, an intemucleotidic linkage is a phosphotriester linkage. In some embodiments, an intemucleotidic linkage is

O

4-0—— O-I-

’ Lm

a phosphorothioate diester linkage (phosphorothioate intemucleotidic linkage, an , typically existing as its anionic form -0P(0)(S )0- at pH e.g., -7 4). It is understood by a person of ordinary skill in the art that an intemucleotidic linkage may exist as an anion or cation at a given pH due to the existence of acid or base moieties in the linkage. In some embodiments, an intemucleotidic linkage is a non-negatively charged intemucleotidic linkage at a given pH. In some embodiments, an intemucleotidic linkage is a neutral intemucleotidic linkage at a given pH. In some embodiments, a given pH is pH -7.4. In some embodiments, a given pH is in the range of pH about 0, 1 , 2, 3, 4, 5, 6 or 7 to pH about 7, 8, 9, 10, 11, 12, 13 or 14. In some embodiments, a given pH is in the range of pH 5-9. In some embodiments, a given pH is in the range of pH 6-8. hi some embodiments, an intemucleotidic linkage has the structure of formula I, I~a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, Il-d-

1, II-d-2, etc., as described in the present disclosure. In some embodiments, a non-negatively charged intemucleotidic linkage has the structure of formula I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II~a~2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, etc., as described in the present disclosure. In some embodiments, an intemucleotidic linkage is one of, e.g., PNA (peptide nucleic acid) or PMQ (phosphorodiamidate Morpholino oligomer) linkage. In some embodiments, an intemucleotidic linkage comprises a chiral linkage phosphorus. In some embodiments, an intemucleotidic linkage is a chiral I > controlled intemucleotidic linkage. In some embodiments, an intemucleotidic linkage is selected from: s (phosphorothioate), si, s2, s3, s4, s5, s6, s7, s8, s9, slO, si 1, sl2, sl3, sl4, s 15, s 16, sl7 or sl8, wherein each of si, s2, s3, s4, s5, s6, s7, s8, s9, slO, s 11, sl2, s!3, sl4, sl5, sl6, sl7 and s 18 is independently as described in WO 2017/062862.

[00206] Unless otherwise specified, the Rp/Sp designations preceding an oligonucleotide sequence describe the configurations of linkage phosphorus in chirally controlled intemucleotidic linkages sequentially from 5’ to 3’ of the oligonucleotide sequence. For instance, in (Rp, Sp)- ATsCslGA, the phosphorus in the“s” linkage between T and C has Rp configuration and the phosphorus in“s i” linkage between C and G has Sp configuration. In some embodiments,“All-(Rp)” or“Ail-(Sp)” is used to indicate that ail chiral linkage phosphorus atoms in chirally controlled intemucleotidic linkages have the same Rp or Sp configuration, respectively. For instance, All-(Rp)- GsCsCsTsCsAsGsTsCsT ' sGsCsTsTsCsGsCsAsCsC indicates that ail the chiral linkage phosphorus atoms the oligonucleotide have Rp configuration; All-(Sp)-

GsCsCsTsCsAsGsTsCsTsGsCsTsTsCsGsCsAsCsC indicates that ail the chiral linkage phosphorus atoms in the oligonucleotide have 5p configuration.

[00207] Oligonucleotide type: As used herein, the phrase“oligonucleotide type” is used to define oligonucleotides that have a particular base sequence, partem of backbone linkages (i.e , partem of intemucleotidic linkage types, for example, natural phosphate linkages, phosphorothioate intemucleotidic linkages, negatively charged intemucleotidic linkages, neutral intemucleotidic linkages etc), pattern of backbone chiral centers (i.e pattern of linkage phosphorus stereochemistry (Rp/Sp)), and pattern of backbone phosphorus modifications (e.g , pattern of “-X-L-R 1 ” groups in formula I). In some embodiments, oligonucleotides of a common designated“type” are structurally identical to one another.

100208 One of skill in the art will appreciate that synthetic methods of the present disclosure provide for a degree of control during the synthesis of an oligonucleotide strand such that each nucleotide unit of the oligonucleotide strand can be designed and/or selected in advance to have a particular stereochemistry at the linkage phosphorus and/or a particular modification at the linkage phosphorus, and/or a particular base, and/or a particular sugar. In some embodiments, an oligonucleotide strand is designed and/or selected in advance to have a particular combination of stereocenters at the linkage phosphorus. In some embodiments, an oligonucleotide strand is designed and/or determined to have a particular combination of modifications at the linkage phosphorus. In some embodiments, an oligonucleotide strand is designed and/or selected to have a particular combination of bases. In some embodiments, an oligonucleotide strand is designed and/or selected to have a particular combination of one or more of the above structural characteristics. The present disclosure provides compositions comprising or consisting of a plurality of oligonucleotide molecules (e.g., chi rally controlled oligonucleotide compositions). In some embodiments, all such molecules are of the same type. In some embodiments, all such molecules are structurally identical to one another. In some embodiments, provided compositions comprise a plurality of oligonucleotides of different types, typically in pre- determined (non-random) relative amounts.

[00209] Chiral control: As used herein,“chiral control” refers to control of the stereochemical designation of a chiral linkage phosphorus in a chiral intemucleotidic linkage within an oligonucleotide. In some embodiments, a control is achieved through a chiral element that is absent from the sugar and base moieties of an oligonucleotide, for example, in some embodiments, a control is achieved through use of one or more chiral auxiliaries during oligonucleotide preparation as exemplified in the present disclosure, which chiral auxiliaries often are part of chiral phosphoramidites used during oligonucleotide preparation. In contrast to dural control, a person having ordinary skill in the art appreciates that conventional oligonucleotide synthesis which does not use chiral auxiliaries cannot control stereochemistr^ at a chiral intemucleotidic linkage if such conventional oligonucleotide synthesis is used to form the chiral intemucleotidic linkage. In some embodiments, the stereochemical designation of each ural linkage phosphorus a chiral intemucleotidic linkage within an oligonucleotide is controlled.

[00210] Chi rally controlled oligonucleotide composition : The terms “chirally controlled

(stereocontrol led or stereodefmed) oligonucleotide composition”,“chirally controlled (stereocontrolled or stereodefined) nucleic acid composition”, and the like, as used herein, refers to a composition that comprises a plurality of oligonucleotides (or nucleic acids, chirally controlled oligonucleotides or chirally controlled nucleic acids) which share 1) a common base sequence, 2) a common pattern of backbone linkages; 3) a common pattern of backbone chiral centers, and 4) a common pattern of backbone phosphorus modifications (oligonucleotides of a particular type), wherein the plurality of oligonucleotides (or nucleic acids) share the same stereochemistry at one or more chiral intemucleotidic linkages (chirally controlled intemucleotidic linkages, whose chiral linkage phosphorus is Rp or Sp, not a random Rp and Sp mixture as non -chirally controlled intemucleotidic linkages). Level of the plurality of oligonucleotides (or nucleic acids) in a chirally controlled oligonucleotide composition is non-random (pre-determined, controlled). Chirally controlled oligonucleotide compositions are typically prepared through chirally controlled oligonucleotide preparation to stereoselectively form one or more chiral intemucleotidic linkages (e.g., using chiral auxiliaries as exemplified in the present disclosure, compared to non-chi rally controlled (stereorandom, non-stereoselective, racemic) oligonucleotide synthesis such as traditional phosphoramidite-based oligonucleotide synthesis using no chiral auxiliaries or chiral catalysts to purposefully control stereoselectivity). A chirally controlled oligonucleotide composition is enriched, relative to a substantially racemic preparation of oligonucleotides having the common base sequence, the common pattern of backbone linkages, and the common pattern of backbone phosphorus modifications, for oligonucleotides of the plurality. In some embodiments, a chirally controlled oligonucleotide composition comprises a plurality of oligonucleotides of a particular oligonucleotide type defined by: 1) base sequence: 2) pattern of backbone linkages; 3) patern of backbone chiral centers; and 4) patern of backbone phosphorus modifications, wherein it is enriched, relative to a substantially racemic preparation of oligonucleotides having the same base sequence, pattern of backbone linkages, and pattern of backbone phosphorus modifications, for oligonucleotides of the particular oligonucleotide type. As one having ordinary skill in tire art readily appreciates, such enrichment can be characterized in that compared to a substantially racemic preparation, at each chirally controlled intemucleotidi c linkage, a higher level of the linkage phosphorus has the desired configuration. In some embodiments, each chirally controlled intemucleotidic linkage independently has a diastereopurity of at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% with respect to its chiral linkage phosphorus. In some embodiments, each independently has a diastereopurity of at least 90%. In some embodiments, each independently has a diastereopurity of at least 95% In some embodiments, each independently has a diastereopurity of at least 97% In some embodiments, each independently has a diastereopurity of at least 98% In some embodiments, oligonucleotides of a plurality have the same constitution. In some embodiments, oligonucleotides of a plurality have the same constitution and stereochemistry, and are structurally identical.

In some embodiments, the plurality of oligonucleotides in a chi rally controlled oligonucleotide composition share the same base sequence, the same, if any, nucleobase, sugar, and mtemucleotidic linkage modifications, and the same stereochemistry (Rp or Sp) independently at linkage phosphorus chiral centers of one or more chirally controlled intemucleotidic linkages, though stereochemistr^ of certain linkage phosphorus chiral centers may differ. In some embodiments, about 0.1%-10Q%, (e.g., about 1%-100%, 5%-100%, 1Q%-1Q0%, 20%-100%, 3Q%-10Q%, 40%-100%, 5Q%- 100%, 60%-100%, 70%-100%, 80-100%, 90-100%, 95-100%, 50%-90%, or about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, or at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) of all oligonucleotides in a chirally controlled oligonucleotide composition are oligonucleotides of the plurality. In some embodiments, about 0.1%-100%, (e.g., about 1%-10Q%, 5%- 100%, 10%-100%, 20%-100%, 30%-! 00%, 40%~i00%, 50%-100%, 60%-100%, 70%-100%, 80-100%, 90-100%, 95-100%, 50%-90%, or about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, or at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) of all oligonucleotides a chirally controlled oligonucleotide composition that share the common base sequence are oligonucleotides of the plurality. In some embodiments, about 0.1%~!00%, (e.g., about 1 %~ 100%, 5%- 100%, 10%-100%, 20%~1 G0%, 30%-100%, 40%-100%, 50%-100%, 60%-100%, 70%~10G%, 80-100%, 90-100%, 95-100%, 50%-90%, or about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, or at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) of all oligonucleotides in a chirally controlled oligonucleotide composition that share the common base sequence, the common pattern of backbone linkages, and the common pattern of backbone phosphorus modifications are oligonucleotides of the plurality. In some embodiments, about 0.1%-1G0%, (e.g., about 1 %~ 100%, 5%- 100%, 10%-100%, 20%~100%, 30%-100%, 40%-100%, 50%-100%, 60%~100%, 70%-100%, 80-100%, 90-100%, 95-100%, 50%-90%, or about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, or at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) of all oligonucleotides in a chirally controlled oligonucleotide composition, or of all oligonucleotides in a composition that share a common base sequence (e.g., of a plurality of oligonucleotide or an oligonucleotide type), or of all oligonucleotides in a composition that share a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone phosphorus modifications (e.g., of a plurality of oligonucleotide or an oligonucleotide type), or of all oligonucleotides in a composition that share a common base sequence, a common patter of base modifications, a common pattern of sugar modifications, a common pattern of intemucleotidic linkage types, and/or a common pattern of intemucleotidic linkage modifications (e.g., of a plurality of oligonucleotide or an oligonucleotide type), or of all oligonucleotides in a composition that share the same constitution, are oligonucleotides of the plurality hi some embodiments, a percentage is at least (DP) NC! , wherein DP is a percentage selected from 85%-100%, and NCI is the number of chirally controlled intemucleotidic linkage. In some embodiments, DP is at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%. In some embodiments, DP is at least 85%. In some embodiments, DP is at least 90%. hr some embodiments, DP is at least 95%. In some embodiments, DP is at least 96%. In some embodim nts, DP is at least 97%. In some embodiments, DP is at least 98%. In some embodiments, DP is at least 99%. In some embodiments, DP reflects diastereopurity of linkage phosphorus chiral centers chirally controlled intemucleotidic linkages. In some embodiments, diastereopurity of a linkage phosphorus chiral center of an intemucleotidic linkage may be typically assessed using an appropriate dimer comprising such an intemucleotidic linkage and the two nucleoside units being linked by the intemucleotidic linkage. In some embodiments, the plurality of oligonucleotides share the same stereochemistry at about 1-50 (e.g., about MO, 1-20, 5-10, 5-20, 10-15, 10-20, 10-25, 10-30, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, I I, 12, 13, 14, 15, 16, 17, 18, 19, or 20, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, I I, 12, 13, 14, 15, 16, 17, 18, 19, or 20) chiral intemucleotidic linkages. In some embodiments, the plurality of oligonucleotides share the same stereochemistry ' at about Q.1%-100% (e.g. , about 1%~100%, 3%-100%, 10%-10G%, 20%-I00%, 30%- 100%, 40%-100%, 50%-100%, 60%-100%, 7Q%-100%, 80-100%, 90-100%, 95-100%, 50%-9Q%, about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, or at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99%) of chiral intemucleotidic linkages. In some embodiments, each chiral intemucleotidic linkage is a chiral controlled intemucleotidic linkage, and the composition is a completely chirally controlled oligonucleotide composition. In some embodiments, not all chiral intemucleotidic linkages are chiral controlled intemucleotidic linkages, and the composition is a partially chirally controlled oligonucleotide composition. In some embodiments, a chirally controlled oligonucleotide composition comprises predetermined levels of individual oligonucleotide or nucleic acids types. For instance, in some embodiments a chirally controlled oligonucleotide composition comprises one oligonucleotide type at a predetermined level (e.g., as described above). In some embodiments, a chirally controlled oligonucleotide composition comprises more than one oligonucleotide type, each independently at a predetermined level. In some embodiments, a chirally controlled oligonucleotide composition comprises multiple oligonucleotide types, each independently at a predetermined level. In some embodiments, a chirally controlled oligonucleotide composition is a composition of oligonucleotides of an oligonucleotide type, which composition comprises a predetermined level of a plurality of oligonucleotides of the oligonucleotide type.

[00212] Chirally pure: as used herein, the phrase “chirally pure” is used to describe an oligonucleotide or compositions thereof, in which all or nearly all (the rest are impurities) of the oligonucleotide molecules exist in a single diastereomeric form with respect to the linkage phosphorus atoms. In many embodiments, as appreciated by those skilled in the art, a chirally pure oligonucleotide composition is substantially pure in that substantially all of tire oligonucleotides in the composition are structurally identical (being the same stereoisomer).

[00213] Linkage phosphorus: as defined herein, the phrase“linkage phosphorus” is used to indicate that the particular phosphorus atom being referred to is the phosphoms atom present in an intemucleotidic linkage, which phosphoms atom corresponds to the phosphoms atom of a natural phosphate linkage as occurs in naturally occurring DNA and RNA. In some embodiments, a linkage phosphorus atom is in a modified intemucleotidic linkage. In some embodiments, a linkage phosphorus atom is the P of P L of formula I. in some embodiments, a linkage phosphorus atom is chiral .

|00214| P -modification: as used herein, the term“P-modification” refers to any modification at the linkage phosphorus other than a stereochemical modification. In some embodiments, a P- modification comprises addition, substitution, or removal of a pendant moiety covalently attached to a linkage phosphorus. In some embodiments, the“P -modification” is W, Y, Z, or -X-L-R ! of formula I.

[00215] Blockmer: the term “blockmer,” as used herein, refers to an oligonucleotide whose pattern of structural features characterizing each individual nucleotide unit is characterized by the presence of at least two consecutive nucleotide units sharing a common structural feature at the nucleobase, sugar and/or intemucleotidic linkage. By common structural feature is meant common chemistry and/or stereochemistry', e.g , common modifications at nucleobases, sugars, and/or intemucleotidic linkages and common stereochemistry at linkage phosphorus chiral centers. In some embodiments, the at least two consecutive nucleotide units sharing a common structural feature are referred to as a“block”.

[00216] In some embodiments, a blockmer is a“stereoblockmer,” e.g. at least two consecutive nucleotide units have the same stereochemistry at the linkage phosphorus. Such at least two consecutive nucleotide units form a“stereoblock.” For instance, (rip, rip)-ATsCslGA is a stereoblockmer because at least two consecutive nucleotide units, the Ts and the Csl, have the same stereochemistry at the linkage phosphorus (both rip). In the same oligonucleotide (rip, 5p)-ATsCslGA, TsCsl forms a block, and it is a stereoblock.

[00217] hi some embodiments, a blockmer is a“P-modification blockmer,” e.g.. at least two consecutive nucleotide units have the same modification at the linkage phosphorus. Such at least two consecutive nucleotide units form a“P-modification block”. For instance, (Rp, rip)~ATsCsGA is a P- modification blockmer because at least two consecutive nucleotide units, the Ts and the Cs, have the same P-modification (i.e., both are a phosphorothioate diester). In the same oligonucleotide of {Rp, rip)- ATsCsGA, TsCs forms a block, and it is a P-modification block.

[00218] In some embodiments, a blockmer is a“linkage blockmer,” e.g., at least two consecutive nucleotide units have identical stereochemistry and identical modifications at the linkage phosphorus. At least two consecutive nucleotide units form a“linkage block”. For instance, (Rp, Ap)~ATsCsGA is a linkage blockmer because at least two consecutive nucleotide units, the Ts and the Cs, have the same stereochemistry (both Rp) and P-modification (both phosphorothioate). In the same oligonucleotide of (Rp, Ap)-ATsCsGA, TsCs forms a block, and it is a linkage block.

100219] In some embodiments, a blockmer is a“sugar modification blockmer,” e.g., at least two consecutive nucleotide units have identical sugar modifications. In some embodiments, a sugar modification blockmer is a 2’-F blockmer wherein at least two consecutive nucleotide units have 2’-F modification at their sugars. In some embodiments, a sugar modification blockmer is a 2’ -OR blockmer wherein at lead two consecutive nucleotide units independently have 2 -OR modification at their sugars, wherein each R is independent as described in tire present disclosure. In some embodiments, a sugar modification blockmer is a 2’-QMe blockmer wherein at least two consecutive nucleotide units have 2 - OMe modification at their sugars. In some embodiments, a sugar modification blockmer is a 2’-MGE blockmer wherein at lead two consecutive nucleotide units have 2’-MOE modification at their sugars. In some embodiments, a sugar modification blockmer is a LNA blockmer wherein at least two consecutive nucleotide units have LNA sugars.

[00220] In some embodiments, a blockmer comprises one or more blocks independently selected from a sugar modification block, a stereoblock, a P-modification block and a linkage block. In some embodiments, a blockmer is a stereoblockmer with respect to one block, and/or a P-modification blockmer with respect to another block, and/or a linkage blockmer with respect to yet another block.

[00221] Altmer : the term“altmer,” as used herein, refers to an oligonucleotide whose pattern of structural features characterizing each individual nucleotide unit is characterized in that no two consecutive nucleotide units of the oligonucleotide strand share a particular structural feature at the nucleobase, sugar, and/or the internucleotidic phosphorus linkage. In some embodiments, an altmer is designed such that it comprises a repeating pattern. In some embodiments, an altmer is designed such that it does not comprise a repeating pattern.

100222 In some embodiments, an altmer is a“stereoaltmer,” e.g., no two consecutive nucleotide units have the same stereochemistry at the linkage phosphorus. For instance, (Rp, rip, Rp, rip, Rp, rip, Rp, rip, Rp, rip jRp, rip, Rp, rip, Rp, rip, Rp, rip, i¾>)-GsCsCsTsCsAsGsTsCsTsGsCsTsTsCsGsCsAsCsC.

[00223] Gapmer: as used herein, the term“gapmer” refers to an oligonucleotide characterized in that one or more nucleotide units (gap) do not have the structural features (e.g., nucleobase modifications, sugar modifications, internucleotidic linkage modifications, linkage phosphours stereochemistry, etc.) contained by nucleotide units flanking such one or more nucleotide units at both ends. In some embodiments, a gapmer comprises a gap of one or more natural phosphate linkages, independently flanked at both ends by non-natural internucleotidic linkages. In some embodiments, a gapmer is a sugar modification gapmer, wherein the gapmer comprises a gap of one or more nucleotide units comprising no sugar modifications which the flanking nucleotide at both ends contain. In some embodiments, a gapmer comprises a gap, wherein each nucleotide unit in the gap region contains no T -modification that is contained in nucleotide units flanking the gap at both ends. In some embodiments, a provided oligonucleotide comprising a gap, wherein each nucleotide unit in the gap region contains no 2’ -OR modification, while nucleotide units flanking the gap at each end independently comprise a 2’ -OR modification. In some embodiments, a provided oligonucleotide comprising a gap, wherein each nucleotide unit in the gap region contains no 2’-F modification, while nucleotide units flanking the gap at each end independently comprise a 27 -F modification.

[00224] Skipmer : as used herein, the term“skipmer” refers to a type of gapmer which every other internucleotidic phosphorus linkage of the oligonucleotide strand is a phosphate diester linkage (a natural phosphate linkage), for example such as those found in naturally occurring DNA or RNA, and every ' other internucleotidic phosphorus linkage of the oligonucleotide strand is a modified internucleotidic linkage (a non-natural internucleotidic linkage).

[00225] For purposes of this disclosure, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 67th Ed., 1986- 87, inside cover.

|00226| Unless otherwise specified, salts, such as pharmaceutically acceptable acid or base addition salts, stereoisomeric forms, and tautomeric forms, of compounds (e.g., oligonucleotides, agents, etc.) are included. Unless otherwise specified, singular forms“a”,“an”, and“the” include the plural reference unless the context clearly indicates otherwise (and vice versa). Thus, for example, a reference to“a compound” may include a plurality of such compounds.

[00227] Synthetic oligonucleotides provide useful molecular tools in a wide variety of applications. For example, oligonucleotides are useful in therapeutic, diagnostic, research, and new nanomaterials applications. The use of naturally occurring nucleic acids (e.g., unmodified DNA or RNA) is limited, for example, by their susceptibility to endo- and exo-nucleases. As such, various synthetic counterparts have been developed to circumvent these shortcomings. These include synthetic oligonucleotides that contain chemical modification, e.g., base modifications, sugar modifications, backbone modifications, etc., which, among other things, render these molecules less susceptible to degradation and improve other properties of oligonucleotides. Chemical modifications may also lead to certain undesired effects, such as increased toxicides, etc. From a structural point of view, modifications to natural phosphate linkages can introduce chirality, and certain properties of oligonucleotides may be affected by the configurations of the phosphorus atoms that form the backbone of the oligonucleotides.

[00228] in some embodiments, an oligonucleotide or oligonucleotide composition is: a DMD oligonucleotide or oligonucleotide composition; an oligonucleotide or oligonucleotide composition comprising a non-negatively charged internucleotidic linkage; or a DMD oligonucleotide comprising a non-negatively charged internucleotidic linkage. [00229] In some embodiments, the chirality of the backbone (e.g., the configurations of the phosphorus atoms) or inclusion of natural phosphate linkages or non-natural internucieotidic linkages in the backbone and/or modifications of a sugar and/or nucleobase, and/or the addition of chemical moieties can affect properties and activities of oligonucleotides, e.g., the ability of a DMD oligonucleotide (e.g., an oligonucleotide antisense to a Dystrophin (DMD) transcript sequence) to skip one or more exons, and/or other properties of a DMD oligonucleotide, including but not limited to, increased stability, improved pharmacokinetics, and/or decreased immunogenicity, etc. Suitable assays for assessing properties and/or activities of provided compounds, e.g., oligonucleotides, and compositions thereof are widely known in the art and can be utilized in accordance with the present disclosure. For example, to test immunogenicity, various DMD oligonucleotides were tested in mouse serum in vivo and demonstrated minimal activation of cytokines, and various DMD oligonucleotides were tested ex vivo in human PBMC (peripheral blood mononuclear cells) for cytokine activity (e.g., IL-12p4Q, IL-l2p7Q, TL- 1 alpha, IL-lbeta, IL-6, MCP-1, MIP-lalpha, MIP-lheta, and TNF-alpha).

[00230] hi some embodiments, technologies (e.g., oligonucleotides, compositions, and methods of use thereof) of the present disclosure can be utilized to target various nucleic acids (e.g., by hybridizing to a target sequence of a target nucleic acid, and/or providing level reduction, degradation, splicing modulation, transcription suppression, etc. of the target nucleic acid, etc.) In some embodiments, provided technologies are particularly useful for modulating splicing of transcripts, e.g., to increase levels of desired splicing products and/or to reduce levels of undesired splicing products hi some embodiments, provided technologies are particularly useful for reducing levels of transcripts, e.g., pre- mRNA, RNA, etc., and in many instances, reducing levels of products arising from or encoded by such transcripts such as mRNA, proteins, etc.

[00231] In some embodiments, a transcript is pre-mRNA. In some embodiments, a splicing product is mature RNA. In some embodiments, a splicing product is mRNA. In some embodiments, splicing modulation or alteration comprises skipping one or more exons. In some embodiments, splicing of a transcript is improved in that exon skipping increases levels of mRNA and proteins that have improved beneficial activities compared with absence of exon skipping. In some embodiments, an exon causing frameshift is skipped. In some embodiments, an exon comprising an undesired mutation is skipped. In some embodiments, an exon comprising a premature termination codon is skipped. An undesired mutation can be a mutation causing changes in protein sequences; it can also be a silent mutation. In some embodiments, a transcript is a transcript of Dystrophin (DMD).

[00232] In some embodiments, splicing of a transcript is improved in that exon skipping lowers levels of mRNA and proteins that have undesired activities compared with absence of exon skipping. In some embodiments, a target is knocked down through exon skipping which, by skipping one or more exons, causes premature stop codon and/or frameshift mutations. In some embodiments, provided oligonucleotides in provided compositions, e.g., oligonucleotides of a plurality, comprise base modifications, sugar modifications, and/or intemucleotidic linkage modifications. In some embodiments, provided oligonucleotides comprise base modifications and sugar modifications. In some embodiments, provided oligonucleotides comprise base modifications and intemucleotidic linkage modifications. In some embodiments, provided oligonucleotides comprise sugar modifications and intemucleotidic modifications. In some embodiments, provided compositions comprise base modifications, sugar modifications, and intemucleotidic linkage modifications. Example chemical modifications, such as base modifications, sugar modifications, intemucleotidic linkage modifications, etc. are widely known in the art including but not limited to those described in this disclosure. In some embodiments, a modified base is substituted A, T, C, G or U. In some embodiments, a sugar modification is 2’ -modification in some embodiments, a 2’~modification is 2-F modification. In some embodiments, a 2 '-modification is 2’-OR 1 , wherein R is not hydrogen. In some embodiments, a 2’-modification is 2’ -OR 1 , wherein R is optionally substituted alkyl. In some embodiments, a 2’-modification is 2’-OMe. In some embodiments, a 2 - modification is 2’-MOE, In some embodiments, a modified sugar moiety is a bridged bicyclic or polycyclic ring. In some embodiments, a modified sugar moiety is a bridged bicyclic or polycyclic ring having 5-20 ring atoms wherein one or more ring atoms are optionally and independently heteroatoms. Example ring structures are widely known in the art, such as those found in BNA, LNA, etc. In some embodiments, provided oligonucleotides comprise both one or more modified intemucleotidic linkages and one or more natural phosphate linkages. In some embodiments, oligonucleotides comprising both modified intemucleotidic linkage and natural phosphate linkage and compositions thereof provide improved properties, e.g., activities and toxicities, etc. In some embodiments, a modified intemucleotidic linkage is a chiral intemucleotidic linkage. In some embodiments, a modified intemucleotidic linkage is a phosphorothioate linkage. In some embodiments, a modified intemucleotidic linkage is a substituted phosphorothioate linkage.

[00233] In some embodiments, provided oligonucleotides comprise one or more non -negatively charged intemucleotidic linkages. In some embodiments, a non-negatively charged intemucleotidic linkage is a positively charged intemucleotidic linkage. In some embodiments, a non-negatively charged intemucleotidic linkage is a neutral intemucleotidic linkage. In some embodiments, a modified intemucleotidic linkage (e.g., a non-negatively charged intemucleotidic linkage) comprises optionally substituted triazolyl. In some embodiments, a modified intemucleotidic linkage (e.g., a non-negatively charged intemucleotidic linkage) comprises optionally substituted alkynyl. In some embodiments, a modified intemucleotidic linkage comprises a triazole or alkyne moiety. In some embodiments, a triazole moiety, e.g., a triazolyl group, is optionally substituted. In some embodiments, a triazole moiety, e.g., a triazolyl group) is substituted. In some embodiments, a triazole moiety is unsubstituted. In some embodiments, a modified intemucleotidic linkage comprises an optionally substituted guanidine moiety. In some embodiments, a modified intemucleotidic linkage comprises an optionally substituted cyclic guanidine moiety. In some embodiments, a modified intemucleotidic linkage comprises an optionally

substituted cyclic guanidine moiety and has the structure of: , wherem W is O or S. In some embodiments, W is O. In some embodiments, W is S. In some embodiments, a non -negatively charged intemucleotidic linkage is stereochemically controlled.

[00234] In some embodiments, an intemucleotidic linkage comprising an optionally substituted guanidine moiety is an intemucleotidic linkage of formula I-n-2, 1-n-3, 1-n-4, II-a-2, II-b-1, II-b-2, II- c- 1, II-c-2, II-d-1 , or II-d-2 as described herein. In some embodiments, an intemucleotidic linkage comprising an optionally substituted cyclic guanidine moiety is an intemucleotidic linkage of formula II- a-2, II-b-1, II-b-2, Il-c-1, II-c-2, II-d-1, or II-d-2.

[00235] Among other things, the present disclosure encompasses the recognition that stereorandom oligonucleotide preparations contain a plurality of distinct chemical entities that differ from one another, e.g., in the stereochemical structure of individual backbone linkage phosphorus chiral centers within the oligonucleotide chain. Without control of stereochemistr ' of backbone chiral centers, stereorandom oligonucleotide preparations provide uncontrolled compositions comprising undetermined levels of oligonucleotide stereoisomers with respect to the uncontrolled chiral centers, e.g., chiral linkage phosphorus. Even though these stereoisomers may have the same base sequence, they are different chemical entities at least due to their different backbone stereochemistry, and they can have, as demonstrated herein, different properties, e.g., activities, toxicides, etc. Among other things, the present disclosure provides new oligonucleotide compositions wherein stereochemistry of one or more linkage phosphorus chiral centers are independently controlled (e.g., in chirally controlled intemucleotidic linkages). In some embodiments, the present disclosure provides chirally controlled oligonucleotide compositions which are or contain particular stereoisomers of oligonucleotides of interest.

[00236] In some embodiments, provided oligonucleotides contain increased levels of one or more isotopes. In some embodiments, provided oligonucleotides are labeled, e.g., by one or more isotopes of one or more elements, e.g., hydrogen, carbon, nitrogen, etc. In some embodiments, provided oligonucleotides in provided compositions, e.g, oligonucleotides of a plurality, comprise base modifications, sugar modifications, and/or infemueleotidie linkage modifications, wherein the oligonucleotides contain an enriched level of deuterium. In some embodiments, provided oligonucleotides are labeled with deuterium (replacing - 1 H with - 2 H) at one or more positions. In some embodiments, one or more ¾ of an oligonucleotide or any moiety conj ugated to the oligonucleotide (e.g. , a targeting moiety, lipid, etc.) is substituted with 2 H. Such oligonucleotides can be used in any composition or method described herein.

[00237] In some embodiments, in an oligonucleotide, a pattern of backbone chiral centers can provide improved activity(s) or characteristic(s), including but not limited to: improved skipping of one or more exons, increased stability, increased activity, increased stability and activity, low toxicity, low immune response, improved protein binding profile, increased binding to certain proteins, and/or enhanced delivery.

[00238] In some embodiments, a pattern of backbone chiral centers is or comprises S, SS, SSS,

SSSS, SSSSS, SSSSSS, SSSSSSS, SOS, SSOSS, SSSOSSS, SSSSOSSSS, SSSSSOSSSSS, SSSSSSOSSSSSS, SSSSSSSOSSSSSSS, SSSSSSSSOSSSSSSSS, SSSSSSSSSOSSSSSSSSS, sosososos, ssososososs, sssososososss, ssssosososossss, sssssososososssss,

SSSSSSOSOSOSOSSSSSS, SOSOSSOOS, SSOSOSSOOSS, SSSOSOSSOOSSS, ssssosossoossss, sssssosossoosssss, ssssssosossoossssss, sosoosoos, ssosoosooss, sssosoosoosss, ssssosoosoossss, sssssosoosoosssss,

SSSSSSOSOOSOOSSSSSS, SOSOSSOOS, ssosossooso, sssosossoosos, ssssosossoososs, sssssosossoososss, ssssssosossoosossss, sosoosooso, ssosoosoosos, sssosoosoosos, ssssosoosoososs, sssssosoosoososss, ssssssosoosoosossss, ssosossoo, sssosossoos, ssssosossoos, sssssosossooss, ssssssosossoosss, ossssssosossoosss, oossssssosossoos, oossssssosossooss,

OOSSSSSSOSOSSOOSSS, OOSSSSSSOSOSSOOSSSS, OOSSSSSSOSOSSOOSSSSS, and/or OOSSSSSSOSOSSOOSSSSSS, RS, SR, SRS, SRSS, SSRS, RR, RRR, RRRR, RRRRR, SRR, RRS, SRRS, SSRRS, SRRSS, SRRR, RRRS, SRRRS, SSRRRS, SSRRRS, RSRRR, SRRRSR. SSSRSSS, SSSSRSSSS, SSSSSRSSSSS, SSSSSSRSSSSSS, SSSSSSSRSSSSSSS, SSSSSSSSRSSSSSSSS, SSSSSSSSSRSSSSSSSSS, SRSRSRSRS, SSRSRSRSRSS, SSSRSRSRSRSSS, SSSSRSRSRSRSSSS, SSSSSRSRSRSRSSSSS, SSSSSSRSRSRSRSSSSSS, SRSRSSRRS, SSRSRSSRRSS, SSSRSRSSRRSSS, SSSSRSRSSRRSSSS, SSSSSRSRSSRRSSSSS, SSSSSSRSRSSRRSSSSSS,

SRSRRSRRS, SSRSRRSRRSS, SSSRSRRSRRSSS, SSSSRSRRSRRSSSS, SSSSSRSRRSRRSSSSS, SSSSSSRSRRSRRSSSSSS, SRSRSSRRS, SSRSRSSRRSR, SSSRSRSSRRSRS, SSSSRSRSSRRSRSS, SSSSSRSRSSRRSRSSS, SSSSSSRSRSSRRSRSSSS, SRS RRS RRRR, SSRSRRSRRSRS, SSSRSRRSRRSRS, SSSSRSRRSRRSRSS, SSSSSRSRRSRRSRSSS, SSSSSSRSRRSRRSRSSSS, SSRSRSSRR, SSSRSRSSRRS, SSSSRSRSSRRS, SSSSSRSRSSRRSS, SSSSSSRSRSSRRSSS, RSSSSSSRSRSSRRSSS, RRSSSSSSRSRSSRRS, RRSSSSSSRSRSSRRSS, RRSSSSSSRSRSSRRSSS, RRSSSSSSRSRSSRRSSSS, RRSSSSSSRSRSSRRSSSSS, (R) n (S) m , (S) t (R) r , (0) t (R) n (S) m , (S (0) m , (0) m (S) t , (S) t (R) n (S) m , (S) t (0) m (S) n , (S) t (0) m , wherein t, m and n are independently 1 to 20, O is a non- chiral internucleotidic linkage, R is a Rp chiral internucleotidic linkage, and S is an Sp chiral intemucleotidic linkage. In some embodiments, the non-ehiral center is a phosphodiester linkage. In some embodiments, the chiral center in a Sp configuration is a phosphorothioate linkage.

[00239] In some embodiments, the 5’-end region of provided oligonucleotides, e.g., a 5’ -wing, comprises a stereochemistry pattern of S, SS, SSS, SSSS, SSSSS, SSSSSS, or SSSSSS. In some embodiments, each S is or represents an Sp phosphorothioate intemucleotidic linkage. In some embodiments, the 5’ -end region of provided oligonucleotides, e.g., a 5’ -wing, comprises a stereochemistry pattern of S, SS, SSS, SSSS, SSSSS, SSSSSS, or SSSSSS, wherein the first S represents the first (the 5’-end) intemucleotidic linkage of a provided oligonucleotide. In some embodiments, one or more nucleotidic units comprising an Sp intemucleotidic linkage in the 5’ -end region independently comprise -F. In some embodiments, each nucleotidic unit comprising an Sp intemucleotidic linkage in the 5’-end region independently comprises -F. In some embodiments, one or more nucleotidic units comprising an .Sp intemucleotidic linkage in the 5 -end region independently comprise a sugar modification. In some embodiments, each nucleotidic unit comprising an Sp intemucleotidic linkage in the 5’ -end region independently comprises a sugar modification. In some embodiments, each 2’- modification is the same. In some embodiments, a sugar modification is a 2’-modification. In some embodiments, a 2’-modification is 2’-QR l . In some embodiments, a 2’-modification is 2’-F. In some embodiments, the 3’-end region of provided oligonucleotides, e.g., a 3’-wing, comprises a stereochemistry pattern of S, SS, SSS, SSSS, SSSSS, SSSSSS, or SSSSSS. In some embodiments, each S is or represents an Sp phosphorothioate internucleotidic linkage. In some embodiments, the 3’-end region of provided oligonucleotides, e.g., a 3’-wing, comprises a stereochemistry pattern of S, SS, SSS, SSSS, SSSSS, SSSSSS, or SSSSSS, wherein the last S represents the last (the 3’-end) intemucleotidic linkage of a provided oligonucleotide. In some embodiments, each S represents an Sp phosphorothioate intemucleotidic linkage. In some embodiments, one or more nucleotidic units comprising an Sp internucleotidic linkage in the 3’-end region independently comprise -F. In some embodiments, each nucleotidic unit comprising an Sp internucleotidic linkage in the 3 -end region independently comprises -F. In some embodiments, one or more nucleotidic units comprising an Sp intemucieotidic linkage in the 3’-end region independently comprise a sugar modification. In some embodiments, each nucleotidic unit comprising an Sp internucleotidic linkage in the 3’-end region independently comprises a sugar modification. In some embodiments, each 2’-modification is the same. In some embodiments, a sugar modification is a 2’ -modification. In some embodiments, a 2’-modification is 2’-OR 1 . In some embodiments, a 2’-modification is 2’-F. In some embodiments, provided oligonucleotides comprise both a 5’-end region, e.g., a 5’-wing, and a 3’-end region, e.g., a 3’-end wing, as described herein. In some embodiments, the 5’-end region comprises a stereochemistry pattern of SS, wherein the first S represents the first mtemucleotidic linkage of a provided oligonucleotide, the 3’-end region comprises a stereochemistry pattern of SS, wherein one or more nucleotidie unit comprising an rip mtemucleotidic linkage in the 5’- or 3’-end region comprise -F. In some embodiments, the 5’-end region comprises a stereochemistry pattern of SS, wherein the first S represents the first mtemucleotidic linkage of a provided oligonucleotide, the 3’-end region comprises a stereochemistry pattern of SS, wherein one or more nucleotidie unit comprising an rip intemucleotidic linkage in the 5’- or 3’-end region comprise a 2’- F sugar modification. In some embodiments, provided oligonucleotides further comprise a middle region between the 5’-end and 3’-end regions, e.g., a core region, which comprises one or more natural phosphate linkages. In some embodiments, provided oligonucleotides further comprise a middle region between the 5’-end and 3’-end regions, e.g., a core region, which comprises one or more natural phosphate linkages and one or more intemucleotidic linkages. In some embodiments, a middle region comprises one or more sugar moieties, wherein each sugar moiety independently comprises a 2’-OR 1 modification. In some embodiments, a middle region comprises one or more sugar moieties comprising no 2’-F modification. In some embodiments, a middle region comprises one or more rip intemucleotidic linkages. In some embodiments, a middle region comprises one or more rip intemucleotidic linkages and one or more natural phosphate linkages. In some embodiments, a middle region comprises one or more .tip intemucleotidic linkages hi some embodiments, a middle region comprises one or more Rp intemucleotidic linkages and one or more natural phosphate linkages. In some embodiments, a middle region comprises one or more rip intemucleotidic linkages and one or more rip intemucleotidic linkages.

[00240] In some embodiments, provided oligonucleotides comprise one or more modified intemucleotidic linkages. In some embodiments, provided oligonucleotides comprise one or more chiral modified temucleotidic linkages. In some embodiments, provided oligonucleotides comprise one or more chirally controlled chiral modified intemucleotidic linkages. In some embodiments, provided oligonucleotides comprise one or more natural phosphate linkages. In some embodiments, provided oligonucleotides comprise one or more modified intemucleotidic linkages and one or more natural phosphate linkages hi some embodiments, a modified intemucleotidic linkage is a phosphorothioate linkage. In some embodiments, each modified intemucleotidic linkage is a phosphorothioate linkage. In some embodiments, a modified intemucleotidic linkage comprises a triazole, substituted triazole, alkyne or Trng. [00241] In some embodiments, the present disclosure pertains to a nucleic acid which comprises a modified internucleotidic linkage comprising a triazole or aJkyne moiety. In some embodiments, the present disclosure pertains to a nucleic acid which comprises a modified internucleotidic linkage comprising an optionally substituted triazolyl or alkynyl. In some embodiments, such a nucleic acid is a siRNA, double-straned siRNA, single-stranded siRNA, oligonucleotide, gapmer, skipmer, blockmer, antisense oligonucleotide, antagomir, microRNA, pre-microRNA, antimir, supemiir, ribozyme, U1 adaptor, RNA activator, RNAi agent, decoy oligonucleotide, triplex forming oligonucleotide, aptamer or adjuvant. In some embodiments, the present disclosure pertains to an oligonucleotide which comprises a modified internucleotidic linkage comprising a triazole or alkyne moiety. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which comprises a modified internucleotidic linkage comprising a triazole or alkyne moiety. In some embodiments, the present disclosure pertains to a nucleic acid which comprises a modified internucleotidic linkage comprising a triazole moiety. In some embodiments, the present disclosure pertains to a nucleic acid which comprises a modified internucleotidic linkage comprising optionally substituted triazolyl. In some embodiments, the present disclosure pertains to a nucleic acid which comprises a modified internucleotidic linkage comprising a substituted triazole moiety. In some embodiments, the present disclosure pertains to a nucleic acid which comprises a modified internucleotidic linkage comprising an alkyne moiety. In some embodiments, the present disclosure pertains to a nucleic acid or oligonucleotide which comprises, at a 5’ end, a structure of

the formula: wherein W is O or S. In some embodiments, an oligonucleotide is a single-stranded siRNA which comprises, at a 5’ end, a

structure of the formula: wherein W is O or S. In some embodiments, a modified internucleotidic linkage is any modified internucleotidic linkage described in Krishna et al. 2012 J. Am. Chem. Soc. 134: 11618-11631.

[00242] In some embodiments, the present disclosure pertains to a nucleic acid which comprises a modified internucleotidic linkage which comprises a guanidine moiety. In some embodiments, the present disclosure pertains to a nucleic acid which comprises a modified internucleotidic linkage which comprises a cyclic guanidine moiety. In some embodiments, the present disclosure pertains to a nucleic acid which comprises a modified internucleotidic linkage which comprises a cyclic guanidine moiety and has the structure of: , wherein W is O or S. In some embodiments, a neutral intemucleotidic linkage or intemucleotidic linkage comprising a cyclic guanidine is chirally controlled. In some embodiments, a nucleic acid comprising a non-negatively charged intemucleotidic linkage or a modified intemucleotidic linkage comprising a cyclic guanidine moiety is a siRNA, double-straned siRNA, single -stranded siRNA, oligonucleotide, gapmer, skipmer, blockmer, antisense oligonucleotide, antagomir, microRNA, pre-microRNA, antimir, supermir, ribozyme, Ul adaptor, RNA activator, RNAi agent, decoy oligonucleotide, triplex forming oligonucleotide, aptamer or adjuvant. In some embodiments, the present disclosure pertains to an oligonucleotide which comprises a modified intemucleotidic linkage which comprises a cyclic guanidine moiety. In some embodiments, the present disclosure pertains to an oligonucleotide which comprises a modified intemucleotidic linkage which has

the structure of: , wherein W is O or S In some embodiments, a neutral intemucleotidic linkage or intemucleotidic linkage comprising a cyclic guanidine moiety is chirally controlled. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which comprises a modified intemucleotidic linkage comprising a cyclic guanidine moiety. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which comprises a modified

intemucleotidic linkage which has the structure of: , wherein W is O or S. In some embodiments, a neutral intemucleotidic linkage or intemucleotidic linkage comprising a cyclic guanidine moiety is chirally controlled. In some embodiments, the present disclosure pertains to a nucleic acid which comprises a modified intemucleotidic linkage comprising a cyclic guanidine moiety. In some embodiments, the present disclosure pertains to a nucleic acid which comprises a modified

intemucleotidic linkage which has the structure of: , wherein W is O or S. In some embodiments, the present disclosure pertains to a nucleic acid or oligonucleotide which comprises, at a 5’ end, a structure comprising a cyclic guanidine moiety. In some embodiments, the present disclosure pertains to a nucleic acid or oligonucleotide which comprises, at a 5’ end, a structure of the formula:

, wherein W is O or S. In some embodiments, the oligonucleotide is a single -stranded siRNA which comprises, at a 5’ end, a structure comprising a cyclic guanidine moiety. In some embodiments, the oligonucleotide is a single-stranded siRNA which comprises, at a 5’ end, a structure of

the formula: , wherein W is O or S. In some embodiments, the intemucleotidic linkage

o a transcript, and change the splicing pattern of the transcript. In some embodiments, provided oligonucleotides provides exon skipping of an exon, with efficiency greater than a comparable oligonucleotide under one or more suitable conditions, e.g., as described herein. In some embodiments, a provided skipping efficiency is at least10%, 2.0%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190% more than, or 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50 or more fold of, that of a comparable oligonucleotide under one or more suitable conditions, e.g., as described herein. In some embodiments, a comparable oligonucleotide is an oligonucleotide which has fewer or no chirally controlled intemucleotidic linkages and/or fewer or no non -negatively charged intemucleotidic linkages but is otherwise identical.

|00244| In some embodiments, the present disclosure demonstrates that 2’-F modifications, among other things, can improve exon-skipping efficiency. In some embodiments, the present disclosure demonstrates that Sp intemucleotidic linkages, among other things, at the 5’- and 3’-ends can improve oligonucleotide stability. In some embodiments, the present disclosure demonstrates that, among other things, natural phosphate linkages and/or Rp intemucleotidic linkages can improve removal of oligonucleotides from a system. As appreciated by a person having ordinar skill in the art, various assays known in the art can be utilized to assess such properties in accordance with the present disclosure.

[00245] In some embodiments, provided oligonucleotides comprise one or more modified sugar moieties. In some embodiments, a modified sugar moiety comprises a 2’ -modification. In some embodiments, a modified sugar moiety comprises a 2’-modification. In some embodiments, a T- modification is 2’-OR\ In some embodiments, a 2 '-modification is a 2’-OMe. In some embodiments, a 2’-modification is a 27-MOE In some embodiments, a 2’ -modification is an LNA sugar modification. In some embodiments, a 2’ -modification is 2’-F. In some embodiments, each sugar modification is independently a 2’-modification. In some embodiments, each sugar modification is independently 2’-OR‘ or 2’-F. In some embodiments, each sugar modification is independently 2 -QR 1 or 2’-F, wherein R 1 is optionally substituted C ]-6 alkyl. In some embodiments, each sugar modification is independently 2’-OR 1 or 2’-F, wherein at least one is 2’-F. In some embodiments, each sugar modification is independently 2’- OR 1 or 2’-F, wherein R 1 is optionally substituted (% 6 alkyl, and wherein at least one is 2’-OR 5 . In some embodiments, each sugar modification is independently 2’-OR 1 or 2’-F, wherein at least one is 2’-F, and at least one is 2’-OR 1 . In some embodiments, each sugar modification is independently 2’ -OR 1 or 2’-F, wherein R 1 is optionally substituted C l-6 alkyl, and wherein at least one is 2’-F, and at least one is 2 -OR 1 [00246] In some embodiments, 5% or more of the sugar moieties of provided oligonucleotides are modified. In some embodiments, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, or more of the sugar moieties of provided oligonucleotides are modified. In some embodiments, each sugar moiety of provided oligonucleotides is modified in some embodiments, a modified sugar moiety comprises a 2’-modification. In some embodiments, a modified sugar moiety comprises a 2’ -modification. In some embodiments, a 2’-modification is 2’-OR 1 . In some embodiments, a 2’-modification is a 2’-OMe. hi some embodiments, a T -modification is a 2’-MOE. In some embodiments, a T -modification is an LNA sugar modification. In some embodiments, a 2’~modification is 2’-F. In some embodiments, each sugar modification is independently a 2’-inodification In some embodiments, each sugar modification is independently 2’-OR 1 or 2’-F In some embodiments, each sugar modification is independently 2’-OR 1 or 2’-F, wherein R 1 is optionally substituted C |-6 alkyl. In some embodiments, each sugar modification is independently 2’-OR 1 or 2’-F, wherein at least one is 2’-F. In some embodiments, each sugar modification is independently 2’ -OR 1 or 2’-F, wherein R' is optionally substituted (% 6 alkyl, and wherein at least one is 2’-OR 1 In some embodiments, each sugar modification is independently 2’-OR 1 or 2’-F, wherein at least one is 2’-F, and at least one is 2’-OR 1 . In some embodiments, each sugar modification is independently 2’-OR 1 or 2’-F, wherein R ! is optionally substituted C ]-6 alkyl, and wherein at least one is 2’~F, and at least one is 2’~QR 1 .

[00247] In some embodiments, provided oligonucleotides comprise one or more 2’~F In some embodiments, provided oligonucleotides comprise two or more 2’-F.

[00248] In some embodiments, provided oligonucleotides comprise alternating 2’-F modified sugar moieties and 2’ -OR 1 modified sugar moieties. In some embodiments, provided oligonucleotides comprise alternating 2’-F modified sugar moieties and 2’-OMe modified sugar moieties, e.g., [(2’~F)(2’~ OMe)]x, [(2’-OMe)(2’-F)]x, etc., wherein x is 1-50. In some embodiments, provided oligonucleotides comprise at least two pairs of alternating 2'-F and 2'-OMe modifications. In some embodiments, provided oligonucleotides comprises alternating phosphodiester and phosphorothioate intemucleotidie linkages, e.g., [(PO)(PS)]x, [(PS)(PO)]x, etc., wherein x is 1 -50. In some embodiments, provided oligonucleotides comprise at least two pairs of alternating phosphodiester and phosphorothioate intemucleotidie linkages.

[00249] In some embodiments, provided oligonucleotides comprise one or more natural phosphate linkages and one or more modified intemucleotidie linkages. In some embodiments, provided oligonucleotides comprise one or more natural phosphate linkages and one or more modified intemucleotidie linkages and one or more non-negatively charged intemucleotidie linkages.

100250 In some embodiments, the present disclosure provides an oligonucleotide composition comprising a plurality of oligonucleotides, wherein:

oligonucleotides of the plurality have the same base sequence; and

oligonucleotides of the plurality comprise one or more modified sugar moieties, or comprise one or more natural phosphate linkages and one or more modified intemucleotidie linkages.

[00251] In some embodiments, oligonucleotides of a plurality comprise one or more modified sugar moieties. In some embodiments, provided oligonucleotides comprise one or more modified sugar moieties. In some embodiments, provided oligonucleotides comprise 2 or more modified sugar moieties. In some embodiments, provided oligonucleotides comprise 3 or more modified sugar moieties.

[00252] In some embodiments, provided compositions alter transcript splicing so that an undesired target and/or biological function are suppressed.

[00253] In some embodiments, provided compositions alter transcript splicing so a desired target and/or biological function is enhanced.

[00254] hi some embodiments, each oligonucleotide of a plurality comprises one or more modified sugar moieties and modified intemucleotidie linkages.

[00255] In some embodiments, each oligonucleotide of a plurality comprises no more than about

25 consecutive unmodified sugar moieties

[00256] In some embodiments, each oligonucleotide of a plurality comprises no more than about

95% unmodified sugar moieties. In some embodiments, each oligonucleotide of a plurality comprises no more than about 90% unmodified sugar moieties. In some embodiments, each oligonucleotide of a plurality comprises no more than about 85% unmodified sugar moieties. In some embodiments, each oligonucleotide of a plurality comprises no more than about 15 consecutive unmodified sugar moieties.

[00257] In some embodiments, each oligonucleotide of a plurality comprises no more than about

95% unmodified sugar moieties

100258] In some embodiments, each oligonucleotide of a plurality comprises two or more modified internucleotidic linkages.

[00259] In some embodiments, about 5% of the intemueleotidie linkages in each oligonucleotide of a plurality are modified intemucleotidic linkages.

[00260] In some embodiments, each oligonucleotide of a plurality comprises no more than about

25 consecutive natural phosphate linkages. In some embodiments, each oligonucleotide of a plurality comprises no more than about 20 natural phosphate linkages.

[00261] In some embodiments, oligonucleotides of a plurality comprise no natural DNA nucleotide units. In some embodiments, oligonucleotides of a plurality comprise no more than 30 natural DMA nucleotides. In some embodiments, oligonucleotides of a plurality comprise no more than 30 consecutive DNA nucleotides.

[00262] In some embodiments, compared to a reference condition, provided chirally controlled oligonucleotide compositions are surprisingly effective. In some embodiments, desired biological effects (e.g , as measured by increased levels of desired mKNA, proteins, etc., decreased levels of undesired mRNA, proteins, etc.) can be enhanced by more than 5, 10, 15, 20, 25, 30, 40, 50, or 100 fold. In some embodiments, a change is measured by increase of a desired mRNA level compared to a reference condition. In some embodiments, a change is measured by decrease of an undesired mRNA level compared to a reference condition. In some embodiments, a reference condition is absence of oligonucleotide treatment. In some embodiments, a reference condition is a stereorandom composition of oligonucleotides having the same base sequence and chemical modifications.

[00263] In some embodiments, a desired biological effect is: improved skipping of one or more exons, increased stability, increased activity, increased stability and activity, low toxicity, low immune response, improved protein binding profile, increased binding to certain proteins, and/or enhanced deliver],’. In some embodiments, a desired biological effect is enhanced by more than 2 fold, 3 fold, 4 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 11 fold, 12 fold, 13 fold, 14 fold, 15 fold, 20 fold, 25 fold, 30 fold, 35 fold, 40 fold, 45 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, 100 fold, 200 fold, or 500 fold.

[00264] In some embodiments, the structure of a DMD oligonucleotide is or comprises a wing- core-wing, wing-core, or core-wing structure. In some embodiments, a 5’ -wing is a 5’ -end region. In some embodiments, a 3 -wing is a 3’-end region. In some embodiments, a core is a middle region. In some embodiments, a 5’-end region is a 5’-wing region. In some embodiments, a 3’-end region is a 3’- wing region. In some embodiments, a middle region is a core region.

[00265] In some embodiments, an oligonucleotide having a wing-core-wing structure is designated a gapmer. In some embodiments, a gapmer is asymmetric, in that the chemistry of one wing is different from the chemistry of the other wing. In some embodiments, a gapmer is asymmetric, in that the chemistry of one wing is different from the chemistry of the other wing, wherein the wings differ in sugar modifications and/or intemudeotidic linkages, or patterns thereof. In some embodiments, a gapmer is asymmetric, in that the chemistry of one wing is different from the chemistr ' of the other wing, wherein the wings differ in sugar modifications, wherein one wing comprises a sugar modification not present in the other wing; or both wings each comprise a sugar modification not found in the other wing; or both wings comprise different patterns of tire same types of sugar modifications; or one wing comprises only one type of sugar modification, while the other wing comprises two types of sugar modifications; etc.

[00266] In some embodiments, an intemudeotidic linkage between a wing region and a core region is considered part of the wing region. In some embodiments, an intemudeotidic linkage between a 5’-wing region and a core region is considered part of tire wing region hr some embodiments, an intemudeotidic linkage between a 3’ -wing region and a core region is considered part of the wing region. In some embodiments, an intemudeotidic linkage between a wing region and a core region is considered part of the core region. In some embodiments, an intemudeotidic linkage between a 5’-wing region and a core region is considered part of the core region. In some embodiments, an intemudeotidic linkage between a 3’-wing region and a core region is considered part of the core region.

[00267] In some embodiments, a region (e.g , a wing region, a core region, a 5’-end region, a middle region, a 3’-end region, etc.) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more nucleoside units.

[00268] In some embodiments, provided oligonucleotides comprise two wing and one core regions. In some embodiments, provided oligonucleotides comprises a 5’-wing-core-wing-3’ structure. In some embodiments, provided oligonucleotides are of a 5’-wing-core-wing-3’ gapmer structure. In some embodiments, die two wing regions are identical. In some embodiments, the two wing regions are different. In some embodiments, the two wing regions are identical in chemical modifications. In some embodiments, the two wing regions are identical in 2’-modifications. In some embodiments, the two wing regions are identical in intemudeotidic linkage modifications. In some embodiments, the two wing regions are identical in patterns of backbone chiral centers hi some embodiments, the two wing regions are identical in pattern of backbone linkages. In some embodiments, the two wing regions are identical in pattern of backbone linkage types. In some embodiments, the two wing regions are identical in pattern of backbone phosphorus modifications.

[00269] A wing region can be differentiated from a core region in that a wing region contains a different structure feature than a core region. For example, in some embodiments, a wing region differs from a core region in that they' have different sugar modifications, base modifications, intemudeotidic linkages, intemudeotidic linkage stereochemistry, etc. In some embodiments, a wing region differs from a core region in that they have different 2’ -modifications of the sugars. [00270] In some embodiments, a region (e.g., a wing region, a core region, a 5’ -end region, a middle region, a 3’ -end region, etc.) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, or more modified intemucieotidic linkages. In some embodiments, a region comprises 2 or more modified intemucieotidic linkages. In some embodiments, a region comprises 3 or more modified intemucieotidic linkages. In some embodiments, a region comprises 4 or more modified intemucieotidic linkages in some embodiments, a region comprises 5 or more modified intemucleotidic linkages. In some embodiments, a region comprises 6 or more modified intemucieotidic linkages. In some embodiments, a region comprises 7 or more modified intemucieotidic linkages. In some embodiments, a region comprises 8 or more modified intemucieotidic linkages. In some embodiments, a region comprises 9 or more modified intemucieotidic linkages. In some embodiments, a region comprises 10 or more modified intemucieotidic linkages.

[00271] In some embodiments, provided oligonucleotides comprise consecutive nucleoside units each of which comprises no 2’-OR 1 modifications (wherein R 1 is not hydrogen). In some embodiments, provided oligonucleotides comprise consecutive nucleoside units whose 2’-positions are independently unsubstituted or substituted with 2’-F. In some embodiments, such an oligonucleotide is a DMD oligonucleotide. In some embodiments, each of the consecutive nucleoside units is independently preceded and/or followed by a modified intemucieotidic linkage. In some embodiments, each of die consecutive nucleoside units is independently preceded and/or followed by a phosphorothioate linkage. In some embodiments, each of the consecutive nucleoside units is independently preceded and/or followed by a chirally controlled modified intemucieotidic linkage. In some embodiments, each of the consecutive nucleoside units is independently preceded and/or followed by a chirally controlled phosphorothioate linkage.

[00272] In some embodiments, a modified intemucieotidic linkage has the structure of formula I,

I-a, I-b, I-c, I-n-1, 1-n-2, 1-n-3, I-n~4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, III, etc., or a salt form thereof. In some embodiments, a modified intemucieotidic linkage has a structure of formula I or a salt form thereof. In some embodiments, a modified intemucieotidic linkage has a structure of formula I-a or a salt form thereof.

[00273] In some embodiments, a modified intemucieotidic linkage is a non-negatively charged intemucieotidic linkage. In some embodiments, a modified intemucieotidic linkage is a positively- charged intemucieotidic linkage. In some embodiments, a modified intemucieotidic linkage is a neutral intemucieotidic linkage. In some embodiments, a non-negatively charged intemucieotidic linkage has the structure of formula I, I-a, I-b, I-c, I-n-1, i n-2. 1-n-3, i n- 4. II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II- c-2, II-d-1, II-d-2, etc., or a salt form thereof. In some embodiments, a non-negatively charged intemucieotidic linkage comprises an optionally substituted 3-20 membered heterocyclyl or heteroaryl group having 1-10 heteroatoms. In some embodiments, a non-negatively charged internucleotidic linkage comprises an optionally substituted 3-2.0 membered heterocyclyl or heteroaryl group having 1-10 heteroatoms, wherein at least one heteroatom is nitrogen. In some embodiments, such a heterocyclyl or heteroaryl group is of a 5 -membered ring. In some embodiments, such a heterocyclyl or heteroaryl group is of a 6-membered ring.

[00274] In some embodiments, a non-negatively charged internucleotidic linkage comprises an optionally substituted 5-20 membered heteroaryl group having 1-10 heteroatoms. In some embodiments, a non-negatively charged internucleotidic linkage comprises an optionally substituted 5-20 membered heteroaryl group having 1-10 heteroatoms, wherein at least one heteroatom is nitrogen. In some embodiments, a non-negatively charged internucleotidic linkage comprises an optionally substituted 5-6 membered heteroaryl group having 1-4 heteroatoms, wherein at least one heteroatom is nitrogen. In some embodiments, a non-negatively charged internucleotidic linkage comprises an optionally substituted 5- membered heteroaryl group having 1-4 heteroatoms, wherein at least one heteroatom is nitrogen. In some embodiments, a heteroaryl group is directly bonded to a linkage phosphorus hi some embodiments, a non-negatively charged internucleotidic linkage comprises an optionally substituted triazolyl group. In some embodiments, a non-negatively charged internucleotidic linkage comprises an unsubstituted triazolyl group, e.g some embodiments, a non-negatively charged internucleotidic

N~N linkage comprises a substituted triazolyl group, e.g.,

[00275] In some embodiments, a non-negatively charged internucleotidic linkage comprises an optionally substituted 5-20 membered heterocyclyl group having 1-10 heteroatoms. In some embodiments, a non-negatively charged internucleotidic linkage comprises an optionally substituted 5-20 membered heterocyclyl group having 1-10 heteroatoms, wherein at least one heteroatom is nitrogen. In some embodiments, a non-negatively charged internucleotidic linkage comprises an optionally substituted 5-6 membered heterocyclyl group having 1-4 heteroatoms, wherein at least one heteroatom is nitrogen. In some embodiments, a non-negatively charged internucleotidic linkage comprises an optionally substituted 5 -membered heterocyclyl group having 1-4 heteroatoms, wherein at least one heteroatom is nitrogen. In some embodiments, at least two heteroatoms are nitrogen. In some embodiments, a heterocyclyl group is directly bonded to a linkage phosphorus. In some embodiments, a heterocyclyl group is bonded to a linkage phosphorus through a linker, e.g., =N- when the heterocyclyl group is past of a guanidine snoiety who directed bonded to a linkage phosphorus through its =N-. In some embodiments, a non-negatively charged internucleotidic linkage comprises an optionally substituted group. In some embodiments, a non-negatively charged intemucleotidic linkage comprises an

optionally substituted group. In some embodiments, a non-negatively charged intemucleotidic

linkage comprises an substituted group. In some embodiments, a non-negatively charged

intemucleotidic linkage comprises group. In some embodiments, each R is independently optionally substituted Ci -20 alkyl. In some embodiments, each R 1 is independently optionally substituted C-._ 6 alkyl in some embodiments, each R 1 is independently methyl. In some embodiments, the two R 1 groups are different; for example, in some embodiments, one R 1 is methyl, and the other is

-CH 2 (CH 2 ) 10 CH 3 .

[00276] In some embodiments, a modified intemucleotidic linkage, e.g., a non-negatively charged intemucleotidic linkage, comprises a triazole or alkyne moiety, each of which is optionally substituted. In some embodiments, a modified intemucleotidic linkage comprises a triazole moiety. In some embodiments, a modified intemucleotidic linkage comprises a unsubstituted triazole moiety. In some embodiments, a modified intemucleotidic linkage comprises a substituted triazole moiety. In some embodiments, a modified intemucleotidic linkage comprises an alkyl moiety hi some embodiments, a modified intemucleotidic linkage comprises an optionally substituted alkynyl group. In some embodiments, a modified intemucleotidic linkage comprises an unsubstituted alkynyl group. In some embodiments, a modified intemucleotidic linkage comprises a substituted alkynyl group. In some embodiments, an alkynyl group is directly bonded to a linkage phosphorus.

[00277] In some embodiments, an oligonucleotide comprising a non-negatively charged intemucleotidic linkage can comprise any structure, format, or portion thereof described herein. In some embodiments, an oligonucleotide comprising a non-negatively charged intemucleotidic linkage can comprise any structure, format, or portion thereof described herein as being a component of a DMD oligonucleotide. In some embodiments, any structure, fonnat, or portion thereof described as being a component of any DMD oligonucleotide can be used in any oligonucleotide comprising a non-negatively charged intemucleotidic linkage, whether or not that oligonucleotide targets DMD or not, or whether die oligonucleotide is capable of mediating skipping of a DMD exon or not. In some embodiments, an oligonucleotide comprising a non -negatively charged intemucleotidic is double-stranded or single- stranded.

[00278] In some embodiments, a provided oligonucleotide composition is characterized in that, when it is contacted with the transcript in a transcript splicing system, splicing of the transcript is altered relative to that observed under reference conditions selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof. In some embodiments, a desired splicing product is increased 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 fold or more. In some embodiments, a desired splicing reference is absent (e.g., cannot be reliably detected by quantitative PCR) under reference conditions. In some embodiments, as exemplified in the present disclosure, levels of the plurality of oligonucleotides, e.g., a plurality of oligonucleotides, in provided compositions are pre-determined.

[00279] In some embodiments, provided oligonucleotides, e.g., oligonucleotides of a plurality in a provided composition, comprise two or more regions. In some embodiments, provided comprise a 5’ -end region, a 3’ -end region, and a middle region in between. In some embodiments, provided oligonucleotides have two wing and one core regions. In some embodiments, provided oligonucleotides are of a wing-core-wing structure. In some embodiments, the two wing regions are identical. In some embodiments, the two wing regions are different. In some embodiments, a 5 -end region is a 5 -wing region. In some embodiments, a 5’ -wing region is a 5’-end region. In some embodiments, a 3’-end region is a 3’ -wing region. In some embodiments, a 3’ -wing region is a 3’ -end region. In some embodiments, a core region is a middle region.

[00280] In some embodiments, a region (e.g., a 5’-wing region, a 3’-wing, a core region, a 5’-end region, a middle region, etc.) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, or more nucleoside units. In some embodiments, a region comprises 2 or more nucleoside units. In some embodiments, a region comprises 3 or more nucleoside units. In some embodiments, a region comprises 4 or more nucleoside units. In some embodiments, a region comprises 5 or more nucleoside units in some embodiments, a region comprises 6 or more nucleoside units. In some embodiments, a region comprises 7 or more nucleoside units in some embodiments, a region comprises 8 or more nucleoside units. In some embodiments, a region comprises 9 or more nucleoside units. In some embodiments, a region comprises 10 or more nucleoside units.

[00281] hi some embodiments, a region (e.g., a 5’ -wing region, a 3’-wing, a core region, a 5’-end region, a middle region, etc.) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more modified intemucleotidic linkages. In some embodiments, a region comprises 2 or more modified intemucleotidic linkages. In some embodiments, the one or more modified internucleotidic linkages are consecutive. In some embodiments, a region comprises 2 or more consecutive modified internucleotidic linkages. In some embodiments, each internucleotidic linkage in a region is independently a modified internucleotidic linkage, wherein each chiral internucleotidic linkage is optionally and independently chirally controlled. In some embodiments, a chiral internucleotidic linkage or a modified internucleotidic linkage has the structure of formula I or a salt form thereof hi some embodiments, a chiral internucleotidic linkage or a modified internucleotidic linkage is a phosphorothioate internucleotidic linkage. In some embodiments, each chiral internucleotidic linkage or a modified internucleotidic linkage independently has the structure of formula I or a salt fonn thereof. In some embodiments, each chiral internucleotidic linkage or a modified internucleotidic linkage is a phosphorothioate internucleotidic linkage. In some embodiments, a region comprises 3 or consecutive modified internucleotidic linkages.

[00282] In some embodiments, a wing region comprises one or more natural phosphate linkages.

In some embodiments, a core region comprises one or more natural phosphate linkages. In some embodiments, a 5’ -end region comprises one or more natural phosphate linkages. In some embodiments, a 3’-end region comprises one or more natural phosphate linkages. In some embodiments, a middle region comprises one or more natural phosphate linkages. In some embodiments, the one or more natural phosphate linkages are consecutive.

[00283] In some embodiments, a natural phosphate linkage follows (e.g., connected to a 3’- position of a sugar moiety) or precedes (e.g., connected to a 5’-position of a sugar moiety) a nucleoside unit whose sugar moiety comprises a 2’~OR 1 modification, wherein R 1 is not hydrogen. In some embodiments, R 1 is optionally substituted Ci 6 aliphatic. In some embodiments, a modified internucleotidic linkage follows (e.g., connected to a 3’-position of a sugar moiety) or precedes (e.g., connected to a 5’-position of a sugar moiety) all or most (e.g., more than 55%, 60%, 70%, 80%, 90%, 95%, etc.) nucleoside units whose sugar moiety comprises no 2’-OR ! modification, wherein R ! is not hydrogen (e.g., those having two 2’-H at the 2’-position, those having a 2’-H and a 2’-F at the 2’-position (2’-F modified), etc.).

[00284] In some embodiments, a region comprises one or more nucleoside units comprising sugar modifications, e.g , 2’-F, 2’ -OR 1 , LNA sugar modifications, etc. In some embodiments, each sugar in a region is independently modified. In some embodiments, each sugar moiety in a wing, a 5’-end region, and/or a 3’-end region is modified. In some embodiments, a modification is a 2’-modification. In some embodiments, a modification can increase stability, e.g., 2 -QR 1 where in R 1 is not -H (e.g., is optionally substituted C._ 6 aliphatic), LNA sugar modifications, etc. In some embodiments, a region, e.g., a core region or a middle region, comprise no sugar modifications (or no 2’-OR 1 sugar modifications/LNA modifications etc.). In some embodiments, such a core/middle region can fonn a duplex with a RNA for recognition/binding of a protein, e.g., RNase H, for the protein to perform one or more of its functions (e.g., in the case of RNase H, its binding and cleavage of DNA/RNA duplex).

[00285] A region and/or a provided oligonucleotide may have various patterns of backbone chiral centers. In some embodiments, each intemucleotidic linkage in a region is a chirally controlled internucleotidic linkage and is Ap. In some embodiments, the 5 -end and/or the 3’-end intemucleotidic linkage is a chirally controlled intemucleotidic linkage and is »5p. In some embodiments, the pattern of backbone chiral centers of a w g region, a 5’-end region, and/or a 3’ -end region is or comprises a 5’-end and/or a 3’-end intemucleotidic linkage which is a chirally controlled intemucleotidic linkage and is Ap, with the other intemucleotidic linkages in the region independently being an natural phosphate linkage, a modified intemucleotidic linkage, or a chirally controlled intemucleotidic linkage (Sp or Rp). In some embodiments, such patterns provide stability . Many example patterns of backbone chiral centers are described in the present disclosure.

[00286] In some embodiments, the present disclosure provides a chirally controlled oligonucleotide composition comprising a plurality of oligonucleotides defined by having:

1) a common base sequence;

2) a common patern of backbone linkages; and

3) a common pattern of backbone chiral centers, which composition is a substantially pure preparation of a single oligonucleotide in that a controlled level of the oligonucleotides in the composition have the common base sequence and length, the common pattern of backbone linkages, and the common pattern of backbone chiral centers.

1002871 In some embodiments, oligonucleotides having a common base sequence may have the same pattern of nucleoside modifications, e.g. , sugar modifications, base modifications, etc. In some embodiments, a pattern of nucleoside modifications may be represented by a combination of locations and modifications. In some embodiments, all non -chiral linkages (e.g., PO) may be omitted. In some embodiments, oligonucleotides having the same base sequence have the same constitution.

[00288] As understood by a person having ordinary skill in the art, a stereorandom or racemic preparation of oligonucleotides is prepared by nom-stereoseieetive and/or low-stereoselective coupling of nucleotide monomers, typically without using any chiral auxiliaries, chiral modification reagents, and/or chiral catalysts. In some embodiments, in a substantially racemic (or chirally uncontrolled) preparation of oligonucleotides, all or most coupling steps are not chirally controlled in that the coupling steps are not specifically conducted to provide enhanced stereoselectivity. An example substantially racemic preparation of oligonucleotides is the preparation of phosphorothioate oligonucleotides through su!furizing phosphite triesters from commonly used phosphoramidite oligonucleotide synthesis with either tetraethylthiuram disulfide or (TETD) or 3H-1, 2-bensodithiol-3-one 1, 1-dioxide (BDTD), a well- known process in the art. In some embodiments, substantially racemic preparation of oligonucleotides provides substantially racemic oligonucleotide compositions (or chi rally uncontrolled oligonucleotide compositions). In some embodiments, at least one coupling of a nucleotide monomer has a diastereo selectivity lower than about 60:40, 70:30, 80:20, 85: 15, 90: 10, 91:9, 92:8, 97:3, 98:2, or 99: 1. In some embodiments, each internucleotidic linkage independently has a diastereoselectivity lower than about 60:40, 70:30, 80:20, 85: 15, 90: 10, 91:9, 92:8, 97:3, 98:2, or 99: 1. In some embodiments, a diastereoselectivity is lower than about 60:40. In some embodiments, a diastereoselectivity is lower than about 70:30. In some embodiments, a diastereoselectivity is lower than about 80:20 In some embodiments, a diastereoselectivity is lower than about 90: 10. In some embodiments, a diastereoselectivity is lower than about 91:9. In some embodiments, at least one internucleotidic linkage has a diastereoselectivity lower than about 90: 10. In some embodiments, at least two internucleotidic linkages have a diastereoselectivity lower than about 90: 10. In some embodiments, at least three internucleotidic linkages have a diastereoselectivity lower than about 90: 10. In some embodiments, at least four internucleotidic linkages have a diastereoselectivity lower than about 90: 10. In some embodiments, at least five internucleotidic linkages have a diastereoselectivity lower than about 90: 10. In some embodiments, each internucleotidic linkage independently has a diastereoselectivity lower than about 90: 10. In some embodiments, a non-chirally controlled internucleotidic linkage has a diastereomeric purity no more than 90%, 85%, 80%, 75%, 70%, 65%, 60%, or 55%. hi some embodiments, the purity is no more than 90%. In some embodiments, the purity is no more than 85%. In some embodiments, the purity is no more than 80%

100289 In contrast, in chirally controlled oligonucleotide composition, at least one and typically each chirally controlled internucleotidic linkage, such as those of oligonucleotides of chirally controlled oligonucleotide compositions, independently has a diastereomeric purity of 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more with respect to the chiral linkage phosphorus. In some embodiments, a diastereomeric purity is 95% or more. In some embodiments, a diastereomeric purity is 96% or more. In some embodiments, a diastereomeric purity is 97% or more. In some embodiments, a diastereomeric purity is 98% or more. In some embodiments, a diastereomeric purity is 99% or more. Among other things, technologies of the present disclosure routinely provide chirally controlled internucleotidic linkages with high diastereomeric purity.

[00290] As appreciated by a person having ordinary skill in the art, diastereoselectivity of a coupling or diastereomeric purity (diastereopunty) of an internucleotidic linkage can be assessed through the diastereoselectivity of a dimer fonnation/diastereomeric purity of the internucleotidic linkage of a dimer formed under the same or comparable conditions, wherein the dimer has the same 5’- and 3’- nucleosides and internucleotidic linkage. [00291] In some embodiments, the present disclosure provides chirally controlled (and/or stereochemically pure) oligonucleotide compositions comprising a plurality of oligonucleotides defined by having:

1) a common base sequence;

2) a common pattern of backbone linkages; and

3) a common pattern of backbone chiral centers, which composition is a substantially pure preparation of a single oligonucleotide in that at least about 10% of the oligonucleotides in the composition have the common base sequence and length, the common pattern of backbone linkages, and the common pattern of backbone chiral centers.

[00292] In some embodiments, the present disclosure provides chirally controlled oligonucleotide composition of a plurality of oligonucleotides, wherein the composition is enriched, relative to a substantially racemic preparation of the same oligonucleotides, for oligonucleotides of a single oligonucleotide type. In some embodiments, the present disclosure provides chirally controlled oligonucleotide composition of a plurality of oligonucleotides wherein the composition is enriched, relative to a substantially racemic preparation of the same oligonucleotides, for oligonucleotides of a single oligonucleotide type defined by:

1) base sequence;

2) pattern of backbone linkages;

3) pattern of backbone chiral centers; and

4) pattern of backbone phosphorus modifications.

100293 In some embodiments, the present disclosure provides a chirally controlled oligonucleotide composition comprising a plurality of oligonucleotides of a particular oligonucleotide type defined by:

1 ) base sequence;

2) pattern of backbone linkages;

3 ) pattern of backbone chiral centers; and

4) pattern of backbone phosphorus modifications.

wherein the composition is enriched, relative to a substantially racemic preparation of oligonucleotides having the same base sequence and length, for oligonucleotides of the particular oligonucleotide type.

[00294] In some embodiments, oligonucleotides having a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers have a common pattern of backbone phosphorus modifications and a common pattern of base modifications. In some embodiments, oligonucleotides having a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers have a common pattern of backbone phosphorus modifications and a common pattern of nucleoside modifications. In some embodiments, oligonucleotides having a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers have identical structures

100295 In some embodiments, oligonucleotides of an oligonucleotide type have a common pattern of backbone phosphorus modifications and a common pattern of sugar modifications in some embodiments, oligonucleotides of an oligonucleotide type have a common patern of backbone phosphorus modifications and a common pattern of base modifications. In some embodiments, oligonucleotides of an oligonucleotide type have a common pattern of backbone phosphorus modifications and a common pattern of nucleoside modifications. In some embodiments, oligonucleotides of a particular type have the same constitution. In some embodiments, oligonucleotides of an oligonucleotide type are identical.

[00296] In some embodiments, a chi rally controlled oligonucleotide composition is a substantially pure preparation of an oligonucleotide type in that oligonucleotides in the composition that are not of the oligonucleotide type are impurities form the preparation process of said oligonucleotide type, m some case, after certain purification procedures.

[00297] In some embodiments, at least about 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or

95% of the oligonucleotides in the composition have a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers.

[00298] In some embodiments, oligonucleotides having a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers have a common pattern of backbone phosphoms modifications. In some embodiments, oligonucleotides having a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers have a common patern of backbone phosphoms modifications and a common patern of nucleoside modifications. In some embodiments, oligonucleotides having a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers have a common pattern of backbone phosphorus modifications and a common pattern of sugar modifications. In some embodiments, oligonucleotides having a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone chiral centers have a common pattern of backbone phosphorus modifications and a common pattern of base modifications. In some embodiments, oligonucleotides having a common base sequence, a common patern of backbone linkages, and a common pattern of backbone chiral centers are identical.

[00299] In some embodiments, purity of a chirally controlled oligonucleotide composition of an oligonucleotide type is expressed as the percentage of oligonucleotides in the composition that are of the oligonucleotide type. In some embodiments, at least about 10% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 20% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 30% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 40% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 50% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 60% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 70% of tire oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 80% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 90% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 92% of the oligonucleotides in a chirally controlled oligonucleotide composition are of tire oligonucleotide type. In some embodiments, at least about 94% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 95% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 96% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the same oligonucleotide type. In some embodiments, at least about 97% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 98% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type. In some embodiments, at least about 99% of the oligonucleotides in a chirally controlled oligonucleotide composition are of the oligonucleotide type.

[00300] In some embodiments, purity of a chirally controlled oligonucleotide composition can be controlled by stereoselectivity of each coupling step in its preparation process. In some embodiments, a coupling step has a stereoselectivity (e.g., diastereoselectivity) of 60% (60% of the new internucleotidic linkage formed from the coupling step has the intended stereochemistry ' ). After such a coupling step, the new internucleotidic linkage formed may be referred to have a 60% purity. In some embodiments, each coupling step has a stereoselectivity of at least 60%. In some embodiments, each coupling step has a stereoselecti vity of at least 70%. In some embodiments, each coupling step has a stereoselectivity of at least 80%. In some embodiments, each coupling step has a stereoselectivity of at least 85%. In some embodiments, each coupling step has a stereoselectivity of at least 90%. In some embodiments, each coupling step has a stereoselectivity of at least 91%. In some embodiments, each coupling step has a stereoselectivity of at least 92%. In some embodiments, each coupling step has a stereoselectivity of at least 93%. In some embodiments, each coupling step has a stereoselectivity of at least 94%. In some embodiments, each coupling step has a stereoselectivity of at least 95%. In some embodiments, each coupling step has a stereoselectivity of at least 96%. In some embodiments, each coupling step has a stereoselectivity of at least 97%. In some embodiments, each coupling step has a stereoselectivity of at least 98%. In some embodiments, each coupling step has a stereoselectivity of at least 99%. In some embodiments, each coupling step has a stereoselectivity of at least 99.5%. In some embodiments, each coupling step has a stereoselectivity of virtually 100%. In some embodiments, a coupling step has a stereoselectivity of virtually 100% in that all detectable product from the coupling step by an analytical method (e.g., NMR, HPLC, use of a nuclease which stereoselectively cleaves phosphorothioates, etc) has the intended stereoselectivity. In some embodiments, stereoselectivity ' of a chiral intemucleotidic linkage in an oligonucleotide may be measured through a model reaction, e.g. formation of a dimer under essentially the same or comparable conditions wherein the dimer has the same intemucleotidic linkage as the chiral intemucleotidic linkage, the 5’-nucleoside of the dimer is the same as the nucleoside to the 5 - end of the chiral intemucleotidic linkage, and the 3’-nucleoside of the dimer is the same as the nucleoside to the 3’-end of the chiral intemucleotidic linkage (e.g., for fU*SfU*SfC*SfU. through the dimer of flJ*SfC). As appreciated by a person having ordinary skill in the art, percentage of oligonucleotides of a particular type having n chirally controlled intemucleotidic linkages in a preparation may be calculated as DP 1 * DP 2 *DP 3 * ... DP“, wherein each of DP 1 , DP 2 , DP 3 , ... , and DP" is independently the diastereomeric purity of the I st , 2 m , 3 ,d , ... , and n i1 chirally' controlled intemucleotidic linkage. In some embodiments, each of DP 1 , DP 2 , DP 3 , ... , and DP" is independently 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 97% or 99% or more. . In some embodiments, each of DP 1 , DP 2 , DP 3 , ... , and DP” is independently 95% or more.

[00301] In some embodiments, in provided compositions, at least 0.5%, 1%, 2%, 3%, 4%, 5%,

6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 97% or 99% of oligonucleotides that have the base sequence of a particular oligonucleotide type (defined by 1) base sequence; 2) pattern of backbone linkages; 3} pattern of backbone chiral centers; and 4} pattern of backbone phosphorus modifications) are oligonucleotides of the particular oligonucleotide type. In some embodiments, at least 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 97% or 99% of oligonucleotides that have the base sequence, the pattern of backbone linkages, and the pattern of backbone phosphorus modifications of a particular oligonucleotide type are oligonucleotides of the particular oligonucleotide type. [00302] In some embodiments, oligonucleotides of a particular type in a chirally controlled oligonucleotide composition is enriched at least 5 fold (oligonucleotides of the particular type have a fraction of 5*(l/2") of oligonucleotides that have the base sequence, the pattern of backbone linkages, and the pattern of backbone phosphorus modifications of the particular oligonucleotide type, wherein n is the number of chiral internucleotidic linkages; or oligonucleotides that have the base sequence, the pattern of backbone linkages, and the pattern of backbone phosphorus modifications of the particular oligonucleotide type but are not of the particular oligonucleotide type are no more than [l -(l/2 u )]/5 of oligonucleotides that have the base sequence, the pattern of backbone linkages, and the pattern of backbone phosphorus modifications of the particular oligonucleotide type) compared to a stereorandom preparation of the oligonucleotides (oligonucleotides of the particular type are typically considered to have a fraction of 1/2" of oligonucleotides that have the base sequence, the pattern of backbone linkages, and the pattern of backbone phosphorus modifications of the particular oligonucleotide type, wherein n is the number of chiral internucleotidic linkages, and oligonucleotides that have the base sequence, the pattern of backbone linkages, and the pattern of backbone phosphorus modifications of the particular oligonucleotide type but are not of the particular oligonucleotide type are typically considered to have a fraction of [l-(l/2 n )] of oligonucleotides that have the base sequence, the pattern of backbone linkages, and tire pattern of backbone phosphorus modifications of the particular oligonucleotide type). In some embodiments, the enrichment is at least 20 fold. In some embodiments, the enrichment is at least 30 fold. In some embodiments, the enrichment is at least 40 fold. In some embodiments, the enrichment is at least 50 fold. In some embodiments, the enrichment is at least 60 fold. In some embodiments, the enrichment is at least 70 fold. In some embodiments, the enrichment is at least 80 fold. In some embodiments, the enrichment is at least 90 fold in some embodiments, the enrichment is at least 100 fold. In some embodiments, the enrichment is at least 20,000 fold. In some embodiments, the enrichment is at least (1.5)" In some embodiments, the enrichment is at least (1.6) ® In some embodiments, the enrichment is at least (1.7)“. In some embodiments, the enrichment is at least (1 1)" In some embodiments, the enrichment is at least (1.8) n . In some embodiments, the enrichment is at least (1.9) n In some embodiments, the enrichment is at least 2 n . In some embodiments, tire enrichment is at least 3". in some embodiments, the enrichment is at least 4“. In some embodiments, the enrichment is at least 5". In some embodiments, the enrichment is at least 6“. In some embodiments, the enrichment is at least 7" In some embodiments, the enrichment is at least 8“ In some embodiments, the enrichment is at least 9". In some embodiments, the enrichment is at least 10 n . In some embodiments, the enrichment is at least 15 n In some embodiments, the enrichment is at least 20". In some embodiments, the enrichment is at least 25". In some embodiments, the enrichment is at least 30 n In some embodiments, the enrichment is at least 40". In some embodiments, the enrichment is at least 50”. In some embodiments, the enrichment is at least 100 n In some embodiments, enrichment is measured by increase of the fraction of oligonucleotides of the particular oligonucleotide type in oligonucleotides that have the base sequence, the pattern of backbone linkages, and the pattern of backbone phosphorus modifications of the particular oligonucleotide type. In some embodiments, an enrichment is measured by decrease of the fraction of oligonucleotides that have the base sequence, the pattern of backbone linkages, and the pattern of backbone phosphorus modifications of the particular oligonucleotide type but are not of the particular oligonucleotide type in oligonucleotides that have the base sequence, the pattern of backbone linkages, and the pattern of backbone phosphorus modifications of the particular oligonucleotide type.

[00303] In some embodiments, provided oligonucleotides are antisense oligonucleotides. In some embodiments, provided oligonucleotides are siRNA oligonucleotides hi some embodiments, a provided chirally controlled oligonucleotide composition is of oligonucleotides that can he antisense oligonucleotide, antagomir, microRNA, pre-microRNA, antimir, supermir, ribozyme, Ul adaptor, RNA activator, RNAi agent, decoy oligonucleotide, triplex forming oligonucleotide, aptamer or adjuvant. In some embodiments, a chirally controlled oligonucleotide composition is of antisense oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of siRNA oligonucleotides in some embodiments, a chirally controlled oligonucleotide composition is of antagomir oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of microRNA oligonucleotides hi some embodiments, a chirally controlled oligonucleotide composition is of pre- microRNA oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of antimir oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of supermir oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of ribozyme oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of Ul adaptor oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of RNA activator oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of RNAi agent oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of decoy oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of triplex forming oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of aptamer oligonucleotides. In some embodiments, a chirally controlled oligonucleotide composition is of adjuvant oligonucleotides.

[00304] In some embodiments, a provided oligonucleotide comprises one or more chiral, modified phosphate linkages. In some embodiments, provided chirally controlled (and/or stereochemieally pure) preparations are of oligonucleotides that include one or more modified backbone linkages, bases, and/or sugars.

[00305] In some embodiments, provided chirally controlled (and/or stereochemieally pure) preparations are of a stereochemical purity of greater than about 80%. In some embodiments, provided chirally controlled (and/or stereochemically pure) preparations are of a stereochemical purity of greater than about 85%. In some embodiments, provided chirally controlled (and/or stereochemically pure) preparations are of a stereochemical purity of greater than about 90%. In some embodiments, provided chirally controlled (and/or stereochemically pure) preparations are of a stereochemical purity of greater than about 91%. In some embodiments, provided chirally controlled (and/or stereochemically pure) preparations are of a stereochemical purity of greater than about 92%. in some embodiments, provided chirally controlled (and/or stereochemically pure) preparations are of a stereochemical purity of greater than about 93%. In some embodiments, provided chirally controlled (and/or stereochemically pure) preparations are of a stereochemical purity of greater than about 94%. In some embodiments, provided chirally controlled (and/or stereochemically pure) preparations are of a stereochemical purity of greater than about 95%. In some embodiments, provided chirally controlled (and/or stereochemically pure) preparations are of a stereochemical purity of greater than about 96%. In some embodiments, provided chirally controlled (and/or stereochemically pure) preparations are of a stereochemical purity of greater than about 97%. in some embodiments, provided chirally controlled (and/or stereochemically pure) preparations are of a stereochemical purity of greater than about 98%. In some embodiments, provided chirally controlled (and/or stereochemically pure) preparations are of a stereochemical purity of greater than about 99%.

[00306] In some embodiments, at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%,

55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% of the mtemucleotidic linkages of an oligonucleotide are independently chiral internucleotidic linkages. In some embodiments, ail chiral, modified internucleotidic linkages are chiral phosphorothioate mtemucleotidic linkages. In some embodiments, all chiral, modified internucleotidic linkages except non-negatively charged internucleotidic linkages are chiral phosphorothioate temucleotidic linkages. In some embodiments, each chiral internucleotidic linkage is chirally controlled. In some embodiments, at least about 10, 20, 30, 40, 50, 60, 70, 80, or 90% chiral internucleotidic linkages of an oligonucleotide are chirally controlled and are of the Sp conformation hi some embodiments, at least about 10, 20, 30, 40, 50, 60, 70, 80, or 90% phosphorothioate internucleotidic linkages of an oligonucleotide are chirally controlled and are of the Sp conformation. In some embodiments, the percentage is at least about 10%. In some embodiments, the percentage is at least about 20%. In some embodiments, the percentage is at least about 30%. In some embodiments, the percentage is at least about 40%. In some embodiments, the percentage is at least about 50%. In some embodiments, the percentage is at least about 60%. In some embodiments, the percentage is at least about 70%. In some embodiments, the percentage is at least about 80%. In some embodiments, the percentage is at least about 90%. [00307] In some embodiments, at least about 10, 20, 30, 40, 50, 60, 70, 80, or 90% chiral intemucieotidie linkages of an oligonucleotide are chirally controlled and are of the Rp conformation in some embodiments, at least about 10, 20, 30, 40, 50, 60, 70, 80, or 90% chiral phosphorothioate intemucieotidie linkages of an oligonucleotide are chirally controlled and are of the Rp conformation. In some embodiments, the percentage is at least about 10%. In some embodiments, the percentage is at least about 20%. In some embodiments, the percentage is at least about 30%. In some embodiments, no more than 10, 20, 30, 40, 50, 60, 70, 80, or 90% chiral intemucieotidie linkages of an oligonucleotide are chirally controlled and are of the Rp conformation. In some embodiments, no more than 10, 20, 30, 40, 50, 60, 70, 80, or 90% phosphorothioate intemucieotidie linkages of an oligonucleotide are of the Rp conformation. In some embodiments, the percentage is no more than 10%. In some embodiments, the percentage is no more than 2.0%. In some embodiments, the percentage is no more than 30%.

[00308] In some embodiments, provided chirally controlled (and/or stereochemically pure) compositions are of oligonucleotides that contain one or more modified bases. In some embodiments, provided chirally controlled (and/or stereochemically pure) compositions are of oligonucleotides that contain no modified bases. As appreciated by those skilled in the art, many types of modified bases can be utilized in accordance with the present disclosure. Example modified bases are described herein.

[00309] In some embodiments, oligonucleotides of provided compositions comprise at least 2, 3,

4, 5, 6, 7, 8, 9 or 10 natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise at least one natural phosphate linkage. In some embodiments, oligonucleotides of provided compositions comprise at least two natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise at least three natural phosphate linkages.

[00310] hr some embodiments, oligonucleotides of provided compositions comprise 1, 2, 3, 4, 5,

6, 7, 8, 9 or 10 natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise one natural phosphate linkage. In some embodiments, oligonucleotides of provided compositions comprise two natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise three natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise four natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise five natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise six natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise seven natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise eight natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise nine natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise ten natural phosphate linkages. [00311] In some embodiments, oligonucleotides of provided compositions comprise at least 2, 3,

4, 5, 6, 7, 8, 9 or 10 consecutive natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise at least two consecutive natural phosphate linkages. In some embodiments, oligonucleotides of provided compositions comprise at least three consecutive natural phosphate linkages.

[00312] In some embodiments, oligonucleotides of the present disclosure have at least 8, 9, 10,

11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, or 75 nucleobases in length. In some embodiments, oligonucleotides of the present disclosure comprises at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, or 75 nucleobases in length, wherein each nucleobase is independently optionally substituted A, T, C, G, U, or a tautomer thereof.

[00313] In some embodiments, provided compositions comprise oligonucleotides containing one or more residues which are modified at the sugar moiety. In some embodiments, provided compositions comprise oligonucleotides containing one or more residues which are modified at the 2’ position of the sugar moiety (referred to herein as a‘ -modification”). Examples of such modifications are described herein and include, but are not limited to, 2 , ~OMe, 2’-MOE, 2 , ~LNA, 2’-F, FRNA, FANA, S-cEt, etc. In some embodiments, provided compositions comprise oligonucleotides containing one or more residues which are 2’-modified. For example, in some embodiments, provided oligonucleotides contain one or more residues which are T -O-m ethoxy ethyl (2 , -MOE)-modified residues. In some embodiments, provided compositions comprise oligonucleotides which do not contain any 2’ -modifications. In some embodiments, provided compositions are oligonucleotides which do not contain any 2’-MOE residues. That is, in some embodiments, provided oligonucleotides are not MOE-modified. Additional example sugar modifications are described in the present disclosure.

[00314] In some embodiments, one or more is one. In some embodiments, one or more is two. In some embodiments, one or more is three. In some embodiments, one or more is four. In some embodiments, one or more is five. In some embodiments, one or more is six. In some embodiments, one or more is seven. In some embodiments, one or more is eight. In some embodiments, one or more is nine. In some embodiments, one or more is ten. In some embodiments, one or more is at least one. In some embodiments, one or more is at least two. In some embodiments, one or more is at least three. In some embodiments, one or more is at least four. In some embodiments, one or more is at least live. In some embodiments, one or more is at least six. in some embodiments, one or more is at least seven. In some embodiments, one or more is at least eight in some embodiments, one or more is at least nine. In some embodiments, one or more is at least ten.

[00315] In some embodiments, a base sequence, e ., a common base sequence of a plurality of oligonucleotide, a base sequence of a particular oligonucleotide type, etc., comprises or is a sequence complementary to a gene or transcript (e.g , of Dystrophin or DMD). In some embodiments, a common base sequence comprises or is a sequence 100% complementar ' to a gene. In some embodiments, a common base sequence comprises or is a sequence complementary to a characteristic sequence element of a gene, which characteristic sequences differentiate the gene from a similar sequence sharing homology with the gene. In some embodiments, a common base sequence comprises or is a sequence 100% complementary to a characteristic sequence element of a gene, which characteristic sequences differentiate the gene from another allele of the gene. In some embodiments, a common base sequence comprises or is a sequence 100% complementary to a characteristic sequence element of a gene, which characteristic sequences differentiate the gene from a similar sequence sharing homology with the gene. In some embodiments, a common base sequence comprises or is a sequence complementary ' to characteristic sequence element of a target gene, which characteristic sequences comprises a mutation that is not found in other copies of the gene, e.g. , the wild-type copy of the gene, another mutant copy the gene, etc. In some embodiments, a common base sequence comprises or is a sequence 100% complementary to characteristic sequence element of a target gene, which characteristic sequences comprises a mutation that is not found in other copies of the gene, e.g. , the wild-type copy of the gene, another mutant copy the gene, etc. In some embodiments, a common base sequence comprises or is a sequence 100% complementary to a characteristic sequence element of a gene, which characteristic sequences differentiate the gene from another allele of the gene. In some embodiments, a characteristic sequence element is a mutation. In some embodiments, a characteristic sequence element is a SNP |00316j In some embodiments, a chiral intemucleotidic linkage has the structure of formula I, I-a,

I-b, I-c, I-n-1, 1-n-2, I-n-3, ϊ-ii-4, II, II-a-1, II-a-2, II-fa-1, II-b-2, 11-c-l, II-c-2, II-d-1, II-d-2, PI, etc., or a salt form thereof. In some embodiments, linkage phosphorus of chiral intemucleotidic linkages are chi rally controlled. In some embodiments, a chiral intemucleotidic linkage is phosphorothioate intemucleotidic linkage. In some embodiments, each chiral intemucleotidic linkage in an oligonucleotide of a provided composition independently has the structure of formula I. In some embodiments, each chiral intemucleotidic linkage in an oligonucleotide of a provided composition independently has the structure of formula II. In some embodiments, each chiral intemucleotidic linkage in an oligonucleotide of a provided composition independently has the structure of formula III. In some embodiments, each chiral intemucleotidic linkage in an oligonucleotide of a provided composition is a phosphorothioate intemucleotidic linkage.

[00317] As appreciated by those skilled in the art, intemucleotidic linkages, e.g., those of formula

I, natural phosphate linkages, phosphorothioate intemucleotidic linkages, etc may exist in their salt forms depending on pH of their environment. Unless otherwise indicated, such salt forms are included in the present application when such intemudeotidic linkages are referred to.

[00318] In some embodiments, oligonucleotides of the present disclosure comprise one or more modified sugar moieties. In some embodiments, oligonucleotides of the present disclosure comprise one or more modified base moieties. As known by a person of ordinary skill in the art and described in the disclosure, various modifications can be introduced to sugar and base moieties. For example, in some embodiments, a modification is a modification described in US9006198, W02014/012081, WO/2015/107425, and WO/2017/062862, the sugar and base modifications of each of which are incorporated herein by reference.

100319] In some embodiments, a sugar modification is a 2’ -modification. Commonly used 2’- modifications include but are not limited to 2’-OR 1 , wherein IV is not hydrogen. In some embodiments, a modification is 2’-OR, wherein R is optionally substituted aliphatic. In some embodiments, a modification is 2’-OMe. In some embodiments, a modification is 2’-(?-MOE. In some embodiments, the present disclosure demonstrates that inclusion and/or location of particular chirally pure intemudeotidic linkages can provide stability improvements comparable to or better than those achieved through use of modified backbone linkages, bases, and/or sugars. In some embodim nts, a provided single oligonucleotide of a provided composition has no modifications on the sugars. In some embodiments, a provided single oligonucleotide of a provided composition has no modifications on 2’-positions of tire sugars (i.e., the two groups at the 2 -position are either -H/-H or -H/-ΌH). In some embodiments, a provided single oligonucleotide of a provided composition does not have any 2’-MOE modifications.

[00320] In some embodiments, a 2’-modification is -O-L- or -L- which connects the 2’-carbon of a sugar moiety to another carbon of a sugar moiety. In some embodiments, a 2’-rnodification is -O-L- or -L- which connects the 2’-carbon of a sugar moiety to the 4’-carbon of a sugar moiety. In some embodiments, a T -modification is S'-cEt In some embodiments, a modified sugar moiety is an LNA sugar moiety.

100321 ] In some embodiments, a 2’-rnodification is -F. In some embodiments, a 2’-modification is FANA. In some embodiments, a 2 -modification is FRNA.

[00322] In some embodiments, a sugar modification is a 5’-modification. In some embodiments, a modification is S’-R 1 , wherein R 1 is not hydrogen. In some embodiments, a sugar modification is 5’~R, wherein R is not hydrogen and is otherwise as described in the present disclosure. In some embodiments, a sugar modification is 5’-R, wherein R is optionally substituted C j-6 aliphatic. In some embodiments, a sugar modification is 5’~R, wherein R is optionally substituted C-._ 6 alkyl. In some embodiments, a sugar modification is 5’~R, wherein R is optionally substituted methyl. In some embodiments, a sugar modification is 5’-R, wherein R is optionally substituted methyl, -wherein no substituents of the methyl group comprises a carbon atom. In some embodiments, a 5’-modification is methyl. In some embodiments, each substituent is independently halogen. In some embodiments, a substituted 5’ -carbon is diastereomerically pure. In some embodiments, a substituted 5’ -carbon has the R configuration. In some embodiments, a substituted 5’ -carbon has the S configuration. In some embodiments, a 5’- modifi cation is 5’-(i?)-Me. In some embodiments, a 5’ -modification is 5 -(<S)-Me.

[00323] In some embodiments, a sugar moiety has one and no more than one modification at a position, e.g., a 2’ -position, 5’-position, etc. In some embodiments, a T -modification takes the position corresponding to the position of the 2 -OH in a natural RNA sugar moiety. In some embodiments, a T- modification takes the position corresponding to the position of the 2’-H in a natural RNA sugar moiety.

100324] In some embodiments, a sugar modification changes tire size of the sugar ring. In some embodiments, a sugar modification changes the conformation of the sugar ring. In some embodiments, a sugar modification is the sugar moiety in FHNA.

[00325] In some embodiments, a sugar modification replaces a sugar moiety with another cyclic or acyclic moiety. Examples of such moieties are widely known in the art, including but not limited to those used in Morpholine, glycol nucleic acids, etc.

Certain Embodiments of Intern ucleotidic Linkages, Chirally Controlled Oligonucleotides and Ckirally Controlled Oligonucleotide Compositions

[00326] Among other things, the present disclosure provides chirally controlled oligonucleotides and chirally controlled oligonucleotide compositions. In some embodiments, the present disclosure provides chirally controlled oligonucleotides and chirally controlled oligonucleotide compositions which are of high crude purity hi some embodiments, the present disclosure provides chirally controlled oligonucleotides, and chirally controlled oligonucleotide compositions which are of high diastereomeric purity. Chirally controlled oligonucleotides are oligonucleotides comprise one or more chirally controlled intemucleotidic linkages, such as oligonucleotides of a plurality in chirally controlled oligonucleotide compositions. In some embodiments, chirally controlled oligonucleotides comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more chirally controlled intemucleotidic linkages. In some embodiments, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more chiral intemucleotidic linkages of a chirally controlled oligonucleotide are independently chirally controlled intemucleotidic linkages. In some embodiments, each chiral intemucleotidic linkage in a chirally controlled oligonucleotide is a chirally controlled intemucleotidic linkage, and a chirally controlled oligonucleotide is diastereomerically pure.

100327 In some embodiments, a chirally controlled oligonucleotide composition is a substantially pure composition of an oligonucleotide type in that oligonucleotides in the composition that are not of the oligonucleotide type are impurities. In some embodiments, such impurities are formed during the preparation process of oligonucleotides of said oligonucleotide type, in some case, after certain purification procedures.

[00328] In some embodiments, the present disclosure provides oligonucleotides comprising one or more diastereomerically pure intemucleotidic linkages with respect to the chiral linkage phosphorus (e.g., linkage phosphorus of chirally controlled intemucleotidic linkages). In some embodiments, the present disclosure provides oligonucleotides comprising one or more diastereomerically pure intemucleotidic linkages having the structure of fonnula I, I-a, I-b, I-c, I-n-1 , 1-n-2, 1-n-3, 1-n-4, II, Il-a- 1, II-a-2 II-b-1, II-b-2, II-e-1, II-c-2, II-d-1, II-d-2, III, etc., or a salt fomi thereof. In some embodiments, the present disclosure provides oligonucleotides comprising one or more diastereomerically pure intemucleotidic linkages with respect to the chiral linkage phosphorus, and one or more natural phosphate linkages (unless otherwise indicated, reference in the present application to intemucleotidic linkages, such as natural phosphate linkages and other types of intemucleotidic linkages when applicable, includes salt fomis of such linkages). Thus, diastereomerically pure intemucleotidic linkages here include salt fomis of diastereomerically pure intemucleotidic linkages; natural phosphate linkages here include salt forms of natural phosphate linkages. A person having ordinary skill in the art appreciates that many intemucleotidic linkages, such as natural phosphate linkages, exist as salt fomis when at physiological pH, in many buffers (e.g., PBS buffers having a pH around 7, e.g., PH 7.4), etc.). In some embodiments, the present disclosure provides oligonucleotides comprising one or more diastereomerically pure intemucleotidic linkages having the structure of formula I, I-a, I-b, I-c, I-n-1, 1- n-2, I-n-3, I-n-4, II, II-a-1 , II-a-2, II-b-1, II-b-2, II-c-1 , II-c-2, II-d-1, II-d-2, III, etc., or a salt form thereof, and one or more natural phosphate linkages. In some embodiments, the present disclosure provides oligonucleotides comprising one or more diastereomerically pure intemucleotidic linkages having the structure of formula I-c, and one or more phosphate diester linkages. In some embodiments, such oligonucleotides are prepared by using stereoselective oligonucleotide synthesis, as described in this application, to form designed diastereomerically pure intemucleotidic linkages with respect to the chiral linkage phosphorus.

[00329] In some embodiments, an oligonucleotide of the present disclosure comprises at least one intemucleotidic linkage, e.g., a modified (non-natural) intemucleotidic linkage (e.g., non-negatively charged intemucleotidic linkage) within or at the terminus (e.g. 5’ or 3’) of the oligonucleotide. In some embodiments, an oligonucleotide comprises a P-modiilcation moiety within or at the terminus (e.g. 5’ or 3’) of the oligonucleotide.

100330] In some embodiments, an oligonucleotide of the present disclosure comprises at least one clurally controlled intemucleotidic linkage within the oligonucleotide. In some embodiments, an oligonucleotide of the present disclosure comprises at least one chirally controlled internucleotidic linkage within the oligonucleotide, and at least one natural phosphate linkage. In some embodiments, an oligonucleotide of the present disclosure comprises at least one chirally controlled internucleotidic linkage within the oligonucleotide, at least one natural phosphate linkage, and at least one phosphorothioate internucleotidic linkage. In some embodiments, an oligonucleotide of the present disclosure comprises at least one chirally controlled internucleotidic linkage within the oligonucleotide, and at least one phosphorothioate triester internucleotidic linkage. In some embodiments, an oligonucleotide of the present disclosure comprises at least one chirally controlled internucleotidic linkage within the oligonucleotide, at least one natural phosphate linkage, and at least one phosphorothioate triester internucleotidic linkage.

[00331] In some embodiments, an oligonucleotide of the present disclosure compri ses at least two chirally controlled internucleotidic linkages within the oligonucleotide that have different stereochemistry and/or different P-modifications relative to one another. In some embodiments, such at least two internucleotidic linkages have different stereochemistry. In some embodiments, such at least two internucleotidic linkages have different P-modifications. In some embodiments, an oligonucleotide of the present disclosure comprises at least two chirally controlled internucleotidic linkages within the oligonucleotide that have different P-modifications relative to one another, and at least one natural phosphate linkage. In some embodiments, an oligonucleotide of the present disclosure comprises at least two chirally controlled internucleotidic linkages within the oligonucleotide that have different P- modifications relative to one another, at least one natural phosphate linkage, and at least one phosphorothioate internucleotidic linkage. In some embodiments, an oligonucleotide of the present disclosure comprises at least two chirally controlled internucleotidic linkages within the oligonucleotide that have different P-modifications relative to one another, and at least one phosphorothioate triester internucleotidic linkage. In some embodiments, an oligonucleotide of the present disclosure comprises at least two chirally controlled internucleotidic linkages within the oligonucleotide that have different P- modifications relative to one another, at least one natural phosphate linkage, and at least one phosphorothioate triester internucleotidic linkage.

[00332] In certain embodiments, an internucleotidic linkage (e.g., a modified (non-natural) internucleotidic linkage wdien formula I is not a natural phosphate linkage) has the structure of formula I:

I

or a salt fonn thereof, wherein: P L is P(=W), P, or P—B(R’ )3;

W is O, N( l . R ' l. S or Se;

each of R 1 and R 5 is independently -H, -L-R’, halogen, -CN, -N0 2 , -L-Si(R’) 3 , -OR’, -SR’, or M R ? ,

each of X, Y and Z is independently -0-, -S-, -Ni-L-R 5 )-, or L;

each L is independently a covalent bond, or a bivalent, optionally substituted, linear or branched group selected from a Ci. 30 aliphatic group and a Ci. 30 heteroaliphatie group having 1-10 heteroatoms, wherein one or more methylene units are optionally and independently replaced with C ]-6 alkylene, C s-6 alkenylene, cºc , a bivalent C r -C 6 heteroaliphatie group having 1-5 heteroatoms, --C(R’) -, -Cy-, -0-, -S , -S-S-, -N(R’)-, -C(O)-, -C(S)-, -C(NR’)-, -C(0)N(R’)-, -N(R’)C(0)N(R’)-,

-N(R’)C(0)0-, -S(O)-, -S(0) 2 - -S(0) 2 N(R’)-, -C(0)S-, -C(0)0-, -P(0)(OR’)-, -P(0)(SR’)- -P(0)(R ) , -P(0)(NR’)-, -P(S)(OR’)-, Pi S H SR } . P{S){ R ) . -P(S)(NR’)-, Pi R ) . -P(OR’)- -P(SR’)-, Pi N R ) . -P(OR’)[B(R’) 3 ]-, -0P(0)(0R’)0-, -0P(0)(SR’)0-, -0P(0)(R’)0- -0P(0)(NR’)0-, 0P(0R )0 — OP(SR’)0— , -OP(NR’)0- 0P( R )0 . or -OP(OR’)[B(R’) 3 JO-, and one or more CH or carbon atoms are optionally and independently replaced with Cy";

each C - is independently an optionally substituted bivalent group selected from a C 3.20 cycloaliphatic ring, a C 6-2 o aryl ring, a 5-20 membered heteroaryl ring having 1 -10 heteroatoms, and a 3- 20 membered heterocyclyl ring having 1-10 heteroatoms;

each Cy L is independently an optionally substituted trivalent or tetravalent group selected from a C 3-2 o cycloaliphatic ring, a C 6.2 o aryl ring, a 5-20 membered heteroaryl ring having 1-10 heteroatoms, and a 3-20 membered heterocyclyl ring having 1-10 heteroatoms;

each R’ is independently -R, -C(0)R, -C(0)OR, or -S(0) 2 R;

each R is independently -H, or an optionally substituted group selected from C-,_ 30 aliphatic, C 1-30 heteroaliphatie having 1-10 heteroatoms, C 6.30 aryl, C 6-3 o arylaliphatic, C 6 30 aryiheteroaliphatic having 1 - 10 heteroatoms, 5-30 membered heteroaryl having 1-10 heteroatoms, and 3-30 membered heterocyclyl having 1-10 heteroatoms, or

two R groups are optionally and independently taken together to form a covalent bond, or two or more R groups on the same atom are optionally and independently taken together with the atom to form an optionally substituted, 3-30 membered, monocyclic, bicyclic or polycyclic ring having, in addition to the atom, 0-10 heteroatoms, or

two or more R groups on two or more atoms are optionally and independently taken together with their intervening atoms to form an optionally substituted, 3-30 membered, monocyclic, bicyclic or polycyclic ring having, in addition to the intervening atoms, 0-10 heteroatoms.

[00333] In some embodiments, a linkage of formula I is chiral at the linkage phosphorus (P in P‘0. In some embodiments, the present disclosure provides a chirally controlled oligonucleotide comprising one or more modified intemucleotidic linkages of formula I. in some embodiments, the present disclosure provides a chirally controlled oligonucleotide comprising one or more modified intemucleotidic linkages of formula I, and wherein individual mtemucleotidic linkages of formula I within the oligonucleotide have different P-modifications relative to one another. In some embodiments, the present disclosure provides a chirally controlled oligonucleotide comprising one or more modified intemucleotidic linkages of formula I, and wherein individual intemucleotidic linkages of formula I within the oligonucleotide have different -X-L-R relative to one another. In some embodiments, the present disclosure provides a chirally controlled oligonucleotide comprising one or more modified intemucleotidic linkages of formula I, and wherein individual intemucleotidic linkages of formula 1 within the oligonucleotide have different X relative to one another. In some embodiments, the present disclosure provides a chirally controlled oligonucleotide comprising one or more modified intemucleotidic linkages of formula I, and wherein individual intemucleotidic linkages of formula I within the oligonucleotide have different -L--R 1 relative to one another. In some embodiments, a chirally controlled oligonucleotide is an oligonucleotide in a provided composition that is of the particular oligonucleotide type. In some embodiments, a chirally controlled oligonucleotide is an oligonucleotide in a provided composition that has the common base sequence and length, the common pattern of backbone linkages, and the common pattern of backbone chiral centers.

[00334] As extensively described herein, in some embodiments, -X-L-R 1 is a moiety useful for oligonucleotide preparation. For example, in some embodiments, -X-L-R is -OCH CH 2 CN (e.g., in non-chirally controlled intemucleotidic linkages); in some embodiments, -X-L-R is of such a structure that H-X-L-R 1 is a chiral auxiliary, optionally capped, as described herein (e.g., DPSE, PSM, etc.: particularly in chirally controlled intemucleotidic linkages, although may also in non-chirally controlled intemucleotidic linkages (e.g., precursors of natural phosphate linkages)).

10001 In some embodiments, a chirally controlled oligonucleotide is an oligonucleotide in a chnally controlled composition that is of a particular oligonucleotide type, and the chirally controlled oligonucleotide is of the type. In some embodiments, a chirally controlled oligonucleotide is an oligonucleotide in a provided composition that comprises a controlled level of a plurality of oligonucleotides that share a common base sequence, a common pattern of backbone linkages, a common pattern of backbone chiral centers, and a common pattern of backbone phosphorus modifications, and the chirally controlled oligonucleotide shares the common base sequence, the common pattern of backbone linkages, the common partem of backbone chiral centers, and the common pattern of backbone phosphorus modifications.

[00335] In some embodiments, the present disclosure provides a chirally controlled oligonucleotide, wherein at least two chi rally controlled intemucleotidic linkages within the oligonucleotide have different P-modifications relative to one another, in that they have different X atoms in their -XLR ! moieties, and/or in that they have different L groups in their -XLR 1 moieties, and/or that they have different R 1 atoms in their -XLR 1 moieties, and/or in that they have different -XLR 1 moieties.

[00336] In some embodiments, the present disclosure provides a chirally controlled oligonucleotide, wherein at least two of the individual intemucleotidic linkages within the oligonucleotide have different stereochemistry and/or different P-modifications relative to one another and the oligonucleotide has a structure represented by the following formula:

[S B n lR B n2S B n3R B n4... S B nxR B nyj

wherein:

each R B independently represents a block of nucleotide units having the R configuration at the linkage phosphorus;

each S independently represents a block of nucleotide units having the S configuration at the linkage phosphorus;

each of ni-ny is zero or an integer, with the requirement that at least one odd n and at least one even n must he non-zero so that the oligonucleotide includes at least two individual intemucleotidic linkages with different stereochemistry relative to one another; and

wherein the sum of nl-ny is between 2 and 200, and in some embodiments is between a lower limit selected from the group consisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more and an upper limit selected from the group consisting of 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, and 200, the upper limit being larger than the lower limit.

[00337] In some such embodiments, each n has the same value; in some embodiments, each even n has the same value as each other even n; in some embodiments, each odd n has the same value each other odd n; in some embodiments, at least two even ns have different values from one another; in some embodiments, at least two odd ns have different values from one another.

[00338] In some embodiments, at least two adjacent ns are equal to one another, so that a provided oligonucleotide includes adjacent blocks of S stereochemistry linkages and R stereochemistry linkages of equal lengths. In some embodiments, provided oligonucleotides include repeating blocks of S and R stereochemistry linkages of equal lengths. In some embodiments, provided oligonucleotides include repeating blocks of S and R stereochemistry' linkages, where at least two such blocks are of different lengths from one another; in some such embodiments each S stereochemistry block is of the same length, and is of a different length from each R stereochemistry' length, which may optionally be of the same length as one another.

[00339] In some embodiments, at least two skip-adjacent ns are equal to one another, so that a provided oligonucleotide includes at least two blocks of linkages of a first stereochemistry' that are equal in length to one another and are separated by a block of linkages of the other stereochemistry, which separating block may be of the same length or a different length from the blocks of first stereochemistry.

[00340] In some embodiments, ns associated with linkage blocks at the ends of a provided oligonucleotide are of the same length. In some embodiments, provided oligonucleotides have terminal blocks of the same linkage stereochemistry. In some such embodiments, the terminal blocks are separated from one another by a middle block of the other linkage stereochemistry.

[00341] hr some embodiments, a provided oligonucleotide of formula

[S B nlR B n2S B n3R B n4...S B nxR B ny] is a stereoblockmer. In some embodiments, a provided oligonucleotide of fonnula [S B nlR B n2S B n3R B n4...S B nxR B ny] is a stereoskipmer. In some embodiments a provided oligonucleotide of formula [S B nl R B n2S B n3R B n4...S B nxR B ny] is a stereoaltmer. In some embodiments, a provided oligonucleotide of formula [S nlR B n2S B n3R B n4...S B nxR B ny] is a gapmer.

[00342] In some embodiments, a provided oligonucleotide of fonnula

[S B nl R B n2S B n3R B n4...S B nxR B ny] is of any of the above described patterns and further comprises patterns of P-modifications. For instance, in some embodiments, a provided oligonucleotide of fonnula [S B nlR B n2S B n3R B n4...S B nxR B ny] and is a stereoskipmer and P-modification skipmer. hr some embodiments, a provided oligonucleotide of formula [S B nlR B n2S B n3R B n4...S B nxR B ny] and is a stereoblockmer and P-modification altmer. In some embodiments, a provided oligonucleotide of formula [S B nlR B n2S B n3R B n4...S B nxR B nyj and is a stereoaltmer and P-modification blockmer.

[00343] In some embodiments, an internucleotidic linkage of formula I has the structure of:

wherein:

P* is an asymmetric phosphorus atom and is either Rp or 5p;

W is O, S or Se;

each of X, Y and Z is independently -O-, -S-, -Nf-L-R 1 )-, or L;

L is a covalent bond or an optionally substituted, linear or branched C -C 3 o alkylene, wherein one or more methylene units of L are optionally and independently replaced by C r -C 6 alkylene, C r -C 6 alkenylene,

_ a -C fi heteroaliphatic moiety, -C(R')r-, -Cy-, -O-, -S-, -S-S-, -N(R')-, -C(O)-, - C(S) , -C(NR')-, -C(0)N(R') , -N(R')C(0)N(R')-, -N(R')C(0)-, -N(R')C(0)0-, -OC(0)N(R')-, 8(0) . 8(0) . S(O) L( K') . -N(R')S(0) 2 - SC 40) ( (0)8 . -OC(O)-, and ( (0)0 : R 1 is halogen, R, or an optionally substituted C -C 5 o aliphatic wherein one or more methylene units are optionally and independently replaced by C ~C 6 alkylene, C r- C 6 alkenylene, cºc , a C --C 6 heteroaliphatic moiety, C(R’) . · . -Cy-, -0-, -S-, -S-S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, - C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(0)-, -N(R')C(0)0-, -OC(0)N(R')-, S{0) . -S(0) r- , -S(0) 2 N(R')-, -N(R')S(0) 2- - SC(0)-, -C(0)S- -0C(0)-, and ( (OK) :

each R' is independently -R, -C(0)R, -C0 2 R, or -SQ 2 R, or:

two R' are taken together with their intervening atoms to form an optionally substituted aryl, carbocyelic, heterocyclic, or heteroaryl ring;

-Cy- is an optionally substituted bivalent ring selected from phenylene, carbocyclylene, arylene, heteroaryleme, and lieteroeyclylene;

each R is independently hydrogen, or an optionally substituted group selected from Ci-C 6 aliphatic, carbocyclyi, and, heteroaryl, and heterocyclyl; and each independently represents a connection to a nucleoside.

[00344] In some embodiments, L is a covalent bond or an optionally substituted, linear or branched C r-- Ci 0 alkylene, wherein one or more methylene units of L are optionally and independently replaced by an optionally substituted Cr--C 6 alkylene, C r- C 6 alkenylene, cºc , - C ( R'> . -Cy-, -0-, -S-, S S . N(R ) . ( ' {();· . -C(S)-, -C(NR’)-, -C(G)N(R'}- -

N(R')C(0)N(R')-, -N(R')C(0)-, -N(R')C(0)0-, -OC(0)N(R')-, -S(O)-, -S(0) 2- , -S(Q) 2 N(R’}-, - N(R')S(0) 2- , -SC(0)-, ( (0)S . ()( !()) . or 00)0 :

R is halogen, R, or an optionally substituted Ci-C 50 aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally substituted Ci-C 6 alkylene, Cr-C 6 alkenylene, — CºC— 5 - C (R') 2 - -Cy-, -0-, -S-, -S-S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, -C(0)N(R')-, - N(R') C(0)N(R') -, -N(R')C(OK -N(R')C(0)0-, -QC(G)N(R')~, S(O) . 8(0) . . -S(0) 2 N(R')-, - N(R')S(0) 2- 8C(0) . C(0)8 . OC(O) . or ( (0)0 :

each R' is independently -R, -C(0)R, -C0 2 R, or -S0 2 R, or:

two R' on the same nitrogen are taken together with their intervening atoms to form an optionally substituted heterocyclic or heteroaryl ring, or

two R' on the same carbon are taken together with their intervening atoms to form an optionally substituted aryl, carbocyelic, heterocyclic, or heteroaryl ring;

-Cy- is an optionally substituted bivalent ring selected from phenylene, carbocyclylene, arylene, heteroarylene, or heterocyclylene;

each R is independently hydrogen, or an optionally substituted group selected from C r- C 6 aliphatic, phenyl, carbocyclyi, aryl, heteroaryl, or heterocyclyl; and each ¾ independently represents a connection to a nucleoside.

[00345] In some embodiments, a chirally controlled oligonucleotide comprises one or more modified intemucleotidic linkages. In some embodiments, a chirally controlled oligonucleotide comprises, e.g., a phosphorothioate or a phosphorothioate triester intemucleotidic linkage. In some embodiments, a chirally controlled oligonucleotide comprises a chirally controlled phosphorothioate triester linkage. In some embodiments, a chirally controlled oligonucleotide comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 chirally controlled phosphorothioate triester intemucleotidic linkages. In some embodiments, a chirally controlled oligonucleotide comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 chirally controlled phosphorothioate intemucleotidic linkages (-0-P(0)(SH)-0- or salt forms thereof).

[00346] hi some embodiments, an oligonucleotide comprises different types of intemucleotidic phosphorus linkages. In some embodiments, a chirally controlled oligonucleotide comprises at least one natural phosphate linkage and at least one modified (non-natural) intemucleotidic linkage. In some embodiments, an oligonucleotide comprises at least one natural phosphate linkage and at least one phosphorothioate. In some embodiments, an oligonucleotide comprises at least one non-negative ly charged intemucleotidic linkage. In some embodiments, an oligonucleotide comprises at least one natural phosphate linkage and at least one non-negative!y charged intemucleotidic linkage. In some embodiments, an oligonucleotide comprises at least one phosphorothioate intemucleotidic linkage and at least one non-negatively charged intemucleotidic linkage. In some embodiments, an oligonucleotide comprises at least one phosphorothioate intemucleotidic linkage, at least one natural phosphate linkage, and at least one non-negatively charged intemucleotidic linkage.

[00347] In some embodiments, an intemucleotidic linkage comprises a chiral auxiliar '. In some embodiments, an intemucleotidic linkage of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, il-d-1, ll-d-2. etc., comprises a chiral auxiliary, wherein P L is P=S. In some embodiments, an intemucleotidic linkage of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1 , II-a-2, II-b-1 , II~b~2, II-c-1, II-c-2, II-d-1, II-d-2, etc., comprises a chiral auxiliary ' , wherein P L is P=0. In some embodiments, a phosphorothioate triester linkage comprises a chiral auxiliary, which, for example, is used to control the stereoselectivity of a reaction. In some embodiments, a phosphorothioate triester linkage does not comprise a chiral auxiliary'. Example chiral auxiliaries that can be utilized in accordance with the present disclosure include those described in US 9394333, US 9744183, US 9605019, US 20130178612, US 20150211006, US 9598458, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2018/237194, WO 2019/055951, the chiral auxiliaries of each of which is incorporated herein by reference. In some embodiments, one or more -X-L-R 1 independently comprise or are an optionally substituted chiral auxiliary. In some embodiments, one or more -X-L-R 1 are each independently of such a structure that H-X-L-R 1 is a chiral reagent/chiral auxiliary described herein (e.g., one having the structure of formula 3-1, formula 3-AA, etc.). In some embodiments, H-X-L-R 1 is a capped chiral reagent/chiral auxiliary described herein (e.g., one having the structure of formula 3-1, formula 3-AA, etc.), winch is capped in that an ammo group of the chiral reagent/chiral auxiliary (e.g., H-W 1 and H-W 2 is or comprises H-NG 5 -) is capped (e.g., forming R l -NG J - (e.g., R’C(0)-NG 5 -, RS(0) 2- NG 3 -, etc.)). In some embodiments, R’ is optionally substituted C I-6 alkyl. In some embodiments, R’ is methyl. In some embodiments, one or more -X-L-R 1 are each independently of

some embodiments, one or more -X-L-R 1 are each independently of such a structure that H-X-L-R 1 is In some embodiments, one or more -X-L-R 1 are each independently of such a

structure that

n some em 5 0C|imen ts one or more -X-L-R 1 are each independently of such a structure that H-X-L-R ! is a compound selected from Tables CA-1, CA-2, CA-3, CA-4, CA-5, CA-6,

CA-7, CA-8, CA-9, CA-10, CA-11, CA-12, or CA-13, or a related (having the same constitution) diastereomer or enantiomer thereof. In some embodiments, one or more -X-L-R 1 are each

independently of such a structure that

some embodiments, one or more -X-L-R 1 are each independently of such a structure that I I X l . R 1 is or . In some embodiments, one or more -X-L-R 1 are each independently of such a

structure that . In some embodiments, one or more -X-L-R 1 are each independently of such a structure that H-X-L-R 1 is a compound selected from Tables CA-1, CA-2, CA-3, CA-4, CA-5, CA-6, CA-7, CA-8, CA-9, CA-10, CA-11, CA-12, or CA-13, or a related (having the same constitution) diastereomer or enantiomer thereof, wherein the -NH- of the 5-membered pyrrolidinyl is replaced with

In some embodiments, one or more -X-L-R 1 are independently some embodiments. one or more are independently

In some embodiments, one or more -X-L-R 1 are each independently of such a structure that H-X-L-R 1 is a compound selected from Tables CA-1, CA-2, CA-3, CA-4, CA-5, CA-6, CA-7, CA-8, CA-9, CA-10, CA-11, CA-12, or CA-I3, or a related (having the same constitution) diastereomer or enantiomer thereof, wherein the connection to the linkage phosphorus is through the alcohol hydroxyl group. In some embodiments, one or more -X-L-R 1

are independently

or . In some embodiments,

R 1 one or more -X-L-R 1 are independently some embodiments, one or more -X-L-R 1

are independently or . In some embodiments, one or more -X-L-R 1 are each independently of such a structure that H-X-L-R 1 is a compound selected from Tables CA-1, CA-2, CA-3, CA-4, CA-5, CA-6, CA-7, CA-8, CA-9, CA-10, CA-11, CA-12, or CA-13, or a related (having the same constitution) diastereomer or enantiomer thereof, wherein the -NH- of the 5-membered pyrrohdinyl is replaced with -NiR 1 )-, and wherein the connection to the linkage phosphorus is through the alcohol hydroxyl group. In some embodiments, one or more -X-L-R 1 are independently or

R 1

and one or more -X-L-R 1 are independently In some embodiments, one or more -X-L-R 1 are independently one or more X i . R 1 are independently some embodiments, one or more -X-L-R are ind ,epend ,ently or and one or more -X-L-R 1 are independently . In some embodiments, R is a capping group utilized in oligonucleotide synthesis. In some embodiments, R 1 is -C(0)-R\ In some embodiments, R 1 is -C(0)-R\ wherein R’ is optionally substituted Ci_ 5 aliphatic. In some embodiments, R s is CiOK ' l 1

[00348] In some embodiments, an oligonucleotide, e.g., a chiraliy controlled oligonucleotide, an oligonucleotide of a plurality, etc. is linked to a solid support. In some embodiments, an oligonucleotide is not linked to a solid support.

100349 In some embodiments, an oligonucleotide comprises at least one natural phosphate linkage and at least two consecutive chiraliy controlled modified intemucleotidic linkages. In some embodiments, a chiraliy controlled oligonucleotide comprises at least one natural phosphate linkage and at least two consecutive chiraliy controlled phosphorothioate intemucleotidic linkages.

100350 In some embodiments, a chiraliy controlled oligonucleotide is a blockmer. In some embodiments, a chiraliy controlled oligonucleotide is a stereoblockmer. In some embodiments, a chiraliy controlled oligonucleotide is a P-modifi cation blockmer. In some embodiments, a chiraliy controlled oligonucleotide is a linkage blockmer.

100351 In some embodiments, a chiraliy controlled oligonucleotide is an altmer. In some embodiments, a chiraliy controlled oligonucleotide is a stereoaltmer. In some embodiments, a chiraliy controlled oligonucleotide is a P-modification altmer. In some embodiments, a chiraliy controlled oligonucleotide is a linkage altmer.

100352 In some embodiments, a chiraliy controlled oligonucleotide is a unirner.

[00353] In some embodiments, in a unimer, all nucleotide units within a strand share at least one common structural feature at the intemucleotidic phosphorus linkage. In some embodiments, a common structural feature is a common stereochemistry at the linkage phosphorus or a common modification at the linkage phosphorus. In some embodiments, a chiraliy controlled oligonucleotide is a stereo unimer. In some embodiments, a chiraliy controlled oligonucleotide is a P-modification unimer. In some embodiments, a chiraliy controlled oligonucleotide is a linkage unimer.

[00354] In some embodiments, a chiraliy controlled oligonucleotide is a gap er.

[00355] In some embodiments, a chiraliy controlled oligonucleotide is a skipmer.

[00356] In some embodiments, the present disclosure provides oligonucleotides comprising one or more modified intemucleotidic linkages independently having the structure of formula I, I-a, I-b, I-c, or a salt form thereof.

[00357] In some embodiments, L is a covalent bond or an optionally substituted, linear or branched C 3- Cio alkyiene, wherein one or more methylene units of L are optionally and independently replaced by an optionally substituted C r-- C 6 alkyiene, C r-- C 6 alkenylene, cºc , -C(R') 2- , -Cy-, -(>- , -S-, -S-S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, -C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(0)-, - N(R')C(0)0-, -OC(0)N(R')-, -S(O)-, -S(0) 2- , -S(0) 2 N(R')-, -N(R')S(0) 2- , S ( ( () ) . -C(0)S-, - OC(O)-, or -C(0)0-;

R is halogen, R, or an optionally substituted Ci-Cso aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally substituted C -C 6 alkyiene, C r- C 6 alkenylene,

N(R') C(0)N(R') -, -N(R')C(OK -N(R')C(0)0-, -OC(0)N(R')-, S(O) . -S(0) 2- , -S(0) 2 N(R')-, - N(R')S(0) 2- , -SC(O)-, C (0)8 . OC(O) . or ( (0)0 :

each R' is independently -R, -C(0)R, -C0 2 R, or -S0 2 R, or:

two R' on the same nitrogen are taken together with their intervening atoms to form an optionally substituted heterocyclic or heteroaryl ring, or

two R' on the same carbon are taken together with their intervening atoms to form an optionally substituted aryl, carbocyclic, heterocyclic, or heteroaryl ring;

-Cy- is an optionally substituted bivalent ring selected from phenylene, carbocyclylene, arylene, heteroaryl ene, or heterocyclylene;

each R is independently hydrogen, or an optionally substituted group selected from C r- C 6 aliphatic, phenyl, carbocyclyl, aryl, heteroaryl, or heterocyclyl; and each independently represents a connection to a nucleoside.

[00358] In some embodiments, a chirally controlled oligonucleotide comprises one or more modified intemucieotidic phosphorus linkages. In some embodiments, a chirally controlled oligonucleotide comprises, e.g., a phosphorothioate or a phosphorothioate triester linkage. In some embodiments, a chirally controlled oligonucleotide comprises a phosphorothioate triester linkage. In some embodiments, a chirally controlled oligonucleotide comprises at least two phosphorothioate triester linkages hi some embodiments, a chirally controlled oligonucleotide comprises at least three phosphorothioate triester linkages. Example modified intemucieotidic phosphorus linkages are described further herein. In some embodiments, a chirally controlled oligonucleotide comprises different intemucieotidic phosphorus linkages. In some embodiments, a chirally controlled oligonucleotide comprises at least one phosphate diester intemucieotidic linkage and at least one modified intemucieotidic linkage. In some embodiments, a chirally controlled oligonucleotide comprises at least one phosphate diester intemucleotidic linkage and at least one phosphorothioate triester linkage. In some embodiments, a chirally controlled oligonucleotide comprises at least one phosphate diester intemucleotidic linkage and at least two phosphorothioate triester linkages. In some embodiments, a chirally controlled oligonucleotide comprises at least one phosphate diester intemucleotidic linkage and at least three phosphorothioate triester linkages.

[00359] In some embodiments, P* is an asymmetric phosphorus atom and is either Rp or »Sp. In some embodiments, P* is Rp. In other embodiments, P* is Sp. In some embodiments, an oligonucleotide comprises one or more intemucleotidic linkages of formula I wherein each P* is independently Rp or Xp. In some embodiments, an oligonucleotide comprises one or more intemucleotidic linkages of formula I wherein each P* is Rp. In some embodiments, an oligonucleotide comprises one or more intemucleotidic linkages of formula I wherein each P* is 5p. In some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula I wherein P* is Rp. In some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula I wherein P* is Sp. In some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula 1 wherein P* is Rp, and at least one intemucleotidic linkage of formula I wherein P* is Sjp.

[00360] In some embodiments, W is O, S, or Se In some embodiments, W is O. In some embodiments, W is S. In some embodiments, W is Se. In some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula I wherein W is O. hi some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula I wherein W is S. In some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula I wherein W is Se.

[00361] In some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula I wherein W is O. In some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula I wherein W is S.

100362 In some embodiments, X is In some embodiments, X is ---S---. In some embodiments, X is -O- or -S---. In some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula I wherein X is -Q-. In some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula I wherein X is -S-. In some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula I wherein X is -O-, and at least one intemucleotidic linkage of formula I wherein X is -S-. In some embodiments, an oligonucleotide comprises at least one intemucleotidic linkage of formula I wherein X is -O-, and at least one intemucleotidic linkage of formula I wherein X is -S-, and at least one intemucleotidic linkage of formula I wherein L is an optionally substituted, linear or branched C j- Cio alkylene, wherein one or more methylene units of L are optionally and independently replaced by an optionally substituted C r-- C 6 alkylene, C r --C 6 alkenylene, , -C(R') 2 -, -Cy-, -0-, -S-, -S-S-, -N(R’)~, -C(O)-, -C(S)-, - C(NR')-, -C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(0)-, -N(R')C(0)0- s -0C(0)N(R')-, S(O) . - S(0) 2— , -S(0) 2 N(R')-, -N(R')S(0) 2 -, SC( O) . -C(0)S-, OC( ( )} . or { (()){) .

100363 In some embodiments, X is -Ny-L-R 1 )--. In some embodiments, X is -b^R 1 )-. In some embodiments, X is -N(R’)~. In some embodiments, X is -N(R)-. In some embodiments, X is -NH-.

[00364] In some embodiments, X is L In some embodiments, X is a covalent bond. In some embodiments, X is or an optionally substituted, linear or branched Ci-C I0 alkylene, wherein one or more methylene units of L are optionally and independently replaced by an optionally substituted C r --C 6 alkylene, C r --C 6 alkenylene, , -C(R') 2~ , -Cy-, -O-, -S-, -S-S-, -N(R’)-, -C(O)-, -C(S)-, - C(NR')-, -C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(0)-, N(R )( (0)0 . -0C(0)N(R')-, S(O) . - S( O ) . S(O) .Xi R') . -N(R')S(0) 2 -, -SC(G)-, C(0)S . OC(O) . or 00)0 . In some embodiments, X is an optionally substituted C r --Ci 0 alkylene or Ci-Ci 0 alkenylene. In some embodiments, X is methylene.

[00365] In some embodiments, Y is -0-. In some embodiments, Y is -S-.

[00366] In some embodiments, Y is -Ni-L-R 1 )--. In some embodiments, Y is -N^R 1 )- In some embodiments, Y is --N(R’)-. In some embodiments, Y is -N(R)-. In some embodiments, Y is -NH-.

[00367] In some embodiments, Y is L. In some embodiments, Y is a covalent bond. In some embodiments, Y is or an optionally substituted, linear or branched C j -C [0 alkylene, wherein one or more methylene units of L are optionally and independently replaced by an optionally substituted Ci C 6 alkylene, C r -C 6 alkenylene,— C ºC— s C( R') , . -Cy-, -0-, S . S S . -N(R')-, -C(O)-, ( (S) . - C(NR')-, -C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(0)-, -N(R')C(0)0-, -0C(0)N(R')-, S(O) . - S( 0) 2 . -S(0) 2 N(R')-, -N(R')S(0) 2 -, SC( O) . -C(0)S-, -OC(O)-, or -C(0)0-. In some embodiments, Y is an optionally substituted Ci-Cio alkylene or Ci-Cio alkenylene. In some embodiments, Y is methylene.

[00368] In some embodiments, Z is -0-. In some embodiments, Z is -S-.

[00369] In some embodiments, Z is -N(-L-R ! )-. In some embodiments, Z is -NCR 1 )-. In some embodiments, Z is -N(R’)-. In some embodiments, Z is -N(R)- . In some embodiments, Z is -NH-.

[00370] In some embodiments, Z is L. In some embodiments, Z is a covalent bond. In some embodiments, Z is or an optionally substituted, linear or branched C r -Cio alkylene, wherein one or more methylene units of L are optionally and independently replaced by an optionally substituted Ci-C 6 alkylene, C -C 6 alkenylene,— c º c ? -C(R') 2 , -Cy-, -0-, -S-, -S-S-, -N(R')-, -C(O)-, -C(S)-, - C(NR')-, -C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(OK -N(R')C(0)0-, -0C(0)N(R')-, -S(O)-, - S(0) 2 -, -S(0) 2 N(R')-, -N(R')S(0) 2 -, -SC(OK ( (O)S . -OC(O)-, or -C(0)0-. In some embodiments, Z is an optionally substituted C I -C LO alkylene or C J -C LO alkenylene. In some embodiments, Z is methylene.

[00371] In some embodiments, L is a covalent bond or an optionally substituted, linear or branched Ci-Cio alkylene, wherein one or more methylene units of L are optionally and independently replaced by an optionally substituted C -C 6 alkylene, C r-- C 6 alkenylene, ^ - C(R') 2- , -Cy-, -Q- , -S-, S S . N{R·) . {·((» . ( (8) . -C(NR')-, -C(0)N(R'>-, -N(R')C(0)N(R ')-, N( R')CiO) . - N(R')C(0)0 , -OC(0)N(R')-, S(O) . S(O) . -S(0) 2 N(R')-, -N(R')S(0) 2- , SOO) . -C(0)S-, - OC(O or -C(0)0-.

[00372] In some embodiments, L is a covalent bond. In some embodiments, L is an optionally substituted, linear or branched C -Cio alkylene, wherein one or more methylene units of L are optionally and independently replaced by an optionally substituted C j -- C 6 alkylene, C.-C 6 alkenylene, C ºC ^ C(R') 2 - -Cy-, -O-, -S-, -S-S-, -N(R')-, -C(O)-, -C(S)-, -C(NR' C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(0)-, -N(R')C(0)0-, -OC(0)N(R')-, -S(O)-, -S(0) 2~ , -S(0) 2 N(R f ) , -N(R')S(0) 2- - SC(O C(0)S , -OCCOK or C(0)0 .

[00373] In some embodiments, L has the structure of-L ] -V-, wherein:

L 1 is an optionally substituted group selected from

C 5 alkylene, Ci-C 6 alkenylene, carboeyclylene, arylene, C r-- C 6 heteroalkylene, heterocyclylene, and heteroarylene;

A

V is selected from O . -S-, -NR’-, C(R’) ¾ - S-S-, -B-S-S-C-, Ά ® A ¾ , or an optionally substituted group selected from C r-- C 6 alkylene, arylene, Cr-C 6 heteroalkylene, heterocyclylene, and heteroarylene;

A is =0, =S, =NR’, or =C(R’) 2 ;

each of B and C is independently -0-, -S-, -NR’-, -C(R’) 2- , or an optionally substituted group selected from C r- C 5 alkylene, carboeyclylene, arylene, heterocyclylene, or heteroarylene; and

each R is independently as defined above and described herein.

wherein Ring Cy’ is an optionally substituted arylene, carbocyclyiene, heteroarylene, or heterocyclylene. In some embodiments, L 1 is optionally substituted In some embodiments, L 1 is

In some embodiments, L 1 is cormected to X. In some embodiments, L 1 is an optionally substituted group selected from the sulfur atom is connect to V. In some embodiments, L 1 is an optionally substituted group selected from , the carbon atom is connect to X

In some embodiments, L has the structure of:

wherein:

E is 0 . S . NR or C(R y ;

— is a single or double bond; the two R L1 are taken together with the two carbon atoms to which they are bound to form an optionally substituted aryl, carbocyclic, heteroaryl or heterocyclic ring; and each R’ is independently as defined above and described herein.

00378 In some embodiments, L has the structure of:

wherein:

( = is O . S . or -NR’;

------- is a single or double bond; and

the two R Li are taken together with the two carbon atoms to which they are bound to form an optionally substituted aryl, C 3 -C. 0 carbocyclic, heteroaryl or heterocyclic ring.

[00379] In some embodiments, L has the structure of:

wherein:

E is -O-, S . -NR’- or ( (R ) . :

D is =N-, =C(F)-, =C(Ci)-, =C(Br)-, ( ' {1} .. =C(CN)-, =C(N0 2 )-, =C(C0 2- (Ci-C 6 aliphatic))-, or =C(CF 3 )-; and

each R’ is independently as defined above and described herein.

[00380] hi some embodiments, L has the structure of:

wherein:

G is -O-,— S— , or -NR’;

D is -N-, ( (F) . OP) . -C(Br)-, C( l) . =C(CN)-, =C(N0 2 )-, =C(C0 2 {C C 6 aliphatic))-, or

=C(CF 3 )-.

[00381] In some embodiments, L has the structure of:

wherein:

E is -O-, S . N R or ( ( R E :

D is =N-, =C(F) ,— C(C1)— , =C(Br) , =C(I)-, =C(CN)-, =C(N0 2 )-, =C(C0 2 -(CrC 6 aliphatic))-, or =C(CF 3 )-; and

each R’ is independently as defined above and described herein.

00382] In some embodiments, L has the structure of:

wherein:

G is -0-, -S-, or -NR’;

D is =N- =C(F) , =C(C1)-, =C(Br)-, =C(I)-, =C(CN)-, =C(NQ 2 )- =C(C0 2 -(C r C 6 aliphatic))-, or

=C(CF 3 )-.

[00383] In some embodiments, L has the structure of:

wherein:

E is -O- S . -NR’- or ( (R ) . :

— is a single or double bond:

the two R L! are taken together with the two carbon atoms to which they are bound to form an optionally substituted aryl, C 3 -Ci 0 carbocyclic, heteroaryl or heterocyclic ring;

and each R’ is independently as defined above and described herein.

[00384] In some embodiments, L has the structure of:

wherein: G is -0-, S . or -NR’;

— is a single or double bond;

the two R 1 are taken together with the two carbon atoms to which they are bound to form an optionally substituted aryl, C 3 -C 10 carbocyclic, heteroaryl or heterocyclic ring;

and each R’ is independently as defined above and described herein.

00385] In some embodiments, L has the structure of:

aliphatic))-, or

=C(CF 3 )-: and

each R is independently as defined above and described herein.

In some embodiments, L has the structure of:

aliphatic))-, or

( (C l· ) and

each R’ is independently as defined above and described herein.

hr some embodiments, L has the structure of:

aliphatic))-, or

=C(CF 3 )-; and each R’ is independently as defined above and described herein

[00388] In some embodiments, L has the structure of:

D is =N- on . 0(1) . =C(Br)-, ==€(!)-, ( ' {( N ) . O NO } . Cf CO · (( ' =-< .. aliphatic))-, or =C(CF 3 )-; and

each R’ is independently as defined above and described herein.

In some embodiments, L has the structure of:

wherein:

E is -0-, -S-, -NR’- or -C(R’) 2 -;

— is a single or double bond;

the two R L1 are taken together with the two carbon atoms to which they are bound to form an optionally substituted aryl, C 3 -C J O carbocyclic, heteroaryl or heterocyclic ring; and each R’ is independently as defined above and described herein.

In some embodiments, L has the structure of:

wherein:

G is— O— ,— S— , or -NR’;

— is a single or double bond;

the two R L1 are taken together with the two carbon atoms to which they are bound to form an optionally substituted aryl, C 3 -Ci 0 carbocyclic, heteroaryl or heterocyclic ring; and each R’ is independently as defined above and described herein.

00391 In some embodiments, L has the structure of:

wherein:

E is -0-, S . N R or C( R h :

D is =N-, =C(F)-, =C(C1)-, =C(Br)-, =C(I)-, =C(CN)-, =C(N0 2 }-, =C(C0 2 -(C ] -C 6 aliphatic))-, or =C(CF 3 ) ; and

each R’ is independently as defined above and described herein.

[00392] In some embodiments, L has the structure of:

wherein:

G is -0-, -S-, or -NR’;

D is =N- =C(F)-, =C(C1)-, =C(Br)- =C(I)-, =C(CN)-, =C(NQ 2 )-, =C(C0 2 -(C C 5 aliphatic))-, or =C(CF 3 )-; and

R’ is as defined above and described herein.

00393] In some embodiments, L has the structure of:

aliphatic))-, or

=C(CT 3 )-; and

each R’ is independently as defined above and described herein.

[00394] In some embodiments, L has the structure of:

wherein:

G is -0--, -S-, or -NR’;

D is =N-, =C(F)-, =C(C1)-, =C(Br)-, =C(I)-, =C(CN)-, =C(NQ 2 }-, =C(C0 2 -(C 3 -C 6 aliphatic))--, or ( {C l· ' ) : and

R’ is as defined above and described herein.

00395] In some embodiments, L has the structure of:

wherein the phenyl ring is optionally substituted. In some embodiments, the phenyl ring is not substituted. In some embodiments, the phenyl ring is substituted.

100396 In some embodiments, L has the structure of:

wherein the phenyl ring is optionally substituted. In some embodiments, the phenyl ring is not substituted. In some embodiments, the phenyl ring is substituted.

[00397] In some embodiments, L has the structure of:

wherein:

— is a single or double bond; and

the two R 1 are taken together with the two carbon atoms to which they are bound to form an optionally substituted aryl, C3-C10 carbocyclic, heteroarl or heterocyclic ring.

100398 In some embodiments, L has the structure of:

wherem: G is -0-, S . or -NR’;

— is a single or double bond; and

the two R 1 are taken together with the two carbon atoms to which they are bound to form an optionally substituted aryl, C 3~ Cio carbocyc!ic, heteroaryl or heterocyclic ring.

[00399] In some embodiments, E is -0-, -S-, -NR’- or -C(R ) 2- , wherein each R’ independently as defined above and described herein. In some embodiments, E is -0-, -S-, or -NR’-. In some embodiments, E is -0-, -S-, or -NH-. In some embodiments, E is -0- In some embodiments, E is— S— . In some embodiments, E is -NH-.

100400] In some embodiments, G is -0-, ---S---, or --NR/, wherein each R’ independently as defined above and described herein. In some embodiments, G is -0-, -S-, or -NH-. In some embodiments, G is -0-. In some embodiments, G is -S-. In some embodiments, G is -NH-.

[00401] In some embodiments, L is L G , wherein:

L J is an optionally substituted C 1 -C 5 alkylene or alkenylene, wherein one or more methylene units are optionally and independently replaced by -0-, -S-,-N(R’)-, -C(Q)-, -C(S)-, -C(NR’)-, ~S(0)~, ---

wherein each of G, R and Ring Cy’ is independently as defined above and described herein.

[00402] In some embodiments, L is -L 3 -S-, wherein L 3 is as defined above and described herein.

In some embodiments, L is -L 3 - O - , wherein L 3 is as defined above and described herein. In some embodiments, L is -L 3 -N(R/)-, wherein each of L 3 and R’ is independently as defined above and described herein. In some embodiments, L is -L 3 -NH-, wherein each of L 3 and R’ is independently as defined above and described herein.

In some embodiments, L 3 is an optionally substituted C 5 alkylene or alkenylene, wherein one or more methylene units are optionally and independently replaced by -0-, -S-,-N(R')-, -C(Q)-, ---

C(S)- , -C(NR')-, -S(G)-, S(O) . or , and each of R’ and Ring Cy is independently as defined above and described herein. In some embodiments, L 3 is an optionally substituted C 5 alkylene.

In some embodiments,

100404 In some embodiments, L 3 is an optionally substituted C 4 alkylene or alkenylene, wherein one or more methylene units are optionally and independently replaced by -Q-, -S-,-N(R')-, -C(Q)--, - C(S) , -C(NR')-, -S(O)--,— S(O) : and each of R’ and Cy is independently as defined above and described herein.

00406] In some embodiments, L’ is an optionally substituted C 3 alkylene or alkenylene, wherein one or more methylene units are optionally and independently replaced by -S-,-N(R')-, -C(O)-, -

C(S> and each of R" and Cy’ is independently as defined above and described herein.

In some embodiments. L is

In some embodiments, L J is an optionally substituted C 2 alkylene or alkenylene, wherein one or more methylene units are optionally and independently replaced by -0-, -S-,-N(R')-, -C(O)-, -

C(S)-, -C(NR' -S(O)-, -S(0) 2 -, , and each of R’ and Cy is independently as defined above and described herein. wherein each of G and Cy’ is

independently as defined above and described herein in some embodiments,

[00411] In some embodiments, L is -L 4 -G-, wherein L 4 is an optionally substituted C j -- C 2 alkylene; and G is as defined above and described herein. In some embodiments, L is L 4 -G , wherein L 4 is an optionally substituted Ci-C 2 alkylene; G is as defined above and described herein; and G is connected to R . In some embodiments, L is -Lf-G-, wherein L 4 is an optionally substituted methylene; G is as defined above and described herein; and G is connected to R 1 . In some embodiments, L is -L 4 - G-, wherein L 4 is methylene; G is as defined above and described herein; and G is connected to R 1 . In some embodiments, L is -L 4 -G-, wherein L 4 is an optionally substituted -(CH 2 ) 2- ; G is as defined above and described herein; and G is connected to R 1 . In some embodiments, L is -I -G-, wherein L 4 is - (CH 2 ) 2- ; G is as defined above and described herein; and G is connected to R 1 .

[00412] In some embodiments, L is , , wherein G is as defined above and described herein, and G is connected to R . In some embodiments, L is . wherein G is as defined above and described herein, and G is connected to R 1 In some embodiments, L is . wherein G is as defined above and described herein, and G is connected to R 1 . In some embodiments, L

is as defined above and described herein

[00414] hi some embodiments, L is -S-R u - or -S-CiQ^-R 1 3 -, wherein R u is an optionally substituted, linear or branched, Ci C 9 alkylene, wherein one or more methylene units are optionally and independently replaced by an optionally substituted C -C 6 alkylene, C -C 6 alkenyiene,— c º c — , - C (R ) · . (V . O . 8 . S S . -N(R')-, -C(O)-, -C(S)- C(XR') . -C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(0)-, -N(R')C(0)0-, -OC(0)N(R')-, -8(0)-, 8(0) . . 8(0) <R') . -N(R')S(0) 2- , 8C(0) . — C(0)S— ,— OC(O)— , or— C(0)0— , wherein each of R’ and -Cy- is independently as defined above and described herein. In some embodiments, L is -S-R L - or -S-C(0)-R L -, wherein R L is an optionally substituted C.-C 6 alkyiene. In some embodiments, L is -S-R^- or -S---C(0)---R L --, wherein R LJ is an optionally substituted Ci C 6 alkenylene. In some embodiments, L is -S-R 1 3 - or -S-C(0)-R L ’-, wherein R LJ is an optionally substituted Ci-C ¾ alkyiene wherein one or more methylene units are optionally and independently replaced by an optionally substituted C j -C 6 alkenylene, arylene, or heteroarylene. In some embodiments, In some embodiments, R iJ is an optionally substituted -S-(C r -C 6 alkenylene)--, --S--(C r --C 6 alkyiene)--, -S-(C j -C 6 alky icnc) ary lone (C , C alkyiene)--, -S-CO-arylene-(C [ -C 6 alkyiene)--, or -S- CO-(Ci-C 6 alkylene)-arylene-(Ci-C 6 alkyiene)-.

In some

In some embodiments

[00417] In some embodiments, the sulfur atom in the L embodiments described above and herein is connected to X. In some embodiments, the sulfur atom in the L embodiments described above and herein is connected to R 5 .

[00418] In some embodiments, R 1 is halogen, R, or an optionally substituted Ci-C ¾ o aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally substituted C -C 6 alkyiene, C 5- C 6 alkenylene,— cºc — , -C(R')2 , -Cy-, -0-, -S-, -S-S-, -N(R')-, - ( ' ( () } .. -C(S)-, -C(NR')-, -C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(0)-, N{R’ )( ' (())() . - OC(0)N(R')-, S(O) . S{ O ) · . -S(0) 2 N(R')- -N(R')S(0) 2 - -SC(O)-, C(0)S .. () ( (()) . or - C(0)0-, wherein each variable is independently as defined above and described herein. In some embodiments, R ! is halogen, R, or an optionally substituted Ci-Cio aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally substituted Ci-C 6 alkyiene, Ci-C 6 alkenylene, --o-c-- ( ( '> , . -Cy- -O-, -S-, -S-S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, -

C(0)N(R')-, -N(R')C(0)N(R')-, X( R )( (O) . -N(R')C(0)0-, -OC(0)N(R')-, -S(O)-, -S(0) 2 -, - S(G) 2 N(R')-, -N(R')S(0) 2~ , -SC(0) , -C(0)S-, -OC(O)--, or -€(0)0-, wherein each variable is independently as defined above and described herein.

[00419] In some embodiments, R ! is hydrogen in some embodiments, R 1 is halogen. In some embodiments R 1 is -F. In some embodiments, R 1 is -Cl. In some embodiments, R l is -Br. In some embodiments, R 1 is -I.

[00420] In some embodiments, R 1 is R wherein R is as defined above and described herein.

[00421] In some embodiments, R 1 is hydrogen. In some embodiments, R ! is an optionally substituted group selected from C -C 50 aliphatic, phenyl, carbocyelyi, aryl, heteroaryl, or heterocyclyl.

100422 In some embodiments, R 1 is an optionally substituted C r-- C 5 o aliphatic. In some embodiments, R 1 is an optionally substituted C J -C LO aliphatic. In some embodiments, R 1 is an optionally substituted C -C 6 aliphatic. In some embodiments, R 1 is an optionally substituted Ci-C 6 alkyl. In some embodiments, R ! is optionally substituted, linear or branched hexyl. In some embodiments, R 1 is optionally substituted, linear or branched pentyl. In some embodiments, R 1 is optionally substituted, linear or branched butyl. In some embodiments, R 1 is optionally substituted, linear or branched propyl. In some embodiments, R 1 is optionally substituted ethyl. In some embodiments, R 1 is optionally substituted methyl.

[00423] In some embodiments, R 5 is optionally substituted phenyl. In some embodiments, R 1 is substituted phenyl. In some embodiments, R 1 is phenyl.

[00424] In some embodiments, R 1 is optionally substituted carbocyelyi. In some embodiments,

R is optionally substituted C 3 -C l0 carbocyelyi. In some embodiments, R 1 is optionally substituted monocyclic carbocyelyi. In some embodiments, R 1 is optionally substituted cycloheptyl. In some embodiments, R 1 is optionally substituted cyclohexyl. In some embodiments, R 1 is optionally substituted cyclopentyl. In some embodiments, R ! is optionally substituted cyclobutyl. In some embodiments, R 1 is an optionally substituted cyclopropyl. In some embodiments, R 1 is optionally substituted bicyclic carbocyelyi .

[00425] In some embodiments, R 1 is an optionally substituted C1-C50 polycyclic hydrocarbon. In some embodiments, R 1 is an optionally substituted C -C 50 polycyclic hydrocarbon wherein one or more methylene units are optionally and independently replaced by an optionally substituted C t -C 6 alkylene, Cr-C 6 alkenylene, -c=c- , -C(R')z-, -Cy- -0-, -S-, -S-S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, - C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(0)-, -N(R')C(0)0-, -OC(0)N(R')~, -S(O)-, -S(0) 2 -, - S(0) 2 N(R')-, -N(R')S(0) 2- , — SC{0)— , — C(0)S— , — OC(O)— , or -C(0)0-, wherein each variable is independently as defined above and described herein. In some embodiments, R 1 is optionally substituted , In some

embodiments, R l is optionally substituted

[00426] In some embodiments, R 1 is an optionally substituted Ci C 5 o aliphatic comprising one or more optionally substituted polycyclic hydrocarbon moieties. In some embodiments, R 1 is an optionally- substituted C1-C50 aliphatic comprising one or more optionally substituted polycyclic hydrocarbon moieties, wherein one or more methylene units are optionally and independently replaced by an optionally substituted Ci-Ce alkylene, Ci-C ¾ alkeny!ene,— c = c — , -C(R')r-, -Cy-, -0-, -S-, -S-S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, -C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(0)-, -N(R')C(0)0-, - OC(0)N(R')-, -S(O)-, -S(0) 2- , -S(0) 2 N(R')-, -N(R')S(0) 2- -SC(Q)-, -C(0)S-, -OC(O)-, or -

( ' (OK) . wherein each variable is independently as defined above and described herein. In some embodiments, R 1 is an optionally substituted Ci-Cso aliphatic comprising one or more optionally-

substituted

, In some

embodiments, R 1 In some embodiments, R 1 is

some mbodiments. R In some

mbodiments,

is an optionally substituted ar l In some embodiments, R 1 is an optionally substituted bieyclic aryl ring.

[00428] In some embodiments, R 1 is an optionally substituted heteroaryl. In some embodiments,

R ! is an optionally substituted 5-6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, sulfur, or oxygen. In some embodiments, R 1 is a substituted 5-6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R 1 is an unsubstituted 5-6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, sulfur, or oxygen.

[00429] In some embodiments, R 1 is an optionally substituted 5 membered monocyclic heteroaryl ring having 1 -3 heteroatoms independently selected from nitrogen, oxygen or sulfur. In some embodiments, R 1 is an optionally substituted 6 membered monocyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[00430] In some embodiments, R 1 is an optionally substituted 5-membered monocyclic heteroaryl ring having 1 heteroatom selected from nitrogen, oxygen, or sulfur. In some embodiments, R 1 is selected from pyrrolyl, furanyl, or thienyl.

[00431] In some embodiments, R 1 is an optionally substituted 5-membered heteroaryl ring having

2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In certain embodiments, R 1 is an optionally substituted 5-membered heteroaryl ring having 1 nitrogen atom, and an additional heteroatom selected from sulfur or oxygen. Example R 1 groups include optionally substituted pyrazolyl, imidazolyl, thiazolyl, isothiazolyi, oxazolyl or isoxazolyl.

[00432] In some embodiments, R ! is a 6-membered heteroaryl ring having 1-3 nitrogen atoms. In other embodiments, R 1 is an optionally substituted 6-membered heteroaryl ring having 1-2 nitrogen atoms. In some embodiments, R 1 is an optionally substituted 6-membered heteroaryl ring having 2 nitrogen atoms. In certain embodiments, R 1 is an optionally substituted 6-membered heteroaryl ring having 1 nitrogen. Example R ! groups include optionally substituted pyridinyl, pyrimidinyl, pyrazinyl, pyridazinyl, triazinyl, or tetraziny! . [00433] In certain embodiments, R 1 is an optionally substituted 8-10 membered bicyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments R 1 is an optionally substituted 5,6-iused heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In other embodiments, R 1 is an optionally substituted 5,6-fused heteroaryl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur hi certain embodiments, R 1 is an optionally substituted 5,6-fused heteroaryl ring having 1 heteroatom independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R ! is an optionally substituted indolyl. In some embodiments, R 1 is an optionally substituted azabicycio[3.2.1]octanyl. In certain embodiments, R 1 is an optionally substituted 5,6-fused heteroaryl ring having 2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R 1 is an optionally substituted azaindolyl. In some embodiments, R 1 is an optionally substituted benzimidazolyi. In some embodiments, R 5 is an optionally substituted benzothiazolyl . In some embodiments, R 1 is an optionally substituted benzoxazolyl. In some embodiments, R 1 is an optionally substituted indazolyi. In certain embodiments, R 1 is an optionally substituted 5,6-fused heteroaryl ring having 3 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[00434] In certain embodiments, R 5 is an optionally substituted 6,6-fused heteroaryl ring having

1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R 1 is an optionally substituted 6,6-fused heteroaryl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In other embodiments, R 1 is an optionally substituted 6,6-fused heteroaryl ring having 1 heteroatom independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R is an optionally substituted quino!inyl. In some embodiments, R 1 is an optionally substituted isoquinolinyl. According to one aspect, R 1 is an optionally substituted 6,6-fused heteroaryl ring having 2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R 1 is a quinazoline or a quinoxaline.

[00435] In some embodiments, R 1 is an optionally substituted heterocyclyl. In some embodiments, R 1 is an optionally substituted 3-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R ! is a substituted 3-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R 5 is an unsubstituted 3-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[00436] In some embodiments, R ! is an optionally substituted heterocyclyl. In some embodiments, R 1 is an optionally substituted 6 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R 1 is an optionally substituted 6 membered partially unsaturated heterocyclic ring having 2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R 1 is an optionally substituted 6 membered partially unsaturated heterocyclic ring having 2 oxygen atoms.

100437 In certain embodiments, R 1 is a 3-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In certain embodiments, R 1 is oxiranyl, oxetanyl, tetrahydrofuranyl, tetrahydropyranyl, oxepaneyl, aziridineyl, azetidineyl, pyrrolidinyl, piperidinyl, azepanyl, thiiranyl, thietanyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, thiepanyl, dioxolanyl, oxathiolanyl, oxazolidinyl, imidazolidinyl, thiazolidinyl, dithiolanyl, dioxanyl, morpholinyl, oxathianyl, piperazinyl, thiomorpholinyl, dithianyl, dioxepanyl, oxazepanyl, oxathiepanyl, dithiepanyl, diazepanyl, dihydrofuranonyl, tetrahydropyranonyl, oxepanonyl, pyrolidinonyl, piperidinonyl, azepanonyl, dihydrothiophenonyl, tetrahydrothiopyranonyi, thiepanonyl, oxazolidinonyi, oxazinanonyl, oxazepanonyl, dioxolanonyl, dioxanonyl, dioxepanony!, oxathiolinonyl, oxathianonyd, oxathiepanonyl, thiazolidinonyl, tliiazinanonyl, thiazepanonyl, imidazolidinonyl, tetrahydropyrimidinonyl, diazepanonyl, imidazolidmedionyl, oxazolidinedionyl, thiazohdinedionyl, dioxolanedionyl, oxathioianedionyl, piperazinedionyl, morpholinedionyl, thiomorpholinedionyl, tetrahydropyranyl, tetrahydrofuranyl, morpholinyl, thiomorpholinyl, piperidinyl, piperazinyl, pyrrolidinyl, tetrahydrothiophenyl, or tetrahydrothiopyranyl. In some embodiments, R 1 is an optionally substituted 5 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[00438] In certain embodiments, R 1 is an optionally substituted 5-6 membered partially unsaturated monocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In certain embodiments, R 1 is an optionally substituted tetrahydropyridinyl, dihydrothiazolyl, dihydrooxazolyl, or oxazolinyl group.

[00439] In some embodiments, R 1 is an optionally substituted 8-10 membered bicyclic saturated or partially unsaturated heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R 1 is an optionally substituted indolinyl. In some embodiments, R 1 is an optionally substituted isoindoiinyl. In some embodiments, I is an optionally substituted 1 , 2, 3, 4-tetrahydroquinoline. In some embodiments, R is an optionally substituted 1, 2, 3, 4- tetrahydroisoquinoline .

[00440] In some embodiments, R 1 is an optionally substituted C -Cio aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally substituted Ci-C 6 alkylene, C 5- C 5 alkenyiene,— c º c — , -C(R')2-, -Cy-, -0-, -S-, -S-S-, -N(R f )-, -C(O)-, -C(S)-, - C(NR')-, -C(0)N(R')-, -N(R')C(0)N(R')-, \(R')C(0) . -N(R')C(0)0-, -OC(0)N(R')-, S(O) . - S(0) 2- , -S(0) 2 N(R')-, -N(R')S(0) 2- , -SC(0)-, -C(0)S-, -0C(0)-, or -C(0)0-, wherein each variable is independently as defined above and described herein. In some embodiments, R 1 is an optionally substituted Cp-Cio aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally-Cy-, -0-, -S-, -S-S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, -C(0)N(R')-, - N (R ') C(0)N (R ') -, -N(R')C(0)-, -N(R')C(0)0-, -0C(0)N(R')-, -S(O)-, -S(0) 2 -, -S(0) 2 N(R')-, -

N(R')S(0) 2 -,— 0C(0)— , or— C(0)0— , wherein each R’ is independently as defined above and described herein. In some embodiments, R 1 is an optionally substituted C.-C-,o aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally-Cy-, -0-, -S-, -S-S-, - N(R')--, -C(O)---, -OC(O)-, or -C(0)0-, wherein each R" is independently as defined above and described herein.

[00443] In some embodiments, R ! comprises a terminal optionally substituted -(CH 2 ) 2 - moiety which is connected to L. Examples of such R ! groups are depicted below:

[00444] In some embodiments, I comprises a terminal optionally substituted -(CH 2 )- moiety which is connected to L Example such R 1 groups are depicted below:

[00445] In some embodiments, R 1 is S R ! .. wherein R 1 2 is an optionally substituted C ]- C 9 aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally substituted C r- C 6 alkylene, C r- C 6 alkenylene,— cºc — , -C(R/) 2- , -Cy-, -()-, -S-, -S-S-, -N(R')-, - C(O)-, -C(S)-, -C(NR')-, -C(0)N(R')-, -N(R')C(0)N(R')~, -N(R')C(0)-, -N(R')C(0)0-, - OC(0)N(R')-, -S(O)-, -S(0) 2- , -S(0) 2 N(R')-, -N(R')S(0) 2- -SC(Q)-, -C(0)S-, -OC(O)-, or - C(0)0-, and each of R’ and -Cy- is independently as defined above and described herein. In some embodiments, R 1 is -S-R L \ wherein the sulfur atom is connected with the sulfur atom in L group.

[00446] In some embodiments, R 1 is -C(0)-R L2 , wherein R 1 2 is an optionally substituted C r- C 9 aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally substituted C -C 6 alkylene, C -C 6 alkenylene,— cºc — , -C(R’)z-, -Cy-, -0-, -S-, -S-S-, -N(R')-, - C(O)-, -C(S)-, -C(NR')-, -C(0)N(R')-, -N(R')C(0)N(R')-, -N(R')C(0)-, -N(R')C(0)0-, - OC(0)N(R')-, 5(0) . 5(0 ) 2 . -S(0) 2 N(R')- -N(R')S(0) 2- -SC(G)-, -C(0)S , ()( ((>) . or -

C(0)0-, and each of R’ and -Cy- is independently as defined above and described herein. In some embodiments, R 1 is -C(0)-R L C wherein the carbonyl group is connected with G in L group. In some embodiments, R 1 is -C(0)-R L , wherein the carbonyl group is connected with the sulfur atom in L group.

[00447] In some embodiments, R 12 is optionally substituted C r-- C 9 aliphatic. hi some embodiments, R L is optionally substituted C ]- C 9 alkyl. In some embodiments, R L2 is optionally substituted C j- C 9 alkenyl. In some embodiments, R L is optionally substituted C 5- C 9 alkynyl. In some embodiments, R L2 is an optionally substituted Ci-C 9 aliphatic wherein one or more methylene units are optionally and independently replaced by -Cy- or -C(Q)-. In some embodiments, R L2 is an optionally substituted C r- C 9 aliphatic wdierein one or more methylene units are optionally and independently replaced by -Cy- In some embodiments, R L2 is an optionally substituted C 5- C 9 aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally substituted heterocycylene . In some embodiments, R L2 is an optionally substituted C -C 9 aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally substituted aryleme. In some embodiments, R L2 is an optionally substituted C 5- C 9 aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally substituted heteroaryl ene. In some embodiments, R L2 is an optionally substituted C r- C 9 aliphatic wlierein one or more methylene units are optionally and independently replaced by an optionally substituted C 3 -C 10 carbocyclylene. In some embodiments, R L2 is an optionally substituted CV-C 9 aliphatic wherein two methylene units are optionally and independently replaced by -Cy- or -C(O)-. In some embodiments, R 1 2 is an optionally substituted C 1 -C 9 aliphatic wherein two methylene units are optionally and independently replaced by -Cy- or -

C(Q)-. Example L2 groups are depicted below:

In some embodiments, R 1 is hydrogen, or an optionally substituted group selected from

O -S-(Ci-Cio aliphatic), Ci-Cio aliphatic, axyl, Ci-C 6 heteroalkyl, heteroaryl and heterocyclyl. In some embodiments, R 1 is aliphatic).

In some embodiments, R 1 is an optionally substituted group selected from -S-(Ci-C 6 aliphatic), Ci-Cm aliphatic, Ci-C 6 heteroaliphatic, aryl, heterocyclyl and heteroaryl.

[00451] In some embodiments, the sulfur atom in the R 1 embodiments described above and herein is connected with the sulfur atom, G, E, or -C(O)- moiety in the L embodiments described above and herein. In some embodiments, the -C(O)- moiety in the R embodiments described above and herein is connected with the sulfur atom, G, E, or -C(O)- moiety in the L embodiments described above and herein.

[00452] In some embodiments, -L-R 1 is any combination of the L embodiments and R 1 embodiments described above and herein.

[00453] in some embodiments, -L-R is -L/’-G-R 1 wherein each variable is independently as defined above and described herein

100454 In some embodiments, -L-R 1 is -L^-G-R 1 wherein each variable is independently as defined above and described herein.

[00455] In some embodiments, -L-R 1 is -L’-G-S-R l L wherein each variable is independently as defined above and described herein.

[00456] In some embodiments, -L-R 1 is -L -G-C(0)-R L2 , wherein each variable is independently as defined above and described herein. me embodiment

, wherein R is an optionally substituted Ci-C 9 aliphatic wherein one or more methylene units are optionally and independently replaced by an optionally substituted C r- C 6 alkylene,

(\ C, alkenylene, CºC— ^ ( ( R ·) . _ ( y . -O-, S . -S-S-, M R’} . -C(O)-, -C(S)-, ( (NR ) . - C(0)N(R')-, -N(R')C(0)N(R')-, -N(R’)C(0)-, N(R ) ( (( ) }( ) . -OC(0)N(R')-, -S(O)-, -S(0) 2- , -

S(0) 2 N(R')-, -N(R')S(0)r-, -SC(O)-,— C(0)S— , -OC(O)-, or -C(0)0-, and each G is independently as defined above and described herein. [00458] In some embodiments, -L-R 1 is -R^-S-S-R 1'7 , wherein each variable is independently as defined above and described herein. In some embodiments, -L-R 1 is wherein each variable is independently as defined above and described herein.

[00459] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00460] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00461] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00462] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00463] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00464] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00465] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00466] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00467] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00468] In some embodiments, -L-R 1 has the structure of:

wherem each variable is independently as defined above and described herein.

[00469] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00470] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00471] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00472] hr some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00473] In some embodiments, -L-R 5 has the structure of:

wherein each variable is independently as defined above and described herein.

[00474] In some embodiments, -L-R 1 has the structure of:

where sach variable is independently as defined above and described herein.

[00475] In some embodiments, -L-R 5 has the structure of:

wherein each variable is independently as defined above and described herein.

[00476] In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

In some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

[00478] hi some embodiments, -L-R 1 has the structure of:

wherein each variable is independently as defined above and described herein.

In some embodiments, -L-R 5 has the structure of:

wherein each variable is independently as defined above and described herein.

In some embodiments, L has the structure of:

wherein each variable is independently as defined above and described herein.

In some embodiments, -X-L-R 1 has the structure of:

wherein:

the phenyl ring is optionally substituted, and

each of R 1 and X is independently as defined above and described herein.

embodiments, -L-R 1 is

100485 In some embodiments, -L-R 1 comprises a terminal optionally substituted -(CH 2 ) 2- moiety which is connected to X. In some embodiments, -L-R 1 comprises a terminal -(CH ? ) ? .- moiety which is connected to X. Examples of such -L-R 1 moieties are depicted below:

[00486] In some embodiments, -L-R 1 comprises a terminal optionally substituted -(CH 2 )- moiety which is connected to X. In some embodiments, -L-R 1 comprises a terminal -(CH 2 )~ moiety which is connected to X. Examples of such -L-R 1 moieties are depicted below :

and X is -S-.

Y is— O— , and Z is -0-.

Cio aliphatic).

In some embodiments, X is -Q- or -S-, and R 1 is

S (C Cio aliphatic).

In some embodiments, X is -O- or -S-, and R ! is i io p - i- 50 aliphatic) .

— S— {Ci— C o aliphatic) or -S-(Ci_C 50 aliphatic).

In some embodiments, -X-L-R 1 has the stmcture wherein die

, , s

X

>

. In some embodiments -X-L-R has the structure of wherein X is O or S, Y’ is -0-, -S- or -NR -, and the moiety is optionally substituted. In

X

some embodiments, X’ is -0-, -S- or -NH-. In some embodiments. is

X . , . In some

X s

embodiments, is In some embodiments, -X-L-R has the

X

structure of R wherein X is O or S, and the moiety is optionally

substituted. In some embodiments, R is R In some

R 1 -Y embodiments, -X-L-R s wherein the is optionally substituted. In

1-Y some embodiments, -X-L-R 1 is wherein the is substituted. In

t 1 -Y some embodiments, -X-L-R 1 is wherein the is uiisubstituted. wherein L * is an optionally substituted group selected from . j: : some embodiments, L x i „s ^¾ Y f Y r ' . , , . In some embodiments, -X-L-R 1 is (CH 3 )3C-S-S-L X -S-. In some embodiments, -X-L-R 1 is R 1 -C(=X’)-Y - C(R)2-S-L X -S . hi some embodiments, -X-L-R 1 is R-C(-X’)-Y’-CHr-S-L^S- . In some

embodiments.

[00499] As will be appreciated by a person skilled in the art, many of the -X-L-R 1 groups described herein are cleavable and can be converted to -X ~ after administration to a subject. In some embodiments, -X-L-R 1 is cleavable. In some embodiments, -X-L-R is -S-L-R 1 , and is converted to - S after administration to a subject. In some embodiments, the conversion is promoted by an enzyme of a subject. As appreciated by a person skilled in the art, methods of determining whether the -S-L-R 1 group is converted to -S after administration is widely known and practiced in the art, including those used for studying drug metabolism and pharmacokinetics.

[00500] hi some embodiments, the intemucleotidic linkage having the structure of formula I is

In some embodiments, the intemueleotidic linkage of formula I has the structure of formula 1-a:

(I-a)

wherein each variable is independently as defined above and described herein.

[00502] hi some embodiments, the intemueleotidic linkage of formula 1 has the structure of formula I-b:

(I-b)

where each variable is independently as defined above and described herein.

[00503] In some embodiments, the intemueleotidic linkage of formula I is an phosphorothioate triester linkage having the structure of formula I-c:

(I-c)

wherein R 1 is not -H when L is a covalent bond.

100504 In some embodiments, the intemueleotidic linkage having the structure of formula I is

c is

In some embodiments, the present disclosure provides a chirally controlled oligonucleotide comprising one or more natural phosphate linkages, and one or more modified intemucieotidie linkages having the formula of I-a, I-b, or I-c.

[00507] In some embodiments, a modified intemucieotidie linkage has the structure of I. In some embodiments, a modified intemucieotidie linkage has the structure of I-a. In some embodiments, a modified intemucieotidie linkage has the structure of I-b. In some embodiments, a modified intemucieotidie linkage has the structure of I-c.

[00508] In some embodiments, a modified intemucieotidie linkage is phosphorothioate intemucieotidie linkage. Examples of intemucieotidie linkages having the stmeture of formula I that can be utilized in accordance with the present disclosure include those described in US 9394333, US 9744183, US 9605019, US 20130178612, US 20150211006, US 9598458, US 20170037399, WO 2017/015555, WO 2017/062862, the intemucieotidie linkages of each of which is incorporated herein by reference. Non-limiting examples of internucleotidic linkages that can be utilized in accordance with the present disclosure also include those described in the art, including, but not limited to, those described in any of: Gryaznov, S ; Chen, J.-K. J Am. Chem. Soc. 1994, 116, 3143, Jones et al. J. Org. Chern. 1993, 58, 2983, Koshkin et al. 1998 Tetrahedron 54: 3607-3630, Lauritsen et al. 2002 Chem. Comm. 5: 530-531, Lauritsen et al. 2003 Bioo. Med. Chem. Lett. 13: 253-256, Mesmaeker et al. Angew. Chem., hit. Ed. Engl. 1994, 33, 226, Petersen et al. 2003 TRENDS Biotech. 21: 74-81, Schultz et al. 1996 Nucleic Acids Res 24: 2966, Ts'o et al Ann. N. Y. Acad. Sci. 1988, 507, 220, and Vasseur et al. J. Am. Chem. Soc 1992, 114, 4006

jOO510j In some embodiments, oligonucleotides comprise one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8,

9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more non-negatively charged internucleotidic linkages hi some embodiments, a non-negatively charged internucleotidic linkage is not negatively charged in that at a given pH in an aqueous solution less than 50%, 40%, 40%, 30%, 20%, 10%, 5%, or 1 % of the internucleotidic linkage exists in a negatively charged salt form. In some embodiments, a pH is about pH 7.4. In some embodiments, a pH is about 4-9. In some embodiments, the percentage is less than 10%. In some embodiments, the percentage is less than 5% in some embodiments, the percentage is less than 1%. In some embodiments, an internucleotidic linkage is a non-negatively charged internucleotidic linkage in that the neutral form of the internucleotidic linkage has no pKa that is no more than about 1, 2, 3, 4, 5, 6, or 7 in water hr some embodiments, no pKa is 7 or less. In some embodiments, no pKa is 6 or less. In some embodiments, no pKa is 5 or less. In some embodiments, no pKa is 4 or less. In some embodiments, no pKa is 3 or less. In some embodiments, no pKa is 2 or less. In some embodiments, no pKa is 1 or less. In some embodiments, pKa of the neutral form of an internucleotidic linkage can be represented by pKa of the neutral form of a compound having the structure of CH 3- the internucleotidic linkage-CH 3 . For example, pKa of the neutral form of an internucleotidic linkage having the structure of formula I may be represented by the pKa of the neutral form of a compound having the structure of

some embodiments, a non-negatively charged internucleotidic linkage is a neutral internucleotidic linkage. In some embodiments, a non-negatively charged internucleotidic linkage is a positively-charged internucleotidic linkage. In some embodiments, a non-negatively charged internucleotidic linkage comprises a guanidine moiety. In some embodiments, a non-negatively charged internucleotidic linkage comprises a heteroaryl base moiety. In some embodiments, a non-negatively charged internucleotidic linkage comprises a triazole moiety. In some embodiments, a non-negatively charged internucleotidic linkage comprises an alkynyl moiety.

[00511] In some embodiments, a non-negatively charged mtemucleotidic linkage, e.g., a neutral mtemucleotidic linkage, comprises -P‘ ' (-N=)-, wherein P 1 is as described in the present disclosure. In some embodiments, a non-negatively charged mtemucleotidic linkage, e.g., a neutral mtemucleotidic linkage, comprises -P(-N=)-. hi some embodiments, a non-negatively charged mtemucleotidic linkage, e.g., a neutral mtemucleotidic linkage, comprises -P(=)(-N=)-. In some embodiments, a non-negatively charged mtemucleotidic linkage, e.g., a neutral mtemucleotidic linkage, comprises -P(=0)(-N=)-. In some embodiments, a non-negatively charged intemucleotidic linkage, e.g., a neutral mtemucleotidic linkage, comprises -P(=S)(-N=)-.

In some embodiments, a non-negatively charged mtemucleotidic linkage, e.g., a neutral

mtemucleotidic linkage, comprises wherein P L is as described in the present disclosure. For example, in some embodiments, P L is P; in some embodiments, P L is P(O); in some embodiments, P L is P(S); etc. In some embodiments, a non-negatively charged mtemucleotidic linkage, e.g., a neutral

intemucleotidic linkage comprises

100513] In some embodiments, a non-negatively charged intemucleotidic linkage has the structure of formula 1, 1-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, Il-d-

1, II-d-2, or a salt form thereof (not negatively charged). In some embodiments, an mtemucleotidic linkage, e.g., a non-negatively charged mtemucleotidic linkage, has the structure of formula I-n-1 or a salt form thereof:

I-n-1 [00514] In some embodiments, X is a covalent bond and -X-Cy-R 1 is -Cy-R 1 . In some embodiments, -Cy- is an optionally substituted bivalent group selected from a 5-20 me inhered heteroaryl ring having 1-10 heteroatoms, and a 3-20 membered heterocyclyl ring having 1-10 heteroatoms. In some embodiments, -Cy- is an optionally substituted bivalent 5-20 membered heteroaryl ring having 1-10 heteroatoms. In some embodiments, -Cy— R 1 is optionally substituted 5-20 membered heteroaryl ring having 1-10 heteroatoms, wherein at least one heteroatom is nitrogen. In some embodiments, -Cy-R 1 is optionally substituted 5 -membered heteroaryl ring having 1-4 heteroatoms, wherein at least one heteroatom is nitrogen. In some embodiments, -Cy-R is optionally substituted 6-membered heteroaryl ring having 1-4 heteroatoms, wherein at least one heteroatom is nitrogen. In some embodiments, -Cy-R is optionally substituted triazolyl.

[00515] In some embodiments, an intemucleotidic linkage, e.g., a non-negatively charged intemucleotidic linkage, has the structure of formula I-n-2 or a salt form thereof:

[00516] In some embodiments, R 1 is R’. In some embodiments, L is a covalent bond. In some embodiments, an intemucleotidic linkage, e.g., a non-negatively charged intemucleotidic linkage, has the structure of formula I-n-3 or a salt form thereof:

I-n-3

[00517] In some embodiments, two R’ on different nitrogen atoms are taken together to form a ring as described. In some embodiments, a formed ring is 5-membered. In some embodiments, a formed ring is 6-membered. In some embodiments, a formed ring is substituted. In some embodiments, the two R’ group that are not taken together to form a ring are each independently R. In some embodiments, the two R’ group that are not taken together to form a ring are each independently hydrogen or an optionally substituted C _ 6 aliphatic. In some embodiments, the two R’ group that are not taken together to form a ring are each independently hydrogen or an optionally substituted Ci 6 alkyl. In some embodiments, the two R’ group that are not taken together to form a ring are the same. In some embodiments, the two R’ group that are not taken together to form a ring are different. In some embodiments, both of them are [00518] In some embodiments, an intemucleotidic linkage, e.g., a non-negatively charged intemucleotidic linkage, has the structure of formula I-n-4 or a salt form thereof:

I-n-4

wherein each of L a and L b is independently L or --X(R 1 )--, and each other variable is independently as described in the present disclosure. In some embodiments, L is a covalent bond, and an intemucleotidic linkage of formula I-n-4 has the structure of:

or a salt form thereof, wherein each variable is independently as described in the present disclosure.

[00519] In some embodiments, L a is -NCR 1 )- In some embodiments, L a is L as described in the present disclosure. In some embodiments, L a is a covalent bond. In some embodiments, L a is -N(R’)-. In some embodiments, L a is -N(R)-. In some embodiments, In some embodiments, L a is

— S ~ . In some embodiments, L a is -S(O)-. In some embodiments, L a is -S(0) 2 -. In some embodiments, L a is ---S(0) 2 N(R )---. hi some embodiments, L b is -NCR 1 )-. In some embodiments, L b is L as described in the present disclosure. In some embodiments, L b is a covalent bond. In some embodiments, L b is -N(R’)-. In some embodiments, L b is -N(R)-. In some embodiments, L° is -0-. In some embodiments, L b is S . In some embodiments, L b is -S(O)-. In some embodiments, L b is -S(0) 2 -. In some embodiments, L b is -S(0) 2 N(R’)-. hi some embodiments, L a and L° are the same. In some embodiments, L a and L b are different. In some embodiments, at least one of L a and L b is -N(R‘)-. In some embodiments, at least one of L a and L b is -0-. In some embodiments, at least one of L a and L b is ~ S ~ . In some embodiments, at least one of L a and L b is a covalent bond. In some embodiments, as described herein, R l is R. In some embodiments, I is -H. hr some embodiments, R l is optionally substituted C._. 0 aliphatic. In some embodiments, R ! is optionally substituted C l-l0 alkyl. In some embodiments, a structure of fonnula I-n-4 is a structure of formula I~n~2. In some embodiments, a structure of formula I-n-4 is a structure of formula I-n-3. In some embodiments, a non-negatively charged intemucleotidic linkage, e.g., a neutral intemucleotidic linkage, has the structure of formula I. In some embodiments, X, e.g., in formula I, II, etc., is -N(-L-R ' ’)-, wherein R 5 is R as described herein. In some embodiments, X is -NH-. In some embodiments, L, e.g., in X L of formula I, II, etc., comprises -S0 2 -. hi some embodiments, L is -S0 2 -. In some embodiments, L is a covalent bond. In some embodiments, L is -C(0)0-(Ci -4 alkylene)- wherein the aikylene is optionally substituted. In some embodiments, L is -C(0)OCH 2- . In some embodiments, R 1 , eg., in formula I, III, etc , comprise an optionally substituted ring. In some embodiments, R 1 is R as described herein. In some embodiments, R 1 is optionally substituted phenyl. In some embodiments, R 1 is 4-methylphenyl. In some embodiments, R 1 is 4-methoxyphenyl. In some embodiments, R 1 is 4-aminophenyl In some embodiments, R 1 is an optionally substituted heteroaliphatic ring. In some embodiments, R 1 is an optionally substituted 3-10 (e ., 3, 4, 5, 6, 7, or 8) membered heteroaliphatic ring. In some embodiments, R 1 is an optionally- substituted 5- or 6-membered saturated monocyclic heteroaliphatic ring having 1-3 heteroatoms. In some embodiments, the ring is -membered. In some embodiments, the ring is 6-membered. In some embodiments, the number of ring heteroatom(s) is 1. In some embodiments, the number of ring heteroatoms is 2. In some embodiments, a heteroatom is oxygen. In some embodiments, R is optionally substituted In some embodiments, is optionally substituted In some

embodiments, In some embodiments, R ! is optionally substituted Ci_ 3 o aliphatic.

In some embodiments, R is optionally substituted C M0 alkyl.

[00520] In some embodiments, an internucleotidic linkage, e.g., a non-negatively charged mtemucleotidic linkage, has the structure of formula II or a salt form thereof:

or a salt form thereof, wherein:

P L is P(=W), P, or P B(R )

W is O, \( i. R ). S or Se;

each of X, Y and Z is independently -0-, -S-, -N(-L-R 5 )-, or L;

R is H, -L-R’, halogen, -CN, -N0 2 , -L-Si(R’) 3 , -OR’, -SR’, or -N(R’) 2 ;

Ring A L is an optionally substituted 3-20 membered monocyclic, hicyclic or polycyclic ring having 0-10 heteroatoms;

each R s is independently -H, halogen, -CN, -N 3 , -NO, ~ ¾ -L-R’, -L-Si(R) 3 , k OR . i. SR . L N( R ) , O 1. R\ O 1. Si(R ) : . -O-L-OR’, 0 S . SR . or -0-L-N(R’) 2 ; g is 0-20;

each L is independently a covalent bond, or a bivalent, optionally substituted, linear or branched group selected from a Ci 30 aliphatic group and a Ci_ 3 o heteroaliphatic group having 1-10 heteroatoms, wherein one or more methylene units are optionally and independently replaced with C ]-6 alkylene, Ci -6 alkenylene, cºc , a bivalent Cr-C 6 heteroaliphatic group having 1-5 heteroatoms, -C(R’) 2 -, -Cy-, -O- S . S S . -N(R’)-, ( (()) . -C(S)- -C(NR’)-, -C(0)N(R’)-, N< R )t (0)X( R ) .

-N(R’)C(0)0-, S(O)--, -S(0) 2 -, S(O) N( R ) . -C(0)S-, -C(0)0-, -P(0)(OR’)- -P(0)(SR’)- -P(0)(R’)-, -P(0)(NR’)-, -P(S)(OR’)-, -P(S)(SR’)-, -P(S)(R’)-, -P(S)(NR’)-, -P(R’)-, -P(OR’)- -P(SR’)-, Pi NR ) . Pi OR ll Bi R ) : ] . -0P(0)(0R’)0- -0P(0)(SR’)0-, -0P(0)(R’)0-,

-0P(0)(NR’)0-, -OP(OR’)0- ( )P(SR )Q . -OP(NR’)0- -OP(R’)0-, or -OP(OR’)[B(R’) 3 ]0- and one or more CH or carbon atoms are optionally and independently replaced with Cy";

each -Cy- is independently an optionally substituted bivalent group selected from a C 3.20 cycloaliphatic ring, a C 6 20 and ring, a 5-20 membered heteroaryl ring having 1 -10 heteroatoms, and a 3- 20 membered heterocyciyi ring having 1-10 heteroatoms;

each Cy L is independently an optionally substituted trivalent or tetravalent group selected from a C 3-20 cycloaliphatic ring, a C 6-2 o aryl ring, a 5-20 membered heteroaryl ring having 1-10 heteroatoms, and a 3-20 membered heterocyciyi ring having 1-10 heteroatoms;

each R is independently -R, -C(Q)R, -C(Q)QR, or -S(Q) 2 R;

each R is independently -H, or an optionally substituted group selected from C-,_ 0 aliphatic, Ci -30 heteroaliphatic having 1-10 heteroatoms, C 6.30 aryl, C 6-3 o arylaliphatic, C 6 3 o arylheteroaliphatic having 1 - 10 heteroatoms, 5-30 membered heteroaryl having 1-10 heteroatoms, and 3-30 membered heterocyciyi having 1-10 heteroatoms, or

two R groups are optionally and independently taken together to form a covalent bond, or, two or more R groups on the same atom are optionally and independently taken together with the atom to form an optionally substituted, 3-30 membered, monocyclic, bi cyclic or polycyclic ring having, in addition to the atom, 0-10 heteroatoms, or

two or more R groups on two or more atoms are optionally and independently taken together with their intervening atoms to form an optionally substituted, 3-30 membered, monocyclic, bi cyclic or polycyclic ring having, in addition to the intervening atoms, 0-10 heteroatoms.

100521 In some embodiments, Ring A" in various structures of the present disclosure is tin optionally substituted aryl ring. In some embodiments, Ring A L is an optionally substituted phenyl ring. In some embodiments, Ring A 1 is an optionally substituted 3-10 (e.g., 3, 4, 5, 6, 7, or 8) membered heteroaliphatic ring. In some embodiments, Ring A L is an optionally substituted 5- or 6-membered saturated monocyclic heteroaliphatic ring having 1-3 heteroatoms. In some embodiments, the ring is 5- membered. In some embodiments, the ring is 6-membered In some embodiments, the number of ring heteroatom(s) is 1 . In some embodiments, the number of ring heteroatoms is 2. In some embodiments, a heteroatom is oxygen. In some embodiments, R s is optionally substituted Ci-C 6 alkyl group. In some embodiments, R * is Me. In some embodiments, R s is OR, wherein R is hydrogen or C -C 6 alkyl group. In some embodiments, R ¾ is OH. hr some embodiments, R ¾ is QMe. In some embodiments, R s is -N(R’) 2 .

In some embodiments, II s is --NH 2 . In some embodiments.

In some embodiments, In some embodiments. , IS

. In some embodiments, an internucleotidic linkage, e.g. a neutral intemucleotidic linkage of

formula which, as one skilled in the art will appreciate, can

exist under certain conditions in the fonn In some embodiments, an intemucleotidic linkage, e.g. a neutral internucleotidic linkage of formula I or II, is n005 (

which, as one skilled in the art will appreciate, can exist under certain conditions in the form In some embodiments, an internucleotidic

linkage, e.g. a neutral internucleotidic linkage of formula

which, as one skilled in the art will appreciate, can exist under certain conditions in the form of

In some embodiments, an internucleotidic linkage, e.g a neutral

internucleotidic linkage of formula which, as one skilled in the art will

appreciate, can exist under certain conditions in a form

[00522] In some embodiments, an internucleotidic linkage, e.g., a non-negatively charged internucleotidic linkage of formula II, has the structure of formula II-a-1 or a salt fonn thereof:

II-a-1

or a salt form thereof.

[00523] In some embodiments, an internucleotidic linkage, e.g., a non-negatively charged internucleotidic linkage of formula II, has the structure of formula II-a-2 or a salt form thereof:

II- a- 2

or a salt form thereof.

[00524] In some embodiments, A L is bonded to -N= or L through a carbon atom. In some embodiments, an intemucleotidic linkage, e.g., a non-negatively charged intemucleotidic linkage of formula II or H-a-l, II-a-2, has the structure of formula II-h-1 or a salt fonn thereof:

II-h-1

[00525] In some embodiments, a structure of formula II- a- 1 or II-a-2 may be referred to a structure of formula Il-a. In some embodiments, a structure of formula II-b-1 or II-b-2 may be referred to a structure of formula H-b. In some embodiments, a structure of formula II-c-1 or II-c-2 may be referred to a structure of formula II-c. In some embodiments, a structure of formula II-d-1 or II-d-2 may be referred to a structure of formula Il-d.

[00526] In some embodiments, A L is bonded to -N= or L through a carbon atom. In some embodiments, an intemucleotidic linkage, e.g., a non-negatively charged intemucleotidic linkage of formula II or II-a-1. II-a-2, has the structure of formula II-b-2 or a salt form thereof:

T !

N R

si

(R " )u

II-b-2

[00527] In some embodiments, Ring A L is an optionally substituted 3-20 membered monocyclic ring having 0-10 heteroatoms (in addition to the two nitrogen atoms for formula II-b). In some embodiments, Ring A L is an optionally substituted 5- membered monocyclic saturated ring.

[00528] In some embodiments, an intemucleotidic linkage, e.g., a non-negatively charged intemucleotidic linkage of formula II, IT-a, or II-b, has the structure of formula II-c-1 or a salt form thereof:

[00529] In some embodiments, an intemue!eotidie linkage, e.g., a non-negatively charged intemucleotidic linkage of formula II, Il-a, or II-b, has the structure of formula II-c-2 or a salt form thereof:

[00530] In some embodiments, an intemucleotidic linkage, e.g., a non-negatively charged intemucleotidic linkage of formula II, H-a, ίΐ-b, or II-c has the structure of formula II-d-1 or a salt form thereof:

II-d-1

[00531] In some embodiments, an intemucleotidic linkage, e.g., a non-negatively charged intemucleotidic linkage of formula II, Il-a, Il-b, or II-c has the structure of formula II-d-2 or a salt form thereof:

[00532] hi some embodiments, each R’ is independently optionally substituted C (-6 aliphatic. In some embodiments, each R’ is independently optionally substituted C ]-6 alkyl. In some embodiments, each R’ is independently -CH 3 . in some embodiments, each R s is -H.

00533] In some embodiments, a non-negatively charged internucleotidic linkage has the structure

,

has the structure . In some embodiments, a non-negatively charged internucleotidic

linkage has the structure some embodiments, a non-negatively charged

intemucleotidic linkage has the structure In some embodiments, a non-

negatively charged internucleotidic linkage has the structure In some

embodiments, a non-negatively charged internucleotidic linkage has the structure

In some embodiments, a non-negatively charged internucleotidic linkage has the structure of . In some embodiments a non-negativelv charged internucleotidic linkage has the structure some embodiments, a non-negatively charged intemucleotidic linkage

has the structure In some embodiments, a non-negatively charged intemucleotidic

linkage has the structure In some embodiments, a non-negatively charged

intemucleotidic linkage has the structure In some embodiments, a non-

negatively charged intemucleotidic linkage has the structure In some embodiments, a non-negatively charged intemucleotidic linkage has the structure of In some embodiments, a non-negatively charged intemucleotidic linkage

has the structure of In some embodiments, a non-negatively charged

intemucleotidic linkage has the structure of In some embodiments a non-

negatively charged intemucleotidic linkage has the structure some embodiments. a non-negatively charged intemucleotidic linkage has the structure In some embodiments, a non-negatively charged intemucleotidic linkage has the structure embodiments, a non-negatively charged intemucleotidic linkage has the structure

in some embodiments, a non-negatively charged intemucleotidic linkage has the structure of ,

has the structure In some embodiments, a non-negatively charged intemucleotidic linkage has the structure In some embodiments, a non-negatively charged intemucleotidic linkage has the structure in some embodiments, a non-negatively charged intemucleotidic linkage has the structure In some embodiments, a non- negatively charged intemudeotidic linkage has the structure . In some embodiments, a non-negatively charged intemudeotidic linkage has the structure of

,

the structure some embodiments, a non-negatively charged intemudeotidic linkage

has the structure In some embodiments, W is O. In some embodiments, W is S. In some embodiments, a non-negatively charged intemudeotidic linkage is chirally controlled. In some embodiments, the linkage phosphorus is Rp. In some embodiments, tire linkage phosphorus is .Sp.

[00534] In some embodiments, each non-negatively charged intemudeotidic linkage or neutral intemudeotidic linkage (e.g., those of formula I~n~l, I-n-2, 1-n-3, 1-n-4, II, II-a-1 , II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, or II-d-2) is independently Rp at its linkage phosphorus. In some embodiments, each negatively charged chiral intemudeotidic linkage is .Sp at its linkage phosphorus. In some embodiments, each phosphorothioate intemudeotidic linkages is Sp at its linkage phosphorus. In some embodiments, each natural phosphate linkage is independently bonded to a sugar comprising a 2’ -OR modification, wherein R is not -H. In some embodiments, each natural phosphate linkage is independently bonded to a sugar comprising a 2’-OR modification, wherein R is not -H, at a 3’-position hi some embodiments, each sugar that contains no 2’-OR modification wherein R is not -H is independently bonded to at least one non-natural phosphate linkages, in many cases, two non-natural natural phosphate linkages. In some embodiments, each 2’-F modified sugar is independently bonded to at least one non-natural phosphate linkages, in many cases, two non-natural natural phosphate linkages. In some embodiments, each non-natural phosphate linkage is a phosphorothioate intemudeotidic linkage. In some embodiments, each non-natural phosphate linkage is a .S'p phosphorothioate intemudeotidic linkage. In some embodiments, each sugar bonded to non-negative ly charged intemucleotidic linkage or neutral intemucleotidic linkage (e g . those of fomiula I-n-1, 1-n-2, 1-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1 , II-c-2, II-d-1, or II-d-2) independently contains no 2 -OR. In some embodiments, each sugar bonded to non-negatively charged intemucleotidic linkage or neutral intemucleotidic linkage (e.g., those of fomiula I-n-1, 1-n-2, 1-n-3, 1-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, or Il-d- 2) is a 2’-F modified sugar.

[00535] In some embodiments, the present disclosure provides a compound, e.g., an oligonucleotide, a chirally controlled oligonucleotide, an oligonucleotide of a provided composition (e.g., of a plurality of oligonucleotides), having the structure of formula O-I:

O-I

or a salt thereof, wherein:

R Ss is independently R’ or -OR ;

each BA is independently an optionally substituted group selected from C 3-30 cycloaliphatic, C 6. 3o aryl, C 5-30 heteroaryl having I -10 heteroatoms, C 3-30 heterocyclyl having 1-10 heteroatoms, a natural nucleobase moiety, and a modified nucleobase moiety;

each II s is independently Ή, halogen, -CN, -N 3 , -NO, -N0 2 , -L-R’, ~-L--Si(R) 3 , L OR , -L-SR’, -L-N(R’) 2 , -0-L-R’, -0-L-Si(R) 3 , -O-L-OR’, -O-L-SR’, or -0-L-N(R’) 2 ;

each s is independently 0-20;

each L s is independently -C(R Ss ) 2- , or L;

each L is independently a covalent bond, or a bivalent, optionally substituted, linear or branched group selected from a C ]-30 aliphatic group and a C. 30 heteroaliphatic group having 1-10 heteroatoms, wherein one or more methylene units are optionally and independently replaced with C j.6 alky!ene, C 5 6

_ Q = Q _

alkenyl ene, - , a bivalent C—C 6 heteroaliphatic group having 1-5 heteroatoms, -C(R’) -, -Cy-,

-0-, S . S S . NCR·} . ( ((}} . -C(S)-, -C(NR’)-, -C(0)N(R’)-, N{ R }C ( 0)N< R ) . -N(R’)C(0)0-, --S(G)-, S(O); . S(()) .N(R ) . ( (O)S . C(0)0 . O OR ) . P(C))(SR ) . -P(0)(R’)-, -P(0)(NR’)-, P(S)(OR’)-, P(S)(SR ) . -P(S)(R’)-, -P(S)(NR’)-, F( R ) . -P(OR’)-, -P(SR’)-, -P(NR )-, -P(OR’)[B(R’) 3 ]- -0P(0)(0R’)0-, -0P(0)(SR’)0-, -0P(0)(R’)0- -0P(0)(NR’)0- -0P(0R’)0- -0P(SR’)0-, -0P(NR’)0- -0P(R’)0-, or OP(OR )| B{ R ), IO . and one or more CH or carbon atoms are optionally and independently replaced with Cy L ;

each -Cy- is independently an optionally substituted bivalent group selected from a C 3.20 cycloaliphatic ring, a C 6 20 an ring, a 5-20 membered heteroaryl ring having 1 -10 heteroatoms, and a 3- 20 membered lieterocyciyi ring having 1-10 heteroatoms;

each Cy L is independently an optionally substituted trivalent or tetravalent group selected from a C 3- 2o cycloaliphatic ring, a C 6-20 ar l ring, a 5-20 membered heteroaryl ring having 1-10 heteroatoms, and a 3-20 membered heterocyclyl ring having 1-10 heteroatoms;

each Ring A is independently an optionally substituted 3-20 membered monocyclic, hicyclic or polycyclic ring having 0-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon;

each L p is independently an intemucleotidic linkage;

z is 1-1000;

L :;E is L or L L ;

R 3El is R’, L R . -OR , or a solid support;

each R is independently -R, -C(0)R, -C(0)OR, or -S(0) 2 R;

each R is independently -H, or an optionally substituted group selected from Ci 30 aliphatic, Ci 30 heteroalrphatic having 1-10 heteroatoms, C 6-30 aryl, C 6-3 o arylaliphatic, C 6-3 o arylheteroaJiphatic having 1- 10 heteroatoms, 5-30 membered heteroaryl having 1-10 heteroatoms, and 3-30 membered heterocyclyl having 1-10 heteroatoms, or

two R groups are optionally and independently taken together to form a covalent bond, or two or more R groups on tire same atom are optionally and independently taken together with the atom to form an optionally substituted, 3-30 membered, monocyclic, bicyclic or polycyclic ring having, in addition to the atom, 0-10 heteroatoms, or

two or more R groups on two or more atoms are optionally and independently taken together with their intervening atoms to form an optionally substituted, 3-30 membered, monocyclic, bicyclic or polycyclic ring having, in addition to the intervening atoms, 0-10 heteroatoms.

[00536] In some embodiments, each L p independently has the structure of formula I, I-a, I-b, I-c,

I-n-1 , 1-n-2, 1-n-3, 1-n-4, II, II-a-1, II-a~2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, III, or a salt form thereof. In some embodiments, each L p independently has the structure of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, 11-c-l, II-c-2, Il-d-1, II-d-2, or a salt form thereof. In some embodiments, each L p independently has the structure of formula I, I-a, I-b, I-c, I-n-1, I-n-2, 1- n~3, II, II-a-1 , II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt fonn thereof. In some embodiments, an intemucleotidic linkage has the structure of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, III, or a salt form thereof. In some embodiments, an intemucieotidic linkage has the structure of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II~a~2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof. In some embodiments, each intemucieotidic linkage independently has the structure of formula I, I-a, I-b, I-e, I- n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, III, or a salt form thereof. In some embodiments, each intemucieotidic linkage independently has the structure of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof. In some embodiments, an intemucieotidic linkage has the structure of formula I, I-a, I- b, I-c, I-n-1, I-n-2, I-n-3, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof. In some embodiments, each intemucieotidic linkage independently has the structure of formula 1,

I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt fonn thereof.

100537 In some embodiments, each BA is independently an optionally substituted group selected from C 5.30 heteroaryl having 1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon, and C 3-30 heterocydyl having 1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus, boron and silicon;

each Ring A is independently an optionally substituted 3-20 membered monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon; and

each L p independently has the structure of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II,

II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, III, or a salt form thereof. In some embodiments, each U independently has the structure of formula I, I-a, I-b, I-e, I-n-1, I-n-2, I-n-3, I-n- 4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof.

[00538] In some embodiments, each BA is independently an optionally substituted C 5.30 heteroaryl having 1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon, wherein the heteroaryl comprises one or more heteroatoms selected from oxygen and nitrogen; each Ring A is independently an optionally substituted 5-10 membered monocyclic or bicyclic saturated ring having 0-5 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon, wherein the ring comprises at least one oxygen atom; and

each 1 independently has the structure of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, U-b-2, II-c-1, II-c-2, II-d-1, II-d-2, III, or a salt form thereof. In some embodiments, each L p independently has the structure of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n- 4, II, II-a-1 , II-a-2, II-b-1 , II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof.

In some embodiments, each BA is independently an optionally substituted A, T, C, G, or U, or an optionally substituted tautomer of A, T, C, G, or U;

each Ring A is independently an optionally substituted 5-7 membered monocyclic or bieyclic saturated ring having one or more oxygen atoms; and

each L p independently has the structure of formula I, I-a, I-b, I-c, I-n-1, S-n-2. I-n-3, I-n-4, II, ll-a-l, II-a-2, II-b-1, U-b-2, li-c-1, II-c-2, II-d-1, II-d-2, III, or a salt form thereof. In some embodiments, each L !> independently has the structure of formula I, I-a, I-b, I-c, I-n-1, 1-n-2, I-n-3, 1-n- 4, II, II- a- 1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof.

[00540] In some embodiments, each BA is independently an optionally substituted or protected nucleobase selected from adenine, cytosine, guanosine, thymine, and uracil and tautomers thereof;

each Ring A is independently an optionally substituted 5-7 membered monocyclic or bicyclic saturated ring having one or more oxygen atoms; and

each L p independently has the structure of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, III, or a salt form thereof. In some embodiments, each L p independently has the structure of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, 1-n- 4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof

[00541] In some embodiments, BA is an optionally substituted group selected from C 3.3 o cycloaliphatic, C 5.30 aryl, C 5 30 heteroaryl having 1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon, C 3-30 heterocyciyl having 1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon, a natural nucleobase moiety, and a modified nucleobase moiety. In some embodiments, BA is an optionally substituted group selected from C 5.30 heteroaryl having 1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon, C 3-30 heterocyciyl having 1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon, a natural nucleobase moiety, and a modified nucleobase moiety. In some embodiments, BA is an optionally substituted group selected from C 5 30 heteroaryl having 1-10 heteroatoms independently selected from oxygen, nitrogen, sulfur, phosphorus and silicon, a natural nucleobase moiety, and a modified nucleobase moiety. In some embodiments, BA is optionally substituted C 5-30 heteroaryl having 1-10 heteroatoms independently selected from oxygen, nitrogen, and sulfur. In some embodiments, BA is optionally substituted natural nucleobases and tautomers thereof hi some embodiments, BA is protected natural nucleobases and tautomers thereof. Various nucleobase protecting groups for oligonucleotide synthesis are known and can be utilized in accordance with the present disclosure. In some embodiments, BA is an optionally substituted nucleobase selected from adenine, cytosine, guanosine, thymine, and uracil, and tautomers thereof. In some embodiments, BA is an optionally protected nucleobase selected from adenine, cytosine, guanosine, thymine, and uracil, and tautomers thereof. [00542] In some embodiments, BA is optionally substituted C 3-30 cycloaliphatic. In some embodiments, BA is optionally substituted C 6-30 aryl. In some embodiments, BA is optionally substituted C3 30 heterocyciyl. In some embodiments, BA is optionally substituted Cs 3 o heteroary!. In some embodiments, BA is an optionally substituted natural base moiety. In some embodiments, BA is an optionally substituted modified base moiety. BA is an optionally substituted group selected from C 3-30 cycloaliphatic, C 6-30 aryl, C 3-30 heterocyciyl, and C 5-30 heteroaryl. In some embodiments, BA is an optionally substituted group selected from C 3.30 cycloaliphatic, C 6-30 aryl, C 3.30 heterocyciyl, C 5-3 o heteroaryl, and a natural nucleobase moiety.

100543 In some embodiments, BA is connected through an aromatic ring. In some embodiments,

BA is connected through a heteroatom. In some embodiments, BA is connected through a r g heteroatom of an aromatic ring. In some embodiments, BA is connected through a ring nitrogen atom of an aromatic ring.

100544 In some embodiments, BA is a natural nucleobase moiety. In some embodiments, BA is an optionally substituted natural nucleobase moiety. In some embodiments, BA is a substituted natural nucleobase moiety. In some embodiments, BA is optionally substituted, or an optionally substituted tautomer of, A, T, C, U, or G. In some embodiments, BA is natural nucleobase A, T, C, U, or G In some embodiments, BA is an optionally substituted group selected from natural nudeobases A, T, C, U, and G.

[00545] In some embodiments, BA is an optionally substituted purine base residue. In some embodiments, BA is a protected purine base residue. In some embodiments, BA is an optionally substituted adenine residue. In some embodiments, BA is a protected adenine residue. In some embodiments, BA is an optionally substituted guanine residue. In some embodiments, BA is a protected guanine residue hi some embodiments, BA is an optionally substituted cytosine residue. In some embodiments, BA is a protected cytosine residue. In some embodiments, BA is an optionally substituted thymine residue. In some embodiments, BA is a protected thymine residue. In some embodiments, BA is an optionally substituted uracil residue. In some embodiments, BA is a protected uracil residue. In some embodiments, BA is an optionally substituted 5-methylcytosine residue. In some embodiments, BA is a protected 5-methylcytosine residue.

[00546] In some embodiments, BA is a protected base residue as used in oligonucleotide preparation. In some embodiments, BA is a base residue illustrated in US 2011/0294124, US 2015/0211006, US 2015/0197540, and WO 2015/107425, each of which is incorporated herein by ¬ re ference.

[00547] In some embodiments, R 5s -L s - is -CH 2 OH. In some embodiments, R 5s -L s - is

-CH(R 5S )-OH, wherein R 3S is as described in the present disclosure. In some embodiments, L s is -CH 2- in some embodiments, L s is -CH(R 3S )- wherein R 5s is not -Ή. In some embodiments, L s is -CH(R Ss )- wherein R 5s is not -H and is otherwise R. In some embodiments, R is optionally substituted Ci_ 6 aliphatic. In some embodiments, R is optionally substituted C 1-6 alkyl. In some embodiments, R is methyl. In some embodiments, ~ CH(R JS )- wherein R ' ” is not -H has is R. In some embodiments, --CH(R & ) wherein R 5 * is not -H has is S

[00548] Example embodiments for variables, e.g., variables of each of the formulae, are additionally described in the present disclosure, and may be independently and optionally combined .

[00549] In some embodiments, the present disclosure provides oligonucleotides and oligonucleotide compositions that are chirally controlled. For instance, in some embodiments, a provided composition contains controlled levels of one or more individual oligonucleotide types, wherein an oligonucleotide type is defined by: 1) base sequence; 2) pattern of backbone linkages; 3) patern of backbone chiral centers; and 4) pattern of backbone P-modifications. in some embodiments, oligonucleotides of the same oligonucleotide type are identical.

100550 In some embodiments, a provided oligonucleotide is an altmer. In some embodiments, a provided oligonucleotide is a P-modification altmer. In some embodiments, a provided oligonucleotide is a stereoaltmer.

[00551] In some embodiments, a provided oligonucleotide is a blockmer. In some embodiments, a provided oligonucleotide is a P-modification blockmer. In some embodiments, a provided oligonucleotide is a stereoblockmer.

[00552] In some embodiments, a provided oligonucleotide is a gapmer.

[00553] In some embodiments, a provided oligonucleotide is a skipmer.

100554 In some embodiments, a provided oligonucleotide is a hemimer. In some embodiments, a hemimer is an oligonucleotide wherein the 5’-end or tire 3’-end has a sequence that possesses a structure feature that the rest of the oligonucleotide does not have. In some embodiments, the 5’ -end or the 3’ -end has or comprises 2 to 20 nucleotides. In some embodiments, a structural feature is a base modification. In some embodiments, a structural feature is a sugar modification. In some embodiments, a structural feature is a P-modification. In some embodiments, a structural feature is stereochemistry' of the chiral intemuc!eotidie linkage. In some embodiments, a structural feature is or comprises a base modification, a sugar modification, a P-modification, or stereochemistry of the chiral intemucleotidic linkage, or combinations thereof. In some embodiments, a hemimer is an oligonucleotide in which each sugar moiety of the 5’ -end sequence shares a common modification. In some embodiments, a hemimer is an oligonucleotide in which each sugar moiety of the 3’-end sequence shares a common modification. In some embodiments, a common sugar modification of the 5’ or 3’ end sequence is not shared by any other sugar moieties in the oligonucleotide. In some embodiments, an example hemimer is an oligonucleotide comprising a sequence of substituted or unsubstituted 2'-0-alkyl sugar modified nucleosides, bicyclic sugar modified nucleosides, b-D-ribonucieosides or b-D- deoxyribonucleosides (for example 2'-MOE modified nucleosides, and LNA™ or ENA™ bicyclic sugar modified nucleosides) at one terminus and a sequence of nucleosides with a different sugar moiety (such as a substituted or unsubstituted 2'-0-alkyl sugar modified nucleosides, bicyclic sugar modified nucleosides or natural ones) at the other terminus. In some embodiments, a provided oligonucleotide is a combination of one or more of unimer, altmer, blockmer, gapmer, hemimer and skipmer. In some embodiments, a provided oligonucleotide is a combination of one or more of unimer, altmer, blockmer, gapmer, and skipmer. For instance, in some embodiments, a provided oligonucleotide is both an altmer and a gapmer. In some embodiments, a provided nucleotide is both a gapmer and a skipmer. One of skill in the chemical and synthetic arts will recognize that numerous other combinations of patterns are available and are limited only by the commercial availability and / or synthetic accessibility of constituent parts required to synthesize a provided oligonucleotide in accordance with methods of the present disclosure. In some embodiments, a hemimer structure provides advantageous benefits. In some embodiments, provided oligonucleotides are S’-hemimers that comprises modified sugar moieties in a 5" -end sequence. In some embodiments, provided oligonucleotides are S’-hemimers that comprises modified 2’ -sugar moieties in a 5’-end sequence.

[00555] In some embodiments, a provided oligonucleotide comprises one or more optionally substituted nucleotides. In some embodiments, a provided oligonucleotide comprises one or more modified nucleotides. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted nucleosides. In some embodiments, a provided oligonucleotide comprises one or more modified nucleosides. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted nucleosides or sugars of LNAs.

[00556] In some embodiments, a provided oligonucleotide comprises one or more optionally substituted nucleobases. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted natural nucleobases. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted modified nucleobases. In some embodiments, a provided oligonucleotide comprises one or more 5-methylcytidine; 5-hydroxymethylcytidine, 5~formyi cytosine, or 5-carboxylcytosine. In some embodiments, a provided oligonucleotide comprises one or more 5- methylcytidine.

1005571 In some embodiments, a provided oligonucleotide comprises one or more optionally substituted sugars. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted sugars found in naturally occurring DNA and RNA In some embodiments, a provided oligonucleotide comprises one or more optionally substituted ribose or deoxyribose. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted ribose or deoxyribose, wherein one or more hydroxyl groups of the ribose or deoxyribose moiety is optionally and independently replaced by halogen, R’, -N(R’) 2 , -OR’, or -SR’, wherein each R’ is independently as defined above and described herein. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted deoxyribose, wherein the T position of the deoxyribose is optionally and independently substituted with R s , halogen, R’, -N(R’) 2 , -OR , or -SR’, wherein each R’ is independently as defined above and described herein. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted deoxyribose, wherein the 2’ position of the deoxyribose is optionally and independently substituted with halogen. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted deoxyribose, wherein the T position of the deoxyribose is optionally and independently substituted with one or more -F. halogen. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted deoxyribose, wherein the 2’ position of the deoxyribose is optionally and independently substituted with -OR’, wherein each R’ is independently as defined above and described herein. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted deoxyribose, wherein the 2’ position of the deoxyribose is optionally and independently substituted with -OR’, wherein each R’ is independently an optionally substituted C -C 6 aliphatic. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted deoxyribose, wherein the T position of the deoxyribose is optionally and independently substituted with -OR’, wherein each R’ is independently an optionally substituted C r- C 6 alkyl. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted deoxyribose, wherein the 2’ position of the deoxyribose is optionally and independently substituted with - OMe. In some embodiments, a provided oligonucleotide comprises one or more optionally substituted deoxyribose, vriierein the T position of the deoxyribose is optionally and independently substituted with - O-methoxyethyl .

[00558] In some embodiments, a provided oligonucleotide is single-stranded oligonucleotide. In some embodiments, a provided oligonucleotide is a hybridized oligonucleotide strand. In certain embodiments, a provided oligonucleotide is a partially hybridized oligonucleotide strand. In certain embodiments, a provided oligonucleotide is a completely hybridized oligonucleotide strand hi certain embodiments, a provided oligonucleotide is a double-stranded oligonucleotide. In certain embodiments, a provided oligonucleotide is a triple-stranded oligonucleotide (e.g., a triplex).

[00559] In some embodiments, a provided oligonucleotide is chimeric. For example, in some embodiments, a provided oligonucleotide is DNA-RNA chimera, DNA-LNA chimera, etc.

[00560] In some embodiments, an oligonucleotide is a chi rally controlled oligonucleotide variant of an oligonucleotide described in WO2012/030683. For example, in some embodiments, a chi rally controlled oligonucleotide variant comprises a chirally controlled version of a chiral intemucleotidic linkage which is not chirally controlled in WO2012/030683. In some embodiments, a chirally controlled oligonucleotide variant comprises one or more chirally controlled intemucleotidic linkages which independently replace one or more natural phosphate linkages or non-chira!ly controlled modified intemucleotidic linkages in WO2012/030683.

[00561] In some embodiments, a provided oligonucleotide is or comprises a portion of GNA,

LNA, PNA, TNA or Morpholine.

[00562] In some embodiments, a provided oligonucleotide is from about 15 to about 25 nucleotide units in length. In some embodiments, a provided oligonucleotide is from about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotide units in length.

[00563] In some embodiments, the present disclosure provides oligonucleotides comprising one or more modified intemucleotidic linkage, which can be chiral at linkage phosphorus and chirally controlled. In some embodiments, an oligonucleotide comprises one or more linkages I, , L PA or L PB , wherein:

5’-sugar 5'-sugar

3'-sugar 3'-sugar

each L P0 is independently

sugar sugar a gajt | orm l ] l reo f

each L PA is independently an intemucleotidic linkage having the structure of

5'~sugar 5'-sugar 5'-sugar 5’-sugar -sugar ^

, or . or a salt form thereof;

each L pli IS independently an intemucleotidic linkage having tire structure of

5‘-sugar 5'-sugar 5'-sugar 5'-sugar -sugar

. or or a salt form thereof;

wherein each other variable is independently as described herein.

5'-sugar -sugar each L f' ° is independently

3'-sugar S'-sugar

. or a salt fonn thereof.

[00565] In some embodiments -O-L-R is ~ OH. In some embodiments, -X-L-R 1 , e.g. in L P0 is -OCH 2 CH 2 CN. In some embodiments, -S L R 1 is -SH. In some embodiments, L iA is a phosphorothioate internucleotidic linkage with the specified stereochemistry. In some embodiments, L f'b is a phosphorothioate internucleotidic linkage with the specified stereochemistry. In some embodiments, X is-O-, and -X-L-R 1 is as described in the present disclosure, e.g., -X-L-R 1 is

wherein each variable is independently in accordance with the present disclosure, or H--X--L--R 1 is a chiral auxiliary as described wherein G 4 and G 5 are taken together to form an optionally substituted ring as described herein. In some embodiments, . In some embodiments, G is -CH 2 Si(R) 3 as described herein. In some embodiments, G 2 is -CH 2 Si(Ph) 2 Me. In some embodiments, G 2 comprises an electron- withdrawing group as described herein, for example, in some embodiments, G 2 is -CH 2 S0 2 R as described herein. In some embodiments. G 2 is -CH 2 S0 2 Ph.

[00566] In some embodiments, N x is \( l . R ) ί . R 1 .. and an intemucleotidic linkage having such a N x group is an intemucleotidic linkage having the structure of fonnula I wherein P L is P=0, Y and Z are -0-, and X is -Ni-L-R 3 )-, wherein the linkage phosphorus stereochemistry is as specified. In some embodiments. N K is and £in intemucleotidic linkage having such a N x group is an intemucleotidic linkage having the structure of formula P, wherein P L is P=0, Y and Z are -0-, and X is -N(-L-R 3 )-, wherein the linkage phosphoras stereochemistry is as specified. In some

embodiments some

mbodiments, In some embodiments, N x is. . In some

Ny N(R 1 )2

:mbodiments, N x is N(R 1 )2 , and an intemucleotidic linkage having such a N x group is an intemucleotidic linkage having the structure of formula I-n-3, wherein P L is P=0, and Y and Z are O , wherein the linkage phosphorus stereochemistry is as specified. In some embodiments, R 1 is optionally

substituted alkyl. In some embodiments, R is methyl. In some embodiments, . In some embodiments, two R 1 on the same nitrogen independently are taken together to form an optionally substituted ring as described herein, e.g., an optionally substituted 5- or 6-membered ring which in addition to the nitrogen atom, has 1 -3 heteroatoms. In some embodiments, the ring is saturated. In some

embodiments, the ring is monocyclic. In some embodiments, In some embodiments.

, Those skilled in the art will appreciate that two N(R l ) 2 groups, in any, in a structure or formula can either be tire same or different. In some embodiments, N x is ^ an intemucleotidic linkage having such a N x group is an intemucleotidic linkage having the structure of formula I-n-4, wherein P is P=0, L is a covalent bond, and Y and Z are -0-, wherein the linkage phosphorus stereochemistry is as specified. In some embodiments, N x is , and an intemucleotidic linkage having such a N x group is an intemucleotidic linkage having the structure of formula II-a-l, wherein P L is P=0, L is a covalent bond, and Y and Z are 0 . wherein the linkage phosphorus stereochemistry is as specified. In some

embodiments, N x and an intemucleotidic linkage having such a N x group is an intemucleotidic linkage having the structure of formula II-b-l, wherein P L is P=0, L is a covalent bond, and Y and Z are -0-, wherein the linkage phosphorus stereochemistry is as specified. In some embodiments, intemucieotidic linkage having such a N x group is an intemucieotidic linkage having the structure of formula II-c-1, wherein P L is P=0, L is a covalent bond, and Y and Z are -0-, wherein the linkage phosphorus stereochemistry is as specified. In some

embodiments, intemucieotidic linkage having such a N x group is an intemucieotidic linkage having the structure of fonnula II-d-1, wherein P L is P=0, L is a covalent bond, and Y and Z are 0 . wherein the linkage phosphorus stereochemistry is as specified. In some embodiments, R’ or R ¾ is optionally substituted alkyl. In some embodiments, R’ or R s is -~CH 3 . in some embodiments, R’ or R'’ is -CH 2 (CH 2 ) ] oCH . In some embodiments, R s -H. In some embodiments, N x

. In some embodiments.

In some embodiments, P=W N is a P” group as described herein. In some embodiments. wherein each variable is as described herein

(tor example, in N x ). In some embodiments, In some embodiments, as described herein R’ or R s is optionally substituted alkyl or -H. In some embodiments, R’ is -CH 3 . In some embodiments, R’ is -CH 2 (CH 2 ) IO CH 3 . In some embodiments, R s is -H. In some embodiments, W N is SO me embodiments, W N is =N-L-R 5 wherein each variable is as described herein. For example, in some embodiments, L is -S0 2 -. In some embodiments, L is -C(0)0CH 2 --. In some embodiments, as described herein, R 5 is or comprise an optionally substituted ring. In some embodiments, II s is R as described herein. In some embodiments, R 5 is optionally substituted phenyl. In some embodiments, R 5 is 4-methyiphenyi. In some embodiments, R 5 is 4-methoxyphenyl. In some embodiments, R 5 is 4-aminophenyl. In some embodiments, R 5 is an optionally substituted heteroaliphatie ring. In some embodiments, R:’ is an optionally substituted 3-10 (e.g., 3, 4, 5, 6, 7, or 8) membered heteroaliphatie ring. In some embodiments, R 5 is an optionally substituted 5- or 6-membered saturated monocyclic heteroaliphatie ring having 1-3 heteroatoms. In some embodiments, the ring is 5 -membered. In some embodiments, the ring is 6-membered. In some embodiments, the number of ring heteroatom(s) is 1. In some embodiments, the number of ring heteroatoms is 2 In some embodiments, a heteroatom is oxygen. In some embodiments, R 5 is optionally substituted In some embodiments, R s is optionally substituted In some

embodiments, In some embodiments, R ' is optionally substituted C ; 0 aliphatic. In some embodiments, is optionally substituted Cm alkyl. In some embodiments, \; N is n some embodiments, W N some embodiments, W is

- OH

ΌH

In some embodiments, W N is 0H In some embodiments, W N is

R 1

R 1 R -Ni

L b — R 1 bl

Q . In some embodiments, W is Q . In In some embodiments, W is

Q . In some embodiments, some embodiments, Q is PF 6 . 5‘-sugar

. In some

5 -sugar

embodiments, -X-L-R 1 in g

In some embodiments. G is

-CH 2 Si(R) 3 as described herein. In some embodiments, G 2 is -CH 2 Si(Ph) 2 Me. In some embodiments,

In some embodiments, in

5‘-sugar

R 1

L g j n some embodiments, G comprises an electron-withdrawing group as described herein. In some embodiments, G 2 is -CH 2 SQ 2 R, wherein R is not -H. In some embodiments, R is optionally substituted phenyl. In some embodiments, G 2 is ( 1 bSO kh. In some embodiments, R is optionally substituted C j.6 aliphatic, e.g., t-butyl. In some embodiments, as described herein, R 1 is -C(0)R’. In some embodiments, R 1 is -C(0)CH 3 . In some embodiments, R 1 is -H.

[00569] In some embodiments, L P0 is a natural phosphate linkage. In some embodiments, L PA is a Rp phosphorothioate intemucleotidic linkage. In some embodiments, L PA is a Rp non-negatively charged intemucleotidic linkage, e.g., nOOl In some embodiments, L PB is a Sp phosphorothioate internucleotidic linkage. In some embodiments, L“ is a Sp non -negatively charged intemucleotidic linkage, e.g., nOOl. In some embodiments, an oligonucleotide comprises one or more linkages L P0 . In some embodiments, an oligonucleotide comprises one or more linkages L PA In some embodiments, an oligonucleotide comprises one or more linkages L ?B . In some embodiments, an oligonucleotide comprises one or more intemucleotidic linkages independently selected from L PB . In some embodiments, each intemucleotidic linkage is independently selected from L P0 , L PA and L PB . In some embodiments, each intemucleotidic linkage is independently selected from L PA and L™. In some embodiments, at least one intemucleotidic linkage is L PA or L™. In some embodiments, each ehirally controlled internucleotidic linkage is independently selected from L PA and L rB .

[00570] In some embodiments, the present disclosure provides oligonucleotides (e.g., ehira!ly controlled oligonucleotides) and compositions thereof (e.g., chirally controlled oligonucleotide compositions), wherein the internucleotidic linkages of the oligonucleotides or regions thereof are or comprise the following consecutive internucleotidic linkages (from 5’ to 3’):

(L /L )t[(L r 7L )n]y(L /L )m, or a combination thereof, wherein:

each L x is independently L PA or L PB : and

each other variable is independently as described herein.

[00571] In some embodiments, internucleotidic linkages of an provided oligonucleotides or regions thereof comprise or are consecutive internucleotidic linkages [(L PA )n(L PB )m]y,

(L PB )t[(L PA )n(L PB )m]y, or (L PB )t[(L P0 )n(L Pb )m |y. In some embodiments, internucleotidic linkages of an provided oligonucleotides or regions thereof comprise or are consecutive internucleotidic linkages In some embodiments, internucleotidic linkages of an provided oligonucleotides or regions thereof comprise or are consecutive internucleotidic linkages [(L PA )(L PB )m]y In some embodiments, internucleotidic linkages of an provided oligonucleotides or regions thereof comprise or are consecutive internucleotidic linkages hi some embodiments, each sugar between two of the consecutive internucleotidic linkages independently contains no 2 '-modification. In some embodiments,

each sugar between two of the consecutive internucleotidic linkages is independently . In some embodiments, n is 1 . In some embodiments, y is 1. In some embodiments, y is 2-10. In some embodiments, t is 1. In some embodiments, t is 2-10. In some embodiments, t is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, n is I, and m is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, t is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, n is 1, and m is 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, t is 2-10, n is I and m is 2-10. In 5'-sugar 5'-sugar

3 -sugar 3 -sugar some embodiments, each I_ PA is independently or . or a salt

sugar '-sugar form thereof. In some embodiments, each L PB is independently or

sugar -sugar

or a salt form thereof. In some embodiments, each L PA is independently

S'-sugar 5 -sugar -sugar

or a salt form thereof.

[00572] In some embodiments, internucleotidic linkages of an provided oligonucleotides or regions thereof comprise or are consecutive internucleotidic linkages (from 5’ to 3’) (L P0 )m(L PA /L PB )n, L P0 (L PA /L PB )n, (L P0 )m(L PB )n, L P0 (L PB )n, [(L P0 )m(L PA /L PB )n]y, [L P0 (L PA /L PB )n]y, [(L P0 )m(L PB )n]y, [L P0 (L PB )n]y, (L PA /L PB )t(L P0 )rn(L PA /L PB )n, (L PA /L PB )tL P0 (L PA /L PB )n, (L PA /L PB )t(L P0 )m(L PB )n, (L PA /L PB )tL P0 (L PB )n, (L PA /L PB )t[(L P0 )m(L PA /L PB )n]y, (L PA /L PB )t[L P0 (L PA /L PB )n]y,

(L pA /L PB )t[(L P0 )m(L PB )n]y, (L PA /L PB )t[L P0 (L PB )n]y, (L P0 )m(L PA /L PB )n(L PA /L PB )t, L P0 (L PA /L PB )n(L PA yL PB )t, ^ ' T PB )n(L FA /L PB )t, L P0 (L PB )n(L FA /L PB )t, [(L P0 )m(L PA /L PB )n]y(L PA /L PB )t, [L P0 (L PA /L PB )n]y(L PA /L PB )t,

-. P0 )m(L PB )n]y(L PA /L PB )t, [L P0 (L PB )n]y(L PA /L PB )t, (l A /l/ B )t[(l 0 )m(L PA /L PB )n]y(L F/ 7L PB )t,

L PB/ T PA \ PA /T PB

/L P P B B )t[(L P0 )m(L PA /L PB )n]y(L P PA A//LT P PB B )·,tL P13

(L rA /L 1 B )t[(L r,J )m(L PB )n]y(L PA /L PB )t,

L PB (L PA /L PB )t[(L P0 )m(L PB )n]y(L PA /L PB )tL PB , (L PA /L PB )t[(L P0 )(L PA /L PB )]y(L PA /L PB )t,

L PB (L PA /L PB )t[(L P0 )(L PA /L PB )]y(L PA /L PB )tL PB , (L PA /L PB }t[(L P0 )(L PB )]y(L PA /L PB )t,

L PB (L PA /L FB )t[(L P0 )(L PB )]y(L PA /L PB )tL FB , or a combination thereof, wherein each variable is independently as described herein. In some embodiments, at least one L PA /L PB of (L PA /L PB )t is L PA . In some embodiments, at least one L PA /L PB of (L PA /L PB )t is L™. In some embodiments, at least one L PA /L PB of (L PA /L PB )t is L pa , and at least one L PA /L PB of (L PA /L PB )t is L PB . In some embodiments, at least one L PA /L PB of (L PA /L PB )m is L Pa . In some embodiments, at least one L PA /L PB of (L PA /L PB )m is L PB . In some embodiments, at least one L PA 7L PB of (L PA /L PB )m is L PA , and at least one L PA /L PB of (L EA /L Pb )m is L E B . In some embodiments, each L PA /L PB of (L PA /L PB )m is L PB . In some embodiments, a sugar bonded to a L P0 linkage at its 3’ -carbon comprises a 2’-modification, wherein the T -modification is not 2’-F. In some

embodiments, a sugar bonded to a L P0 linkage at its 3’ -carbon is independently wherein R /s is not -H or -OH. In some embodiments, each sugar bonded to a I PO

linkage at its 3’ -carbon is independently , wherein R"" is not -H or -OH.

In some embodiments, each sugar bonded to a L P0 linkage at its 3’-carbon is independently wherein R /s is not -H or -OH. In some embodiments, R" s is -H. In some embodiments, R 2 ’ is not -H, -F or -OH. In some embodiments, each sugar bonded to a L P0 linkage at its 3’-carbon is

independently , wherein R s is not ~ H, -F or -OH. In some embodiments, R 2' is -OR, wherein R is optionally substituted C-._ 6 aliphatic. In some embodiments, R is optionally substituted C _ 6 alkyl. In some embodiments, R: s is -OMe. In some embodiments, a 5’ -end sugar, a 3’ -end sugar, and/or a sugar between L PA /L PB and L pA /L PB comprises a 2’-F modification. In some embodiments, a 5’ -end

sugar, a 3’-end sugar, and/or a sugar between wherein R S is -F.

In some embodiments, each sugar comprises a 2’-F is bonded to a modified intemucleotidic linkage, e.g., at its 3 -carbon. In some embodiments, a modified intemucleotidic linkage is L PA or L PB . In some 5'-sugar S’-suqar

3 -sugar 3 -sugar

mbodiments, each L PA is independently or or a salt form

5 -sugar -sugar thereof in some embodiments, each L FB is independently or

5 -sugar

AT *

3'-sugar

each L FA is independently or a salt fonn thereof, and each L FB is independently sugar sugar qj . a gajt p orm thereof. In some embodiments, each modified intemucleotidic linkage in a provided oligonucleotide is independently L !>0 (wherein -X-L-R 1 is not -H),

5 -sugar 5'-sugar 5 -sugar 5'-sugar salt form thereof. In some embodiments, each modified intemucleotidic linkage is independently

5‘-sugar 5 -sugar

R 1 -sugar

or , or a salt fonn thereof. In some embodiments each S’-sugar 5'-sugar

modified intemucleotidic linkage is independently or , or a salt form thereof. In some embodiments, m is 1. In some embodiments, each m is 1. In some embodiments, n is 2 or more. In some embodiments, each n is 2 or more. In some embodiments, t is 1. In some embodiments, t is 2 or more. In some embodiments, t is 3. In some embodiments, t is 4. In some embodiments, t is 5. In some embodiments, t is 6. In some embodiments, t is 7. In some embodiments, t is 8. In some embodiments, t is 9. In some embodiments, t is 10. In some embodiments, each t is independently 2 or more. In some embodiments, each t is independently 3 or more. In some embodiments, each t is independently 4 or more. In some embodiments, each t is independently 5 or more.

[00573] In some embodiments, each of L !>0 , 1_ PA and L™ independently bonds to a 5’ -sugar through its 3’ -carbon, and to a 3’ -sugar through its 5’ -carbon, e.g. , each L PA is independently an

3 -carbon 3‘-carbon

S’-earbon 5‘-carbon intemucleotidic linkage having the structure of

3'-carbon 3'-carbon

S'-carbon 5’-carbon P13

. or or a salt form thereof; each L is independently an

5'-stigar 5'-sugar

S’-sugar 3 -sugar intemucleotidic linkage having the structure of

5‘-sugar 5'-sugar -sugar

or or a salt form thereof. Example sugar structures are described herein, e.g. , in some embodiments, each sugar moiety independently has the structure of wherein each variable is independently as described in the present disclosure.

[00574] In some embodiments, L E’ ° has a pattern, location, number, percentage, etc as described herein for a natural phosphate linkage. In some embodiments, L PA has a pattern, location, number, percentage, etc. as described herein for a Rp intemucleotidic linkage. In some embodiments, a Rp intemucleotidic linkage is a Rp phosphorothioate intemucleotidic linkage. In some embodiments, a Rp intemucleotidic linkage is a Rp non-negatively charged intemucleotidic linkage (e.g., nOOl). In some embodiments, L™ has a pattern, location, number, percentage, etc. as described herein for a Sp intemucleotidic linkage. In some embodiments, a rip intemucleotidic linkage is a rip phosphorothioate intemucleotidic linkage. In some embodiments, a rip intemucleotidic linkage is a rip non-negatively charged intemucleotidic linkage (e.g., nOOl).

[00575] In some embodiments, the present disclosure provides an oligonucleotide, wherein the first intemucleotidic linkage from the 5’ -end is an intemucleotidic linkage of O P , and each other intemucleotidic linkage is independently selected from O p , * FD , * PD S, * PD R, * N , * S and * R, wherein:

5'-suaar S'-sugar 5’-siigar

3 -sugar 3 -sugar 3'-sugar

G 5P is , T L PO , T L PA , T L PB , or a salt form thereof;

each O p is independently L P0 ;

5‘-sugar 5‘-sugar

each is independently

5'-sugar -sugar

, or a salt form thereof; sugar '-sugar

each * PD S is independently or a salt form thereof;

5 -sugar

, - ,,

each * PU R is independently salt form thereof;

5 -sugar 5 -sugar 5'-sugar

3‘sugar 3'-sugar 3’-sugar each * N is independently

, or a salt form thereof;

5‘-sugar -sugar

each * S is independently or a salt form thereof; and

sugar

each * n R I S i ndependently sugar thereof;

wherein each variable in independently as described herein, wherein -X-L-R/ is not

sugar '-sugar O is independently

3‘-sugar 3'-sugar

, L PU , L fa , L™, or a salt form thereof. In some mbodiments, each O p is independently °. In some embodiments, each * PD is independently 5‘-sugar

-sugar

or a salt form thereof. In some embodiments, each * PD S is independently

5’-sugar

-sugar

or a salt form thereof. In some embodiments, each * PD R is independently

,

5'-sugar

-sugar

or a salt form thereof. In some embodiments, each * N R is independently

5‘-sugar

-sugar

or a salt form thereof.

00577] In some embodiments, X is -0-. In some embodiments, -L-R 1 contains an electron- withdrawing group. In some embodiments, -L-R 1 is -CH 2 G 2 , wherein the methylene unit is optionally substituted. In some embodiments, -L-R 1 is -CH(R’)G 2 . In some embodiments, G does not comprise a chiral element, and (f comprises an electron-withdrawing group as described herein, e.g., in some embodiments, G 2 is -CH 2 CN (e.g wherein linkage phosphorus is not chirally controlled). In some embodiments, G 2 comprises a chiral element, e.g., wherein linkage phosphorus is chirally controlled. In some embodiments, -X-L-R 1 is of such a structure that H-X-L-R 1 is a chiral reagent described herein, or a capped chiral reagent described herein wherein an amino group of the chiral reagent (typically of -W 1 -H or -W 2 -H, which comprises an amino group -NHG 5 -) is capped, e.g., with -C(0)R’ (replacing a -H, e.g., -N[-C(0)R , ]G '5 -). In some embodiments, -X-L-R 1 is

R wherein each variable is independently in

accordance with the present disclosure. In some embodiments, wherein each variable is independently in accordance with the present disclosure. In some embodiments, R 1 is -H or -C(0)R\ In some embodiments, wherein R s is -H, e.g., in 0 M \ In some embodiments, R s is ~ C(0)R’ (e.g., in 0 5P ,

O p . * PD S, ’R, * N S, * R, etc.). In some embodiments, R 1 is CH 3 C(0) ~ . In some embodiments, as described herein, G 2 is In some embodiments, G 2 is -C(R) 2 Si(R)3, wherein -C(R) 2 - is optionally substituted -CH 2 -, and each R of -Si(R) 3 is independently an optionally substituted group selected from C MO aliphatic, heterocyclyl, heteroaryl and aiyl. In some embodiments, G is -CH 2 Si(Me)(Ph) 2. In some embodiments, e.g., * !>l) R, etc., G 2 is -CH 2 Si(Me)(Ph) 2 . In some embodiments, G 2 comprises an electron-withdrawing group as described herein. In some embodiments, G 2 is -C(R) 2 S0 2 R\ wherein — C(R) 2— is optionally substituted -CH 2 -, and R' is an optionally substituted group selected from C H0 aliphatic, heterocyclyl, heteroaryl and aryl. In some embodiments, R/ is phenyl. In some embodiments, e.g., in * S, * N R, etc., G 2 is -CH 2 S0 2 Ph.

[00578] In some embodiments, the present disclosure provides an oligonucleotide (“a first oligonucleotide”), which has an identical structure as an oligonucleotide described in a Table herein or an oligonucleotide described in e.g., US 2015021 1006, US 20170037399, US 20180216107, US 20180216108, US 20190008986, WO 2017/015555, WO 2017/015575, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, WO 2017/210647, WO 2018/022473, WO 2018/067973, WO 2018/098264, WO 2018/223056, WO 2018/223073, WO 2018/223081, WO 2018/237194, WO 2019/032607, WO 2019/032612, etc., the oligonucleotide of each of which is incorporated herein by reference (“a second oligonucleotide ), which second oligonucleotide comprises modified internucleotidic linkages, except that compared to the second oligonucleotide, in the first oligonucleotide:

the first internucleotidic linkage from the 5’ -end is an internucleotidic linkage of 0 5p ; and for the rest linkages:

at each location where there is a phosphate linkage in the second oligonucleotide, there is independently a linkage ofO p in the first oligonucleotide;

at each location where there is a stereorandom phosphorothioate linkages in the second oligonucleotide, there is independently a linkage of * PD in the first oligonucleotide;

at each location where there is a S'p phosphorothioate linkage in the second oligonucleotide, there is independently a linkage of * PD S in the first oligonucleotide;

at each location where there is a i?p phosphorothioate linkage in the second oligonucleotide, there is independently a linkage of * W) R in the first oligonucleotide;

at each location where there is a stereorandom non-negatively charged internucleotidic linkage in the second oligonucleotide, there is independently a linkage of * N in the first oligonucleotide;

at each location where there is a 5p non-negatively charged internucleotidic linkage in the second oligonucleotide, there is independently a linkage of * N S in tire first oligonucleotide;

at each location where there is a Rp non-negatively charged internucleotidic linkage in the second oligonucleotide, there is independently a linkage of * N R in the first oligonucleotide, and

each nucleobase in the first oligonucleotide is optionally and independently protected (e.g., as in oligonucleotide synthesis), and each additional chemical moiety, if any, in the first oligonucleotide is optionally and independently protected (e.g. , -OH in a carbohydrate moiety protected as -OAc).

[00579] In some embodiments, at each location where there is a phosphate linkage in the second oligonucleotide, there is independently a linkage of O p in the first oligonucleotide; at each location where there is a stereorandom phosphorothioate linkages in the second oligonucleotide, there is independently a linkage of * ?D in the first oligonucleotide; at each location where there is a ¾) phosphorothioate linkage in the second oligonucleotide, there is independently a linkage of * PD S in the first oligonucleotide; at each location there is a Rp phosphorothioate linkage in the second oligonucleotide, there is independently a linkage of piS R in the first oligonucleotide; at each location there is a stereorandom non-negatively charged internucleotidic linkage in the second oligonucleotide, there is independently a linkage of * in the first oligonucleotide; at each location there is a Sp non-negatively charged internucleotidic linkage in the second oligonucleotide, there is independently a linkage of * N S in the first oligonucleotide; at each location there is a Rp non-negatively charged intemucleotidie linkage in the second oligonucleotide, there is independently a linkage of * N R in the first oligonucleotide, and each nucleobase in the first oligonucleotide is optionally and independently protected (e.g., as in oligonucleotide synthesis), and each additional chemical moiety, if any, in the first oligonucleotide is optionally and independently protected (e.g. , -OH in a carbohydrate moiety protected as -OAc); wherein each of 0 5P , O p , * PD , * PD S, * PD R, * N , * N S and * n R is independently as described herein. In some embodiments, such an oligonucleotide is linked to a support optionally through a linker, e.g., a CNA linker to CPG. In some embodiments, as appreciated by those skilled in the art, after a removal process of -X-L-R , a linkage of O , O , *‘ , * PD S, * PD R, * n , * k S or * R becomes a linkage it replaces. In some embodiments, such oligonucleotides (e.g., first oligonucleotides) are useful intermediates for preparing their corresponding oligonucleotides (e.g., second oligonucleotides). In some embodiments, the present disclosure provides chirally controlled oligonucleotide composition of a provided first oligonucleotide or a stereoisomer thereof.

100580 In some embodiments, as appreciated by those skilled in the art, W N is of such a structure that its N-moiety has the same non-hydrogen atoms and connections of non-hydrogen atoms as the N- moiety of the non-negatively charged intemucleotidie linkage it replaces (without considering single.

double, or triple bond etc.). For example, in some embodiments, P in * N is (such a * is n00! p ), and its corresponding non-negatively charged intemucleotidie linkage is nOOl.

[00581] In some embodiments, a provided oligonucleotide has the same“Description” as an oligonucleotide listed in a Table herein (e.g.. Table Al), except that:

the oligonucleotide comprises at least one linkage of Q p , and/or at each location in the oligonucleotide where there is a phosphate linkage, there is independently a linkage of Q p , wherein 0 !> is

at each location where there is a stereorandom phosphorothioate linkages, there is independently

a linkage of * PD , wherein

at each location where there is a .Vp phosphorothioate linkage, there is independently a linkage of S’-earbon -carbon

* PD S, wherein * ;

at each location where there is a Rp phosphorothioate linkage, there is independently a linkage of

3 -carbon

* PD R wherein

at each location where there is a stereorandom nOOl, there is independently a linkage of

wherein (as appreciated by those skilled in the art, it is associated with an anion (e.g., Q such as PF 6 (which can be an anion in a modification step)));

at each location where there is a »Sp nOOl, there is independently a linkage of * N S, wherein * N S is carbon '-carbon (as appreciated by those skilled in the art, it is associated with an anion (e.g ,

Q such as PF 6 (which can be an anion in a modification step))); and

at each location where there is a Rp nOOl, there is independently a linkage of * N R, wherein * N R is

n (as appreciated by those skilled in the art, it is associated with an anion (e.g., Q such as PF 6 (which can be an anion in a modification step))); and the oligonucleotide is optionally connected to a solid support, optionally through a linker.

In some embodiments, the oligonucleotide is connected to a solid support, e.g , CPG, polystyrene support, etc. In some embodiments, the oligonucleotide is connected to a solid support through a linker, e.g., a CNA linker. In some embodiments, such an oligonucleotide is an oligonucleotide of formula O-I or a salt form thereof.

Certain Embodiments of Stereochemistry and Pattern of Backbone Chiral Centers

[00582] Among other things, the present disclosure provides oligonucleotides comprising one or more chi rally controlled intemudeotidic linkages. In some embodiments, the present disclosure provides chirally controlled oligonucleotide compositions. In some embodiments, each chiral linkage phosphorus of provided oligonucleotides is independently chirally controlled (stereocontrolled) (e.g., each independently having a stereopurity ' (diastereopurity) of at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% (e.g., as typically assessed using an appropriate dimer comprising an intemudeotidic linkage containing the linkage phosphoms, and the two nucleoside units being linked by the intemudeotidic linkage)). In some embodiments, a stereopurity is at least 90%. In some embodiments, a stereopurity is at least 95%. In some embodiments, a stereopurity is at least 96%. In some embodiments, a stereopurity is at least 97%. In some embodiments, a stereopurity is at least 98% In some embodiments, a stereopurity is at least 99%. With the capability to fully control stereochemistry and other modifications (e.g., base modifications, sugar modifications, intemudeotidic linkage modifications, etc.), the present disclosure provides technologies of improved properties and/or activities compared to corresponding non- chirally controlled technologies.

[00583] In some embodiments, patern of backbone chiral centers of a region, particularly a core region or a middle region, or of an oligonucleotide (e.g., an oligonucleotide of a plurality of oligonucleotides) is or comprises (Np/Op)t[(Rp)n(Sp)m]y, (Np/Op)t[(Op)n(Sp)m]y, (Np/Op)t[(Op/Rp)n(Sp)m]y, (Sp)t[(Rp)n(Sp)m]y, (Sp)t[(Op)n(Sp)m]y, (Sp)t[(Op/Rp)n(Sp)m]y, [(Rp)n(Sp)mjy, [(Op)n(Sp)m]y, [(Op/Rp)n(Sp)m]y, (Rp)t(Np)n(Rp)m, (Rp)t(Sp)n(Rp)m, (Rp)t[(Np/Op)n]y(Rp)m, (Rp)t[(Sp/Np)n]y(Rp)m, (Rp)t[(Sp/Op)n]y(Rp)m, (Np/Op)t(Np)n(Np/Op)m, (Np/Qp)t(Sp)n(Np/Op)m, (Np/Op)t[(Np/Op)n]y(Np/Op)m, (Np/ Op)t[(Sp/ Op)n]y(Np/Op)m,

(Np/Op)t[(Sp/Op)n]y(Np/Qp)m, (Rp/Op)t(Np)n(Rp/Qp)m, (Rp/Op)t(Sp)n(Rp/Op)m,

(Rp/Op)t[(Np/Op)n]y(Rp/Op)m, (Rp/Op)t[(Sp/Op)n]y(Rp/Op)m, or (Rp/Op)t[(Sp/Op)n]y(Rp/Op)m (unless otherwise specified, description of patterns of modifications and stereochemistry are from 5" to 3’ as typically used m the art), wherein rip indicates S configuration of a chiral linkage phosphorus of a chiral modified intemudeotidic linkage, Rp indicates R configuration of a chiral linkage phosphoms of a chiral modified intemudeotidic linkage. Op indicates an achiral linkage phosphoms of a natural phosphate linkage, each Np is independently Rp, or rip, and each of m, n, t and y is independently 1-50 as described in the present disclosure. In some embodiments, a pattern of backbone chiral centers is or comprises [(Rp/Op)n(Sp)m]y. In some embodiments, a patern of backbone chiral centers is or comprises [(Rp)n(Sp)m]y. In some embodiments, a pattern of backbone chiral centers is or comprises

[(Op)n(Sp)m]y. In some embodiments, a pattern of backbone chiral centers is or comprises

(Np/Op)t[(Rp/Op)n(Sp)m]y. In some embodiments, a pattern of backbone chiral centers is or comprises (Np/Op)t[(Rp)n(Sp)m]y. In some embodiments, a patern of backbone chiral centers is or comprises (Np/Op)t[(Op)n(Sp)m]y. In some embodiments, a patern of backbone chiral centers is or comprises (Sp)t[(Rp/Op)n(Sp)m]y. In some embodiments, a pattern of backbone chiral centers is or comprises (Sp)t[(Rp)n(Sp)m]y. In some embodiments, a pattern of backbone chiral centers is or comprises (Sp)t[(Op)n(Sp)m]y. In some embodiments, a pattern of backbone chiral centers is or comprises (Rp)t(Np)n(Rp)m. In some embodiments, a pattern of backbone chiral centers is or comprises

(Rp)t(Sp)n(Rp)m. In some embodiments, a patern of backbone chiral centers is or comprises

(Rp)t[(Np/Op)n]y(Rp)m. In some embodiments, a pattern of backbone chiral centers is or comprises

(Rp)t[(Sp/Np)n]y(Rp)m. In some embodiments, a pattern of backbone chiral centers is or comprises

(Rp)t[(Sp/Op)n]y(Rp)m. In some embodiments, a pattern of backbone chiral centers is or comprises

(Np/0p)t(Np)n(Np/0p)m. In some embodiments, a pattern of backbone chiral centers is or comprises

(Np/Op)t(Sp)n(Np/Op)m. In some embodiments, a pattern of backbone chiral centers is or comprises

(Np/Op)t[(Np/Op)n]y(Np/Op)m. In some embodiments, a pattern of backbone chiral centers is or comprises (Np/Op)t[(Sp/Op)n]y(Np/Op)m. In some embodiments, a pattern of backbone chiral centers is or comprises (Np/Op)t[(Sp/Op)n]y(Np/Op)m. In some embodimen ts, a pattern of backbone chiral centers is or comprises (Rp/Op)t(Np)n(Rp/Op)m. In some embodiments, a pattern of backbone chiral centers is or comprises (Rp/Op)t(Sp)n(Rp/Op)m. In some embodiments, a pattern of backbone chiral centers is or comprises (Rp/Op)t[(Np/Op)n]y(Rp/Op)m. In some embodiments, a pattern of backbone chiral centers is or comprises (Rp/Op)t[(Sp/Op)n]y(Rp/Op)m. In some embodiments, a pattern of backbone chiral centers is or comprises (Rp)(Rp/Op)t[(Sp/Op)n]y(Rp/Op)m(Rp). In some embodiments, n is 1. For example, in some embodiments, a pattern of backbone chiral centers is or comprises (Sp)t[Op(Sp)m]y; in some embodiments, a pattern of backbone chiral centers is or comprises (Sp)t[Rp(Sp)mjy. In some embodiments, y is 1. In some embodiments, m is 2 or more. In some embodiments, t is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, n is 1, and m is 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, t is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, n is 1, and m is 2, 3, 4, 5, 6, 7, 8, 9, or 10. hi some embodiments, there are at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 intemucleotidic linkages preceding, and there are at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 intemucleotidic linkages after the Rp or Op. In some embodiments, there are at least 2 intemucleotidic linkages preceding and/or following. In some embodiments, there are at least 3 intemucleotidic linkages preceding and/or following. In some embodiments, there are at least 4 intemucleotidic linkages preceding and/or following. In some embodiments, there are at least 5 intemucleotidic linkages preceding and/or following. In some embodiments, there are at least 6 intemucleotidic linkages preceding and/or following. In some embodiments, there are at least 7 intemucleotidic linkages preceding and/or following. In some embodiments, there are at least 8 intemucleotidic linkages preceding and/or following in some embodiments, there are at least 9 intemucleotidic linkages preceding and/or following. In some embodiments, there are at least 10 intemucleotidic linkages preceding and/or following. In some embodiments, y is 1. In some embodiments, y is 2 or more. In some embodiments, y is 2, 3, 4, or 5 In some embodiments, y is 2. In some embodiments, y is 3. In some embodiments, y is 4. In some embodiments, y is 5. In some embodiments, a region having such a pattern of backbone chiral centers contains no 2’-modifications on its sugar moieties, wherein the T -modification is 2’-QR i or T- 0-L-, wherein R 1 is not hydrogen and L comprises a carbon atom and connects to another carbon atom of the sugar moiety. In some embodiments, each sugar moiety of a region having such a pattern of

backbone chiral centers is independently a natural DNA sugar moiety appreciated by a person having ordinar ' skill in the art, for a natural DNA sugar moiety in natural DNA, Cl is connected to a base, C3 and C5 are each independently connected to intemucleotidic linkages or -OH (when at the 5’- or 3’ -end)). Certain benefits/advantages provided by such patterns of backbone chiral centers are described in US 20170037399, WO 2017/015555, and WO 2017/062862.

[00584] In some embodiments, y, t, n and m each are independently 1-20 as described in the present disclosure. In some embodiments, y is 1. In some embodiments, y is at least 2, 3, 4, 5, 6, 7, 8, 9,

10, 11, 12, 13, 14, or 15. hi some embodiments, y is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15. In some embodiments, y is 1, 2, 3, 4, 5, 6, 7. 8, 9, or 10. In some embodiments, y is 1. In some embodiments, y is 2. In some embodiments, y is 3. In some embodiments, y is 4. In some embodiments, y is 5. In some embodiments, y is 6. In some embodiments, y is 7. In some embodiments, y is 8. In some embodiments, y is 9. hi some embodiments, y is 10.

[00585] In some embodiments, n is 1. In some embodiments, n is at least 2, 3, 4, 5, 6, 7, 8, 9, 10,

11, 12, 13, 14, or 15 In some embodiments, n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15. In some embodiments, n is 1-10. In some embodiments, n is 1, 2, 3, 4, 5, 6, 7 or 8. In some embodiments, n is 1. hi some embodiments, n is 2, 3, 4, 5, 6, 7 or 8. hi some embodiments, n is 3, 4, 5, 6, 7 or 8. hi some embodiments, n is 4, 5, 6, 7 or 8. In some embodiments, n is 5, 6, 7 or 8. In some embodiments, n is 6, 7 or 8. In some embodiments, n is 7 or 8. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some embodiments, n is 4. In some embodiments, n is 5. In some embodiments, n is 6. In some embodiments, n is 7. hi some embodiments, n is 8. In some embodiments, n is 9. In some embodiments, n is 10.

[00586] In some embodiments, m is 0-50. In some embodiments, m is 1-50. In some embodiments, m is 1 . In some embodiments, m is 2-50. In some embodiments, m is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15. In some embodiments, rn is 2, 3, 4, 5, 6, 7 or 8. In some embodiments, m is 3, 4, 5, 6, 7 or 8. In some embodiments, m is 4, 5, 6, 7 or 8. In some embodiments, m is 5, 6, 7 or 8. In some embodiments, m is 6, 7 or 8. In some embodiments, m is 7 or 8. In some embodiments, m is 0 In some embodiments, m is 1. In some embodiments, m is 2. In some embodiments, m is 3. In some embodiments, m is 4. In some embodiments, m is 5. In some embodiments, m is 6. In some embodiments, m is 7. In some embodiments, rn is 8. In some embodiments, m is 9. In some embodiments, m is 10. In some embodiments, m is 11. In some embodiments, m is 12. In some embodiments, m is 13. In some embodiments, m is 14. In some embodiments, m is 15. In some embodiments, m is 16. In some embodiments, m is 17. In some embodiments, m is 18. In some embodiments, m is 19. In some embodiments, m is 20. In some embodiments, m is 21. In some embodiments, m is 22. In some embodiments, m is 23. In some embodiments, m is 24. In some embodiments, m is 25. In some embodiments, m is at least 2. In some embodiments, m is at least 3. In some embodiments, m is at least 4. In some embodiments, m is at least 5. In some embodiments, m is at least 6. In some embodiments, m is at least 7. In some embodiments, rn is at least 8. In some embodiments, m is at least 9. In some embodiments, m is at least 10. In some embodiments, m is at least 11. In some embodiments, m is at least 12. In some embodiments, m is at least 13. I some embodiments, m is at least 14 In some embodiments, m is at least 15. In some embodiments, m is at least 16. In some embodiments, m is at least 17. In some embodiments, m is at least 18. In some embodiments, m is at least 19. In some embodiments, m is at least 20. In some embodiments, m is at least 21. In some embodiments, m is at least 22. In some embodiments, is at least 23. In some embodiments, m is at least 24. In some embodiments, m is at least 25. In some embodiments, m is at least greater than 25.

100587 In some embodiments, t is 1-20. In some embodiments, t is 1. In some embodiments, t is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15. In some embodiments, t is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15. In some embodiments, t is 1-5. In some embodiments, t is 2. In some embodiments, t is 3 In some embodiments, t is 4. In some embodiments, t is 5 In some embodiments, t is 6. In some embodiments, t is 7. In some embodiments, t is 8. In some embodiments, t is 9. In some embodiments, t is 10. In some embodiments, t is 11. In some embodiments, t is 12. In some embodiments, t is 13. In some embodiments, t is 14. In some embodiments, t is 15. In some embodiments, t is 16. In some embodiments, t is 17. in some embodiments, t is 18 In some embodiments, t is 19. In some embodiments, t is 20. [00588] In some embodiments, each of t and m is independently at least 2, 3, 4, 5, 6, 7, 8, 9, 10,

11, 12, 13, 14, or 15. In some embodiments, each of t and m is independently at least 3. In some embodiments, each of t and m is independently at least 4. In some embodiments, each of t and m is independently at least 5. In some embodiments, each of t and m is independently at least 6. In some embodiments, each of t and m is independently at least 7. In some embodiments, each of t and m is independently at least 8. In some embodiments, each of t and m is independently at least 9. In some embodiments, each of t and m is independently at least 10.

[00589] In some embodiments, provided oligonucleotides comprises a block, e.g , a first block, a

5’-wing, etc., that has a pattern of backbone chiral centers of or comprising a t-section, e.g., (Sp)t, (Rp)t, (Np/Op)t, (Rp/Op)t, etc., a block, e.g., a second block, a core, etc., that has a pattern of backbone chiral centers of or comprising a y~ or n-section, e.g., (Np)n, (Sp)n, [(Np/Op)n]y, [(Rp/Op)n]y, [(Sp/Op)n]y, etc., and a block, e.g., a third block, a 3’-wing, etc., that has a pattern of backbone chiral centers of or comprising a m-section, e.g., (Sp)m, (Rp)m, (Np/Op)m, (Rp/()p)rn, etc.

[00590] In some embodiments, a t-, y-, n-, or m-section that comprises Np or Rp, e.g., (Rp)t,

(Np/Op)t, (Rp/Op)t, (Np)n, [(Np/Op)n]y, [(Rp/Op)n]y, (Rp)m, (Np/Op)m, (Rp/Op)m, etc. independently comprises at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, or 95%, or 100% Rp In some embodiments, a t- or m-section that comprises Np or Rp independently comprises at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, or 95%, or 100% Rp. In some embodiments, provided oligonucleotides comprise at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%,

90%, or 95%, or 100% Rp. In some embodiments, a percentage is at least 10%. In some embodiments, a percentage is at least 20%. In some embodiments, a percentage is at least 30%. In some embodiments, a percentage is at least 40%. In some embodiments, a percentage is at least 50%. In some embodiments, a percentage is at least 60%. In some embodiments, a percentage is at least 70%. In some embodiments, a percentage is at least 75% In some embodiments, a percentage is at least 80%. In some embodiments, a percentage is at least 85%. In some embodiments, a percentage is at least 90%. In some embodiments, a percentage is at least 95%. In some embodiments, a percentage is 100%.

[00591] In some embodiments, each sugar moiety bonded to a Rp or Op linkage phosphorus at 3’ independently comprises a modification. In some embodiments, each sugar moiety bonded to a Rp or Op linkage phosphorus at 5’ independently comprises a modification. In some embodiments, each sugar moiety bonded to a Rp linkage phosphorus at 3’ independently comprises a modification. In some embodiments, each sugar moiety bonded to a Rp linkage phosphorus at 5’ independently comprises a modification. In some embodiments, each sugar moiety bonded to an Op linkage phosphorus at 3’ independently comprises a modification. In some embodiments, each sugar moiety bonded to an Op linkage phosphorus at 5’ independently comprises a modification. In some embodiments, each sugar moiety bonded to a Sp linkage phosphorus at 3’ independently comprises a modification. In some embodiments, each sugar moiety bonded to a Sp linkage phosphorus at 5’ independently comprises a modification. In some embodiments, each sugar moiety independently comprises a modification. In some embodiments, a modification is a 2’-modification. In some embodiments, a modification is 2’-OR, wherein R is not hydrogen. In some embodiments, a modification is 2’ -OR, wherein R is optionally substituted C )-6 alkyl. In some embodiments, a modification is 2’ -OR, wherein R is substituted C ( _ 6 alkyl. In some embodiments, a modification is 2’ -OR, wherein R is optionally substituted C 2-6 alkyl. In some embodiments, a modification is 2’ -OR, wherein R is substituted C 2-6 alkyl. In some embodiments, R is -CH 2 CH 2 OMe. In some embodiments, a modification is or comprises -L- connecting two sugar carbons, e.g., those found LNA. In some embodiments, a modification is -L- connecting C2 and C4 of a sugar moiety. In some embodiments, L is ( R · ( R(R) . wherein R is as described in the present disclosure. In some embodiments, L is -CH 2 -CH(R)-, wherein R is as described in the present disclosure and is not hydrogen. In some embodiments, L is -CH 2- (i?)-CH(R)-, wherein R is as described in the present disclosure and is not hydrogen hi some embodiments, L is -CH 2--- (5)-CH(R)--, wherein R is as described in the present disclosure and is not hydrogen. In some embodiments, a block, a wing, a core, or an oligonucleotide has sugar modifications as described in the present disclosure.

[00592] In some embodiments, a provided pattern of backbone chiral centers is or comprises

(Rp/Sp)-(A11 Rp or All Sp)-(Rp/Sp), wherein each Rp/Sp is independently Rp or Sp. In some embodiments, a provided pattern of backbone chiral centers is or comprises (Rp)-(All Sp)-(Rp). In some embodiments, a provided pattern of backbone chiral centers is or comprises (Sp)-(All Sp)-(Sp). In some embodiments, a provided pattern of backbone chiral centers is or comprises (Sp)-(All Rp)-(Sp). In some embodiments, a provided pattern of backbone chiral centers is or comprises (Rp/Sp)-(repeating (Sp)m(Rp)n)-(Rp/Sp). In some embodiments, a provided pattern of backbone chiral centers is or comprises (Rp/Sp)-(repeatmg SpSpRp)-(Rp/Sp).

[00593] In some embodiments, provided oligonucleotides comprise one or more blocks, characterized by base modifications, sugar modifications, types of intemudeotidic linkages, stereochemistry of linkage phosphorus, etc. In some embodiments, provided oligonucleotides comprises or are of a 5’-first block-second block-third block-3’ structure. In some embodiments, a first block is a 5’ -wing. In some embodiments, a first block is 5’ -end region. In some embodiments, a second block is a core. In some embodiments, a second block is a middle region between a 5’-end and a 3’-end region. In some embodiments, a third block a 3’-wing. In some embodiments, a third block is a 3’-end region. Each of a 5’-wing, 5’-end region, core, middle region, 3’-wing, and 3’-end region can independently be a block.

[00594] In some embodiments, provided oligonucleotides comprises or are of a 5’-wing-core- wing-3’, 5’-wing-core-3’ or 5’-core-w g~3’ structures. In some embodiments, a first block, a second block, a third block, a wing (e.g., a 5’ -wing, a 3’ -wing) and/or a core of provided oligonucleotides are each independently a block or comprise one or more blocks as described in the present disclosure.

[00595] Various blocks, 5’-wings, 3’ -wings and cores can be utilized in accordance with the present disclosure, including those described in US 20150211006, US 2015021 1006, WO 2017015555, WO 2017015575, WO 2017062862, WO 2017160741, blocks, 5’-wings, 3’ -wings and cores of each of which are incorporated herein by reference.

[00596] In some embodiments, a block is a linkage phosphorus stereochemistry block. For example, in some embodiments, a block comprises only Rp, Sp, or Op linkage phosphorus. In some embodiments, a block is a Rp block comprising only Rp linkage phosphorus. In some embodiments, a block is a Rp/Op block comprising only Rp/Op linkage phosphorus. In some embodiments, a block is a Sp/Qp block comprising only Sp/Qp linkage phosphorus hi some embodiments, a block is an Op block. In some embodiments, an oligonucleotide, or a region thereof (a first block, a second block, a third block, a wing, a core, etc.) comprises one or more of a Rp block, a Sp block and/or an Op block. In some embodiments, a block comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more, linkage phosphorus.

[00597] In some embodiments, a block is a sugar modification block. In some embodiments, a block is a 2’ -modification block wherein each sugar moiety of the block independently comprises the 2’- modification. In some embodiments, a 2’ -modification is 2’ -OR wherein R is as described in the present disclosure. In some embodiments, a 2’-modification is a 2’-OR wherein R is not hydrogen. In some embodiments, a 2’-modification is 2’~QMe. In some embodiments, a 2’-modification is 2’~MQE. In some embodiments, a modification is a LNA modification. In some embodiments, an oligonucleotide, or a region thereof (a first block, a second block, a third block, a wing, a core, etc.) comprises one or more sugar modification blocks, each independently of its own sugar modification. In some embodiments, a block comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more, sugar moieties.

100598] As illustrated herein, a block can be of various lengths. In some embodiments, a block is of 1-30, e.g, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleobases in length hi some embodiments, a 5’-first block-second-block-third block-3’, or a 5’-wing-core-wing-3' is of 5-10-5, 3-10-4, 3-10-6, 4-12-4, etc

100599] In some embodiments, an oligonucleotide or a block or region thereof (e.g, a 5’-end region, a 5’-wing, a middle region, a core region, a 3’-end region, a 3’-ring, etc.) comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more, non-negatively charged intemucieotidie linkages as described in the present disclosure. In some embodiments, a provided oligonucleotide comprises two or more, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more, consecutive non-negatively charged mtemucleotidic linkages. In some embodiments, a block or region comprises two or more, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more, consecutive non-negatively charged mtemucleotidic linkages. In some embodiments, the number is 1. In some embodiments, the number is 2. In some embodiments, the number is 3. In some embodiments, the number is 4. In some embodiments, the number is 5. In some embodiments, the number is 6. In some embodiments, the number is 7. In some embodiments, die number is 8. In some embodiments, the number is 9. In some embodiments, the number is 10 or more. In some embodiments, each mtemucleotidic linkage between nucleoside units in a block, e.g., a 5’-end region, a 5’ -wing, is a non- negatively charged mtemucleotidic linkage except the first mtemucleotidic linkage between two nucleoside units of the block from the 5’-end of the block. In some embodiments, each mtemucleotidic linkage between nucleoside units in a block, e.g., a 3 -end region, a 3’-wing, is a non-negatively charged mtemucleotidic linkage except the first mtemucleotidic linkage between two nucleoside units of the block from the 3’-end of the block. In some embodiments, each mtemucleotidic linkage between nucleoside units in a region, e.g., a 5’-end region, a 5’-wing, is a non-negatively charged mtemucleotidic linkage except the first mtemucleotidic linkage between two nucleoside units of the region from the 5’-end of the region. In some embodiments, each mtemucleotidic linkage between nucleoside units in a region, e.g., a 3’-end region, a 3’-wing, is a non-negatively charged mtemucleotidic linkage except the first mtemucleotidic linkage between two nucleoside units of the region from the 3’-end of the region. In some embodiments, each mtemucleotidic linkage in a region or block, e.g., a 5’ -end region, a 5’-wing, a middle region, a core region, a 3’-end region, a 3’-ring, etc., is independently a non-negatively charged intemucieotidie linkage, a natural phosphate mtemucleotidic linkage or a Rp chiral mtemucleotidic linkage. In some embodiments, each intemucieotidie linkage in a region or block is independently a non- negatively charged intemucieotidie linkage, a natural phosphate intemucieotidie linkage or a Rp phosphorothioate intemucieotidie linkage. In some embodiments, about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more of intemucieotidie linkages of an oligonucleotide or a region or block, e.g., a 5’-end region, a 5’-wing, a middle region, a core region, a 3’-end region, a 3’-ring, etc., is independently a non-negatively charged mtemucleotidic linkage, a natural phosphate intemucieotidie linkage or a Rp chiral intemucieotidie linkage. In some embodiments, about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more of intemucieotidie linkages of an oligonucleotide or a region or block is independently a non-negatively charged intemucieotidie linkage, a natural phosphate intemucieotidie linkage or a Rp phosphorothioate intemucieotidie linkage. In some embodiments, about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more of intemucleotidic linkages of an oligonucleotide or a region or block is independently a non-negatively charged intemucleotidic linkage or a natural phosphate intemucleotidic linkage. In some embodiments, about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more of intemucleotidic linkages of an oligonucleotide or a region or block is independently a non-negatively charged intemucleotidic linkage. In some embodiments, the percentage is 45% or more. In some embodiments, the percentage is 50% or more. In some embodiments, the percentage is 60% or more. In some embodiments, the percentage is 70% or more. In some embodiments, the percentage is 80% or more. In some embodiments, the percentage is 90% or more. In some embodiments, a region or block is a wing. In some embodiments, a region or block is a 5’ -wing. In some embodiments, a region or block is a 3’- wing. In some embodiments, a region or block is a core. As described herein, a region or block, e.g., a wing, a core, etc., can have various lengths, e.g., comprising 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nudeobases. In some embodiments, each nucleobase is independently optionally substituted A, T, C, G, U or an optionally substituted tautomer of A, T, C, G, or U.

Length

[00600] As described in the present disclosure, provided oligonucleotides can be of various lengths, e.g., 2-200, 10-15, 10-25, 15-20, 15-25, 15-40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 60, 70, 80, 90, 100, 150, nudeobases in length, wherein each nucleobase is independently optionally substituted A, T, C, G, or U, or an optionally substituted tautomer of A, T, C, G, or U. In some embodiments, provided oligonucleotides, e.g., oligonucleotide of a plurality in chirally controlled oligonucleotide compositions, are 15 nudeobases in length. In some embodiments, provided oligonucleotides are 16 nudeobases in length. In some embodiments, provided oligonucleotides are 17 nudeobases in length. In some embodiments, provided oligonucleotides are 18 nudeobases m length. In some embodiments, provided oligonucleotides are 19 nudeobases in length. In some embodiments, provided oligonucleotides are 20 nudeobases in length hi some embodiments, provided oligonucleotides are 21 nudeobases in length. In some embodiments, provided oligonucleotides are 22 nudeobases in length. In some embodiments, provided oligonucleotides are 23 nudeobases in length. In some embodiments, provided oligonucleotides are 24 nudeobases in length. In some embodiments, provided oligonucleotides are 25 nudeobases in length.

[00601] As described in the present disclosure, provided oligonucleotides, oligonucleotides of a plurality in chirally controlled oligonucleotide compositions, may comprise various modifications, e.g., base modifications, sugar modifications, intemucleotidic linkage modifications, etc. In some embodiments, the oligonucleotide composition comprises at least one modified nucleotide, at least one modified sugar moiety, at least one morpho!ino moiety, at least one 2'-deoxy ribonucleotide, at least one locked nucleotide, and/or at least one bicyclic nucleotide.

Nucleobases

[00602] In some embodiments, a nucleobase is a natural nucleobase. In some embodiments, a nucleobase is a modified nucleobase (non-natural nucleobase). In some embodiments, a nucleobase, e.g., BA, in provided oligonucleotides is a natural nucleobase (e.g., adenine, cytosine, guanosine, thymine, or uracil) or a modified nucleobase derived from a natural nucleobase, e.g., optionally substituted adenine, cytosine, guanosine, thymine, or uracil, or tautomeric forms thereof. Examples include, but are not limited to, uracil, thymine, adenine, cytosine, and guanine, and tautomeric forms thereof, having their respective amino groups protected by protecting groups, e.g, one or more of -R, ~C(0)R, etc. Example protecting groups, including those useful for oligonucleotide synthesis, are widely known in the art and can be utilized in accordance with the present disclosure. In some embodiments, a protected nucleobase and/or derivative is selected from nucleobases with one or more acyl protecting groups, 2-fIuorouracii, 2- fluorocytosine, 5-bromouracil, 5-iodouracil, 2,6-diaminopurine, azacytosine, pyrimidine analogs such as pseudoisocytosine and pseudouracil and other modified nucleobases such as 8-substituted purines, xanthine, or hypoxanthme (the latter two being the natural degradation products). Example modified nucleobases are also disclosed in Chiu and Ranu. RNA, 2003, 9, 1034-1048, Limbach et al Nucleic Acids Research, 1994, 22, 2183-2196 and Revankar and Rao, Comprehensive Natural Products Chemistry, vol. 7, 313. In some embodiments, a modified nucleobase is substituted uracil, thymine, adenine, cydosine, or guanine. In some embodiments, a modified nucleobase is a functional replacement, e.g., in terms of hydrogen bonding and/or base pairing, of uracil, thymine, adenine, cytosine, or guanine in some embodiments, a nucleobase is optionally substituted uracil, thymine, adenine, cytosine, 5-methy!cyiosine, or guanine. In some embodiments, a nucleobase is uracil, thymine, adenine, cytosine, 5-methylcytosine, or guanine.

[00603] In some embodiments, a modified base is optionally substituted adenine, cytosine, guanine, thymine, or uracil. In some embodiments, a modified nucleobase is independently adenine, cytosine, guanine, thymine or uracil, modified by one or more modifications by which:

(1) a nucleobase is modified by one or more optionally substituted groups independently selected from acyl, halogen, ammo, azide, alkyl, alkenyl, alkynyl, aryl, heteroalkyl, heteroalkenyl, heteroalkynyl, heterocyclyl, heteroaryl, carboxyl, hydroxyl, biotin, avidin, streptavidin, substituted silyi, and combinations thereof;

(2) one or more atoms of a nucleobase are independently replaced with a different atom selected from carbon, nitrogen or sulfur;

(3) one or more double bonds in a nudeobase are independently hydrogenated; or

(4) one or more optionally substituted ary] or heteroary! rings are independently inserted into a nudeobase.

[00604] Modified nucleobases also include expanded-size nucleobases in which one or more aryl rings, such as phenyl rings, have been added. Nucleic base replacements described in the Glen Research catalog (available at the Glen Research website); Krueger AT et al, Acc. Chern. Res. , 2007, 40, 141 -150; Kool, ET, Acc. Chem. Res., 2002, 35, 936-943; Benner S.A., et al., Nat. Rev. Genet., 2005, 6, 553-543; Romesberg, F.E., el al. , Gurr. Opin. Chern. Biol., 2003, 7, 723-733; Hirao, I., Curr. Opin. Chem. Biol., 2006, 10, 622-627, are contemplated as useful for oligonucleotides of the present disclosure.

[00605] In some embodiments, modified nucleobases include structures such as, but not limited to, corrin- or porphyrin-derived rings. Porphyrin-derived base replacements have been described in Morales-Rojas, H and Kool, ET, Org. Lett., 2002, 4, 4377-4380. Shown below is an example of a porphyrin-derived ring which can be used as a nudeobase replacement:

[00606] In some embodiments, a modified nudeobase is fluorescent. Examples of such fluorescent modified nucleobases include phenanthrene, pyrene, sti!lbene, isoxanthine, isozanthopterin, terphenyl, terthiophene, benzoterthiophene, coumarin, lumazine, tethered stillbene, benzo-uracil, and naphtho-uracil.

[00607] In some embodiments, a modified nudeobase is a universal base or a degenerate base, e.g., 3-nitropyrrole, 5’-mtroindole, P, K, etc

[00608] In some embodiments, other nucleosides can also be used in technologies disclosed in the present disclosure and include nucleosides that incorporate modified nucleobases, or nucleobases covalently bound to modified sugars. Some examples of nucleosides that incorporate modified nucleobases include 4-acetylcytidine; 5-(carboxyhydroxylmethyl)uridine; 2 ' -G-metliylcjtidine; 5- carboxymethylaminomethyl-2-thiouridine; 5-carboxymethylaminomethyluridine; dihydrouridine; 2 ' -O- methylpseudouridine; beta,D-galactosylqueosine; 2 ' -O-methylguanosine; A^-isopentenyladenosine; 1- methyladenosine; 1-methylpseudouridine; 1-methylguanosine; 1-methylinosine; 2,2-dimethylguanosine; 2-methyladenosine; 2-methylguanosine; L''-methylguanosine: 3-methyl-cytidine; 5-methyicytidine; 5- hydroxymethyicytidine; 5-formylcytosine; 5-carboxy'lcytosine; A' 6 -methyladenosine; 7-methylguanosine; 5-methylaminoethyluridine; 5-methoxyaminomethyl-2-thiouridine; beta,D-mannosylqueosine; 5- methoxycarbonylmethyluridine; 5 -methoxy uridine; 2-methylthio-V°-isopentenyladenosine; iV-((9-beta,D- ribofuranosyl-2-methylthiopurine-6-yl)carbamoyl)threonine; A r -((9-beta,D-ribofuranosylpurine-6-yl)-A r - methylcarbamoyi)threonine; uridine-5 -oxyacetic acid methylester; uridine-5 -oxyacetie acid (v); pseudouridine; queosine; 2-thiocytidine; 5-methyl-2-thiouridine; 2-thiouridine; 4-thiouridine; 5- methyluridine; 2’ -O-methyl-5-methyluridine; and 2’ -Omethyluridine.

[00609] In some embodiments, a nucieobase is optionally substituted A, T, C, G or U, wherein one or more ~ NH 2 are independently and optionally replaced with ---C(---L---R 1 ) 3, one or more -NH- are independently and optionally replaced with -C(-L-R 1 ) 2 -, one or more =N- are independently and optionally replaced with -C(-L-R 1 )-, one or more =CH- are independently and optionally replaced with =N-, and one or more =0 are independently and optionally replaced with =S, =N(-L-R 1 ), or

=C(-L-R 1 ) 2 , wherein two or more -L-R 1 are optionally taken together with their intervening atoms to form a 3-30 membered bicyclic or polycyclic ring having 0-10 heteroatom ring atoms. In some embodiments, a modified nucieobase is optionally substituted A, T, C, G or U, wherein one or more — NH 2 are independently and optionally replaced with -C(-L-R ] ) 3 , one or more -NH- are independently and optionally replaced with -CC-L-R 1 ^-, one or more =N- are independently and optionally replaced with -CX-L-R 1 )-, one or more ( 1 1 are independently and optionally replaced with =N-, and one or more =0 are independently and optionally replaced with =S, =N(-L-R i ), or =C(-L-R 1 ) 2 , wherein two or more -L-R 1 are optionally taken together with their intervening atoms to form a 3-30 membered bicyclic or polycyclic ring having 0-10 heteroatom ring atoms, wherein the modified base is different than the natural A, T, C, G and U. In some embodiments, a nucieobase is optionally substituted A, T, C, G or U. In some embodiments, a modified base is substituted A, T, C, G or U, wherein the modified base is different than the natural A, T, C, G and U.

[00610] In some embodiments, a modified nucieobase may be optionally substituted. In some embodiments, a modified nucieobase contains one or more, e.g. , heteroatoms, alkyl groups, or linking moieties connected to fluorescent moieties, biotin or avidin moieties, or other proteins or peptides. In some embodiments, a nucieobase or modified nucieobase comprises or is conjugated with one or more biomolecule binding moieties such as e.g., antibodies, antibody fragments, biotin, avidin, streptavidin, receptor ligands, or chelating moieties. In some embodiments, a modified nucieobase is modified by substitution with a fluorescent or biomolecuie binding moiety. In some embodiments, a substituent on a nucieobase or modified nucieobase is a fluorescent moiety. In some embodiments, a substituent on a nucleobase or modified nucieobase is biotin or avidin.

[00611] Example nucieobases are also described in US 20110294124, US 20120316224, US

20140194610, US 2015021 1006, US 20150197540, WO 2015107425, WO/2017/015555,

WO/2017/015575, and WO/2017/062862, the nucieobases of each of which is incorporated herein by- reference.

[00612] In some embodiments, oligonucleotides comprise one or more modified sugar moieties beside the natural sugar moieties. In some embodiments, a sugar is a natural sugar. In some embodiments, a sugar is a modified sugar (non-natural sugar). The most common naturally occurring nucleotides are comprised of ribose sugars linked to the nucieobases adenosine (A), cytosine (C), guanine (G), and thymine (T) or uracil (U). Also included in the present disclosure are modified nucleotides wherein an internucleotidic linkage is linked to various positions of a sugar or modified sugar. As non- limiting examples, an internucleotidic linkage can be linked to the 2 ' , 3 , 4 ' or 5 position of a sugar.

1006131 In some embodiments, a sugar nioietv wherein each variable is independently as described in the present disclosure. In some embodiments, a sugar moiety is wherein L s is ( ' ( R ') , wherein each R 's is independently as described in the present

disclosure. hr some embodiments, a sugar moiety has tin structure wherein each variable is independently as described in the present disclosure. In some embodiments, a sugar moiety has the structure wherein each variable is independently as described in the present disclosure.

, wherein each variable is independently as described in the present disclosure. In some embodiments, i nucleoside has the structure of

wherein each variable is independently as described in the present disclosure. In some embodiments, a nucleoside moiety has or comprises the structure wherein each variable is independently as described in the present disclosure. In some embodiments, L s is -CH(R)-, wherein R is as described in the present disclosure. In some embodiments, R is -H. In some embodiments, R is not -H, and 12 is -(R)-CH(R)-. In some embodiments, R is not -H, and L s is -(S)-CH(R)-. In some embodiments, R, as described in the present disclosure, is optionally substituted C ]-6 alkyl. In some embodiments, R is methyl.

00614] Various types of sugar modifications are known and can be utilized m accordance with the present disclosure. In some embodiments, a sugar modification is a 2’-modification (e.g R" ( e.g in

In some embodiments, a 2’-modification is 2’-F. In some embodiments, a 2’- modification is 2’ -OR, wherein R is not hydrogen. In some embodiments, a 2’ -modification is 2’ -OR, wherein R is optionally substituted Ci -6 aliphatic. In some embodiments, a 2’-modification is 2’ -OR, wherein R is optionally substituted Ci -6 alkyl. In some embodiments, a 2’-modification is 2’-OMe. In some embodiments, a T -modification is 2’-MOE. In some embodiments, a 2’-modification is a LNA sugar modification (C2-0-CH 2- C4). In some embodiments, a 2’-modification is (C2-0-C(R) 2- C4), wherein each R is independently as described in the present disclosure. In some embodiments, a T- modifieation is (C2-0-CHR-C4), wherein R is as described in the present disclosure. In some embodiments, a 2’-modification is (C2-0-(i?)-CHR-C4), wherein R is as described in the present disclosure and is not hydrogen. In some embodiments, a 2’~modification is (C2-0-(S)-CHR-C4), wherein is as described in the present disclosure and is not hydrogen. In some embodiments, R is optionally substituted Ci 6 aliphatic. In some embodiments, R is optionally substituted Ci- 5 alkyl. In some embodiments, R is unsubstituted C j-6 alkyl. In some embodiments, R is methyl. In some embodiments, R is ethyl. In some embodiments, a 2’~modification is (C2-0-CHR-C4), wherein R is optionally substituted C ]-6 aliphatic. In some embodiments, a 2’-modification is (C2-0-CHR-C4), wherein R is optionally substituted Ci_ 6 alkyl. In some embodiments, a 2’-modification is (C2-0-CHR-C4), wherein R is methyl. In some embodiments, a 2’-modification is (C2-0-CHR-C4), wherein R is ethyl. In some embodiments, a 2’-modification is (C2-O--(R)-CHR-C4), wherein R is optionally substituted C [-6 aliphatic. In some embodiments, a 2’-modification is (C2-0-(i?)-CHR-C4), wherein R is optionally substituted C j,.6 alkyl. In some embodiments, a 2’-modification is (C2-0~(/?)- CHR-C4), wherein R is methyl. In some embodiments, a 2’-modification is (C2-0-(R)-CHR-C4), wherein R is ethyl. In some embodiments, a 2’-modification is (C2-0-(5)-CHR-C4), wherein R is optionally substituted C._ 6 aliphatic. In some embodiments, a 2’-modification is (C2-0-(.S)-CHR-C4), wherein R is optionally substituted C s 6 alkyl. In some embodiments, a 2’-modification is (C2 0 (5)- CHR-C4), wherein R is methyl. In some embodiments, a 2’-modification is (C2-0-(5)-CHR-C4), wherein R is ethyl. In some embodiments, a 2’-modification is C2-0-(i?)-CH(CH 2 CH 3 )-C4. In some embodiments, a T -modification is C2-0-(5)-CH(CH 2 CH 3 )-C4. In some embodiments, a sugar moiety is a natural DNA sugar moiety. In some embodiments, a sugar moiety is a natural DNA sugar moiety modified at 2’ (2’-modification). In some embodiments, a sugar moiety is an optionally substituted natural DNA sugar moiety. In some embodiments, a sugar moiety is an 2’-substituted natural DNA sugar moiety.

[00615] Many modified sugars can be incorporated within oligonucleotides of the present disclosure. In some embodiments, a modified sugar contains one or more substituents at the 2 ' position including one of the following: -F; -CF 3 , -CN, -N 3 , -NO, -NO , -OR’, -SR’, or -N(R’) 2 , wherein each R’ is independently as described in the present disclosure; -O-tC j- C o alkyl), -S-(Ci-Ci 0 alkyl), -NH- (Ci-Cio alkyl), or -N(C r-- Ci 0 alkyl) 2 ; -O-(C 2- Ci 0 alkenyl), -S-(C 2- Ci 0 alkenyl), -NH-(C 2 -C I0 alkenyl), or -N(C 2~ C IO alkenyl) ? ; -O-(C 2 -Ci 0 alkynyl), -S-(C 2- C 0 alkynyl), -NH-(C 2 -C 0 alkynyl), or -N(C 2- C o alkynyl) 2 ; or -O— (C— C ]0 alkylene)-0— (C -C. 0 alkyl), -O-(Ci-Ci 0 alkylene)-NH-(C ] -C l0 alkyl) or -0-(Ci-Cio alkylene)-NH(Ci-C ]0 alkyi) 2 , M l (C = C,, alkyleneMMCi-Cu, alkyl), or N(C = C,, alkyl) --(Ci-C o alkylene)-0-(Ci-Cio alkyl), wherein the alkyl, alkylene, alkenyl and alkynyl may be substituted or unsubstituted. Examples of substituents include, and are not limited to, -0(CH 2 ) n 0CH 3 , and -0(CH 2 )„NH 2 , wherein n is from 1 to about 10, MOE, DMAOE, and DMAEOE. Certain modified sugars are described in WO 2001/088198, WO/2017/062862, and Martin et al Helv. Chim. Acta , 1995, 78, 486-504. In some embodiments, a modified sugar comprises one or more groups selected from a substituted silyl group, an RNA cleaving group, a reporter group, a fluorescent label, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, a group for improving the phannacodynamic properties of an oligonucleotide, or other substituents having similar properties. In some embodiments, modifications are made at one or more of the the 2 ' , 3 1 , 4 ' , 5 ' , or 6 ' positions of a sugar, including the 3 ' position of a sugar on the 3 ' -terminal nucleoside or in the 5 ' position of the 5 ' -terminal nucleoside. In some embodiments, a RNA comprises a sugar which has, at the 2 ! position, a 2'-OH, or 2'-OR 1 , wherein OR is optionally substituted alkyl, including 2’-OMe.

[00616] In some embodiments, a 2'-modification is 2'-F.

[00617] In some embodiments, the 2’-OH of a ribose is replaced with a substituent (c.g . R 1 including one of the following: -H, -F; -CF 3 , -CN, -N 3 , -NO, -N0 2 , -OR’, -SR’, or -N(R’) 2 , wherein each R’ is independently as defined above and described herein; -0-(C r-- Cio alkyl),— S— (Ci— C i0 alkyl), - NH-(Ci-Cio alkyl), or Nit = (A, alky 1 ) ·: -O-(C 2- C [0 alkenyl), -S-(C 2- C 10 alkenyl), -NH-(C 2- C 10 alkenyl), or -N(C -Cio alkenyl) ? .; -0-(C 2- Cio alkynyl), -S-(C 2- Cio alkynyl), -NH-(C 2 -C ]0 alkynyl), or - N(C 2 -C IO alkynyl) 2 ; or -O— (Ci-Cio alkylene)-0— (Ci-Cio alkyl), -O-(Ci-Ci 0 alkylene)-NH-(Ci-Cio alkyl) or -O-(C I --C L0 alkylene)-NH(C -Cio alkyl) 2 , -NH-(Ci-Cio alkylene)-0-(Ci-Cio alkyl), or -N(C r- C;o alkyl)-(Cr--Cio alkyiene)-0-(Cr-Cio alkyl), wherein the alkyl, alkylene, alkenyl and alkynyl may be substituted or unsubstituted. In some embodiments, the 2’-OH is replaced with -H (deoxyribose). In some embodiments, the 2’-OH is replaced with -F. In some embodiments, the 2 , -OH is replaced with - OR . In some embodiments, the 2’-OH is replaced with -OMe. In some embodiments, the 2’-OH is replaced with -OCH 2 CH 2 OMe.

[00618] In some embodiments, a modified sugars is a sugar in locked nucleic acids (LNAs). In some embodiments, two substituents on sugar carbon atoms are taken together to form a bivalent moiety. In some embodiments, two substituents are on two different sugar carbon atoms. In some embodiments, a formed bivalent moiety has the structure of -L- as defined herein. In some embodiments, -L- is — Q— CH 2— , wherein -CH 2 - is optionally substituted. In some embodiments, -L- is -0-CH 2 -. In some embodiments, -L- is -0-CH(Me)-. In some embodiments, -L- is -0-CH(Et)-. In some embodiments, -L- is between C2 and C4 of a sugar moiety. In some embodiments, a locked nucleic acid sugar has the structure indicated below, wherein R 2s is -OCH 2 C4’-:

[00619] In some embodiments, a modified sugar is an ENA sugar or modified ENA sugar such as those described in, e.g.. Seth et al., I Am Chem Soc. 2010 October 27; 132(42): 14942-14950. In some embodiments, a modified sugar is any of those found in an XNA (xenonucleic acid), for instance, arabinose, anliydrohexitol, threose, 2 , fluoroarabinose, or cyclohexene.

[00620] In some embodiments, a modified sugar is one described in WO 2017/062862.

[00621] In some embodiments, modified sugars are sugar mimetics such as cyclobutyl or cyclopentyl moieties in place of pentofuranosyl. Representative United States patents that teach preparation of such modified sugar structures include, but are not limited to, US Patent Nos.: 4,981,957; 5,118,800; 5,319,080; and 5,359,044. In some embodiments, modified sugars are sugars in which the oxygen atom within the rihose ring is replaced by nitrogen, sulfur, selenium, or carbon. In some embodiments, a modified sugar is a modified ribose wherein the oxygen atom within the ribose ring is replaced with nitrogen, and wherein the nitrogen is optionally substituted with an alkyl group (e.g., methyl, ethyl, isopropyl, etc).

[00622] Non-limiting examples of modified sugars include glycerol, which form glycerol nucleic acid (GNA) analogues. In some embodiments, an GNA analogue is described in Zhang, R et al. , J. Am. Chem. Soc. , 2008, 130, 5846-5847; Zhang L, et al., J. Am. Chem. Soc. , 2005, 127, 4174-4175 and Tsai CH ci a!.. PNAS, 2007, 14598-14603

00623 In some embodiments, another example of a GNA derived analogue, flexible nucleic acid based on the mixed acetal aminal of formyl glycerol, is described in Joyce GF et al., PNAS, 1987,

84, 4398-4402 and Heuberger BD and Switzer C, J Am. Chem. Soc., 2008, 130, 412-413.

[00624] Additional non-limiting examples of modified sugars include hexopyranosyl (6’ to 4’), pentopyranosyl (4’ to 2’), pentopyranosyl (4’ to 3’), or tetrofuranosyl (3’ to 2’) sugars.

[00625] In some embodiments, one or more hydroxyl group in a sugar moiety is optionally and independently replaced with halogen, R’ -N(R’) 2 , -OR’, or -SR’, wherein each R’ is independently as defined above and described herein.

In some embodiments, at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%,

31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%,

49%, 50% or more (e.g, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more), inclusive, of the sugars in an oligonucleotide, e.g., a chirally controlled oligonucleotide, an oligonucleotide of a plurality of oligonucleotide of an oligonucleotide composition, etc. are modified. In some embodiments, sugars of purine nucleosides and in some embodiments, only purine nucleosides, are modified (e.g., about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31 %, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50% or more [e.g., 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more] of the purine nucleosides are modified). In some embodiments, sugars of pyrimidine nucleosides and in some embodiments, only pyrimidine nucleosides, are modified (e.g., about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%,

21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%,

39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50% or more [e.g.. 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more] of the pyrimidine nucleosides are modified). In some embodiments, both purine and pyrimidine nucleosides are modified.

100627 In some embodiments, modified sugars include those described in: A. Eschenmoser,

Science (1999), 284:2118; M. Bohringer et al. f ieri ( ' him. Acta (1992), 75 : 1416- 1477; M. Egli et al, J. Am. Chem. Soe. (2006), 128(33): 10847-56; A. Eschenmoser in Chemical Synthesis: Gnosis to Prognosis, C. Chatgilialoglu and V. Sniekus, Ed., (Kluwer Academic, Netherlands, 1996), p 293; K.-U. Schoning et al, Science (2000), 290: 1347-1351 ; A. Eschenmoser et al, Helv. ( him. Acta (1992), 75:218; J. Hunziker et al, Helv. Chim. Acta ( 1993), 76:259; G. Otting et al, Helv. Chim. Acta (1993), 76:2701; K. Groebke et al Helv. Chim. Acta (1998), 81:375; and A. Eschenmoser, Science (1999), 284:2118. Modifications to the 2' modifications can be found in Verma, S. et al. Annu. Rev. Biochem. 1998, 67, 99-134 and all references therein. In some embodiments, a modified sugar is one described in W02012/030683. In some embodiments, a modified sugar is any modified sugar described in any of: Gryaznov, S; Chen, J.-K. J. Am. Chem. Soc. 1994, 116, 3143; Hendrix et al. 1997 Chem. Eur. J. 3: 110; Hyrup et al. 1996 Bioorg. Med. Chem. 4: 5; Jepsen et al. 2004 Oligo. 14: 130-146; Jones et al. J. Org. Chem. 1993, 58, 2983; Koizumi et al. 2003 Nuc. Acids Res. 12: 3267-3273; Koshkin et al. 1998 Tetrahedron 54: 3607-3630; Kumar et al. 1998 Bioo. Med Chem. Let. 8: 2219-2222; Lauritsen et al. 2002 Chem. Comm 5: 530-531 ; Lauritsen et al. 2003 Bioo. Med. Chem. Lett. 13: 253-256; Mesmaeker et al. Angew. Chem., Int. Ed. Engl. 1994, 33, 226; Morita et al. 2001 Nucl. Acids Res. Supp. 1: 241-242; Morita et al. 2002 Bioo. Med. Chem. Lett. 12: 73-76; Morita et al. 2003 Bioo. Med. Chem. Lett. 2211-2226; Nielsen et al. 1997 Chem. Soc. Rev 73; Nielsen et al. 1997 J Chem. Soc. Perkins Transl. 1: 3423-3433; Obika et al. 1997 Tetrahedron Lett. 38 (50): 8735-8; Obika et al. 1998 Tetrahedron Lett. 39: 5401-5404; Pallan et al. 2012 Chem. Comm. 48: 8195-8197; Petersen et al. 2003 TRENDS Biotech. 21: 74-81; Rajwanshi et al. 1999 Chem. Com un. 1395-1396; Schultz et al. 1996 Nucleic Acids Res. 24: 2966; Seth et al. 2009 J. Med. Chem 52: 10-13; Seth et al. 2010 J. Med Chem. 53: 8309-8318; Seth et al. 2010 J. Org. Chem 75: 1569- 1581; Seth et al. 2012 Bioo. Med. Chem. Lett. 22: 296-299; Seth et al. 2012 Mol. Ther-Nuc. Acids. 1, e47; Seth, Punit P; Siwkowski, Andrew; Allerson, Charles R; Vasquez, Guillermo; Lee, Sam; Prakash, Thazha P; Kinberger, Garth; Migawa, Michael T; Gaus, Hans; Bhat, Ba!krishen; et al. From Nucleic Acids Symposium Series (2008), 52(1 ), 553-554; Singh et al 1998 Chem. Comm. 1247-1248; Singh et al. 1998 J. Org. Chem. 63: 10035-39; Singh et al. 1998 J. Org. Chem. 63: 6078-6079; Sorensen 2003 Chem. Comm. 2130-2131; Ts'o et al. Ann N. Y. Acad. Sci. 1988, 507, 220; Van Aerschot et al. 1995 Angew. Chem. Int. Ed. Engl. 34: 1338; Vasseur et al. J. Am. Chem. Soc. 1992, 114, 4006; WO 20070900071; WO 20070900071; or WO 2016/079181.

[00628] In some embodiments, a modified sugar moiety is an optionally substituted pentose or hexose moiety. In some embodiments, a modified sugar moiety is an optionally substituted pentose moiety. In some embodiments, a modified sugar moiety is an optionally substituted hexose moiety. In some embodiments, a modified sugar moiety is an optionally substituted ribose or hexitol moiety. In some embodiments, a modified sugar moiety is an optionally substituted ribose moiety. In some embodiments, a modified sugar moiety is an optionally substituted hexitol moiety.

[00629] In some embodiments, a sugar is D-2-deoxynbose. In some embodiments, a sugar is beta-D-deoxyribofuranose. In some embodiments, a sugar moiety is a beta-D-deoxyribofuranose moiety. In some embodiments, a sugar is D-ribose In some embodiments, a sugar is beta-D-ribofuranose. In some embodiments, a sugar moiety is a beta-D-ribofuranose moiety. In some embodiments, a sugar is optionally substituted beta-D-deoxyribofuranose or beta-D-ribofuranose. In some embodiments, a sugar moiety is an optionally substituted beta-D-deoxyribofuranose or beta-D-ribofuranose moiety. In some embodiments, a sugar moiety/unit in an oligonucleotide, nucleic acid, etc. is a sugar which comprises one or more carbon atoms each independently connected to an intemucleotidic linkage, e.g., optionally substituted beta-D-deoxyribofuranose or beta-D-ribofuranose whose 5’-C and/or 3’-C are each independently connected to an intemucleotidic linkage (e.g., a natural phosphate linkage, a modified intemucleotidic linkage, a chirally controlled intemucleotidic linkage, etc.).

[00630] In some embodiments, each nucleoside of a provided oligonucleotide comprises a 2’~0~ methoxyethyl sugar modification.

[00631] In some embodiments, the oligonucleotide composition comprises at least one locked nucleic acid (LNA) nucleotide. In some embodiments, the oligonucleotide composition comprises at least one modified nucleotide comprising a modified sugar moiety which is modified at the 2'-position.

100632 In some embodiments, the oligonucleotide composition comprises modified sugar moiety which comprises a 2 -substituent selected from the group consisting of: H, OR, R, halogen, SH, SR, NH 2 , NHR, NR 2 , and ON, wherein R is an optionally substituted C j -C 6 alkyl, alkenyl, or alkynyi and halogen is F, Cl, Br or I.

100633 In some embodiments, a modified nucleobase, sugar, nucleoside, nucleotide, and/or modified intemucleotidic linkage is selected from those described in Ts’o et al. Ann. N. Y. Acad. Sci. 1988, 507, 220; Gryaznov, S ; Chen, J.-K. J. Am. Chem. Soc. 1994, 116, 3143; Mesmaeker et al. Angew. Chem., Int. Ed. Engl . 1994, 33, 226; Jones et al. J. Org Chem. 1993, 58, 2983; Vasseur et al . I. Am . Chem. Soc. 1992, 1 14, 4006; Van Aerschot et al. 1995 Angew. Chem. Int. Ed. Engl. 34: 1338; Hendrix et al. 1997 Chem. Eur. J. 3: 110; Koshkin et al. 1998 Tetrahedron 54: 3607-3630; Hyrup et al. 1996 Bioorg. Med. Chem. 4: 5; Nielsen et al. 1997 Chem. Soc. Rev. 73; Schultz et al. 1996 Nucleic Acids Res. 24: 2966; Ohika et al. 1997 Tetrahedron Lett. 38 (50): 8735-8; Obika et al. 1998 Tetrahedron Lett. 39: 5401- 5404; Singh et al. 1998 Chem. Comm. 1247-1248; Kumar et al. 1998 Bioo. Med. Chem. Let. 8: 2219- 2222; Nielsen et al. 1997 J. Chem. Soc. Perkins Transl. 1 : 3423-3433; Singh et al. 1998 J. Org. Chem. 63: 6078-6079; Seth et al. 2010 J. Org. Chem. 75: 1569-1581 ; Singh et al. 1998 j. Org. Chem 63: 10035-39; Sorensen 2003 Chem. Comm. 2130-2131; Petersen et al. 2003 TRENDS Biotech. 21 : 74-81; Rajwanshi et al. 1999 Chem. Commun. 1395-1396; Jepsen et al. 2004 Oligo. 14: 130-146; Morita et al. 2001 Nucl. Acids Res. Supp. 1 : 241-242; Morita et al. 2002 Bioo. Med. Chem. Lett. 12: 73-76; Morita et al. 2003 Bioo. Med. Chem. Lett. 2211-2226; Koizumi et al. 2003 Nuc. Acids Res. 12: 3267-3273; Lauritsen et al. 2002 Chem. Comm . 5: 530-531 ; Lauritsen et al. 2003 Bioo. Med. Chem. Lett 13: 253-256; WO

20070900071; Seth et al., Nucleic Acids Symposium Series (2008), 52(1), 553-554; Seth et al . 2009 J. Med. Chem. 52: 10-13; Seth et al. 2012 Mol. Ther-Nuc. Acids. 1, e47; Pallan et al. 2012 Chem. Comm. 48: 8195-8197; Seth et al. 2010 J. Med. Chem. 53: 8309-8318; Seth et al. 2012 Bioo. Med. Chem. Lett. 22: 296-299; WO 2016/079181; US 6,326,199; US 6,066,500; and US 6,440,739.

[00634] In some embodiments, sugars and nucleosides include 6 ' -modified bicychc sugars and nucleosides, respectively, that have either (R) or (5)-chirality at the 6' -position, e.g., those described in US Patent No. 7,399,845. In other embodiments, sugars and nucleosides include 5 ' -modified bi cyclic sugars and nucleosides, respectively, that have either (R) or (5)-chirality at the 5 ' -position, e.g., those described in US Patent Application Publication No. 20070287831.

[00635] In some embodiments, modified sugars, nucleobases, nucleosides, nucleotides, and/or internucleotidic linkages are described in U.S. Pat. No. 3,687,808, as well as U.S. Pat. Nos. 4,845,205;

5,130,30; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,457,191; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; 5,681,941; 5,750,692; 6,015,886; 6,147,200; 6,166,197; 6,222,025; 6,235,887; 6,380,368; 6,528,640; 6,639,062; 6,617,438; 7,045,610; 7,427,672; and 7,495,088, the sugars, nucleobases, nucleosides, nucleotides, and internucleotidic linkages of each of which are incorporated by reference.

[00636] In some embodiments, modified sugars, nucleobases, nucleosides, nucleotides, and/or internucleotidic linkages are those described in any of: Gryaznov, S; Chen, J.-K. J. Am. Chem. Soc. 1994, 116, 3143; Hendrix et al. 1997 Chem. Eur. J. 3: 110; Hyrup et al. 1996 Bioorg. Med. Chem. 4: 5; Jepsen et al. 2004 Ohgo. 14: 130-146; Jones et al. J. Org. Chem. 1993, 58, 2983; Koizumi et al. 2003 Nuc. Acids Res. 12: 3267-3273; Koshkin et al. 1998 Tetrahedron 54: 3607-3630; Kumar et al. 1998 Bioo. Med. Chem. Let. 8: 2219-2222; Lauritsen et al. 2002 Chem. Comm. 5: 530-531; Lauritsen et al. 2003 Bioo.

Med. Chem Lett. 13; 253-256; Mesmaeker et al. Angew. Chem , Int. Ed. Engl. 1994, 33, 226; Morita et al. 2001 Nucl . Acids Res. Supp. 1; 241-242; Morita et al. 2002 Bioo. Med. Chem. Lett. 12: 73-76; Morita et al. 2003 Bioo. Med. Chem. Lett. 2211-2226; Nielsen et al. 1997 Chem. Soc. Rev. 73; Nielsen et al. 1997 J. Chem. Soc. Perkins Trans!. 1: 3423-3433; Obika et al. 1997 Tetrahedron Lett. 38 (50): 8735-8; Obika et al. 1998 Tetrahedron Lett. 39: 5401-5404; Pallan et al. 2012 Chem. Comm. 48: 8195-8197; Petersen et al. 2003 TRENDS Biotech. 21: 74-81; Rajwanshi et al. 1999 Chem. Commun. 1395-1396; Schultz et al. 1996 Nucleic Acids Res. 24: 2966; Seth et al. 2009 I. Med. Chem. 52: 10-13; Seth et al. 2010 I. Med. Chem. 53: 8309-8318; Seth et al. 2010 J. Org. Chem. 75: 1569-1581; Seth et al. 2012 Bioo. Med. Chem. Lett. 22: 296-299; Seth et al. 2012 Mol. Ther-Nuc. Acids. 1, e47; Seth, Punit P; Siwkowski, Andrew; Alierson, Charles R; Vasquez, Guillermo; Lee, Sam; Prakash, Thazha P; Kinberger, Garth; Migawa, Michael T; Gaus, Hans; Bhat, Balkrishen; et al. From Nucleic Acids Symposium Series (2008), 52(1), 553-554; Singh et al. 1998 Chem. Comm. 1247-1248; Singh et al. 1998 J. Org. Chem. 63: 10035- 39; Singh et al. 1998 J. Org. Chem. 63: 6078-6079; Sorensen 2003 Chem. Comm. 2130-2131; Ts'o et al. Ann. N. Y. Acad. Sci. 1988, 507, 220; Van Aerschot et al. 1995 Angew. Chem. Int. Ed. Engl. 34: 1338; Vasseur et al. J. Am. Chem. Soc. 1992, 114, 4006; WO 20070900071; WO 20070900071; and WO 2016/079181

100637 In some embodiments, modified sugars, nucleobases, nucleosides, nucleotides, and/or intemucieotidic linkages include, or include those in, HNA, PNA, 2'-F!uoro N3'-P5'-phosphoramidate, LNA, beta-D-oxy-LNA, 2 -0,3 '-C-linked bicyclic, PS-LNA, beta-D-thio-LNA, beta-D-amino-LNA, xylo- LNA [c], alpha-L-LNA, ENA, beta-D-ENA, amide-linked LNA, methylphosphonate-LNA, (R, 5)-cEt, (R, 5)-cMOE, (R, S)-5’-Me-LNA, S-Me cLNA, Methylene-cLNA, 3’-Me-alpha-L-LNA, R- ( f -Me -alpha-L- LNA, S-5’ -Me-alpha-L-LNA, or R-5' -Me -alpha-L-LNA. Certain modified sugars, nucleobases, nucleosides, nucleotides, and/or intemucieotidic linkages are described in US 9394333, US 9744183, US 9605019, US 20130178612, US 2015021 1006, US 9598458, US 20170037399, WO 2017/015555, WO 2 17/062862, the modified sugars, nucleobases, nucleosides, nucleotides, and intemucieotidic linkages of each of which are incorporated herein by reference.

[00638] In some embodiments, the present disclosure provides technologies, e.g., oligonucleotides, compositions, methods, etc., related to the dystrophin (DMD) gene or a product encoded thereby (a transcript, a protein (e.g., various variants of the dystrophin protein), etc.) hi some embodiments, the base sequence of an oligonucleotide is or comprise a sequence which sequence is, or is complementary (e.g , 85%, 90%, 95%, 100%; in many embodiments, 100%) to, a sequence in the DMD gene or a product thereof (e.g., a transcript, rnRNA, etc.) (such an oligonucleotide -DMD oligonucleotide). In some embodiments, such a sequence in the DMD gene or a product thereof comprises 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 20, 31, 32, 33, 34, 35 or more nucleobases. In some embodiments, such a sequence in the DMD gene or a product thereof comprises at least 10 nucleobases. In some embodiments, such a sequence in the DMD gene or a product thereof comprises at least 15 nucleobases. In some embodiments, such a sequence in the DMD gene or a product thereof comprises at least 16 nucleobases. In some embodiments, such a sequence in the DMD gene or a produet thereof comprises at least 17 nucleobases. In some embodiments, such a sequence in the DMD gene or a product thereof comprises at least 18 nucleobases. In some embodiments, such a sequence in the DMD gene or a product thereof comprises at least 19 nucleobases. In some embodiments, such a sequence in the DMD gene or a product thereof comprises at least 2.0 nucleobases. In some embodiments, the present disclosure provides technologies, including DMD oligonucleotides and compositions and methods of use thereof, for treatment of muscular dystrophy, including but not limited to, Duchenne Muscular Dystrophy (also abbreviated as DMD) and Becker Muscular Dystrophy (BMD). In some embodiments, DMD comprises one or more mutations. In some embodiments, such mutations are associated with reduced biological functions of dystrophin protein in a subject suffering from or susceptible to muscular dystrophy.

100639 In some embodiments, the dystrophin (DMD) gene or a product thereof, or a variant or portion thereof, may be referred to as DMD, BMD, CMD3B, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272, MRX85, or dystrophin; External IDs: GMIM: 300377 MGI: 94909; HomoloGene: 20856; Gene Cards: DMD; In Human: Entrez: 1756; Ensembl: ENSG00000198947; UniProt: PI 1532; RefSeq (mRNA): NM_000109; NM_004006; NM_004007; N : 004009; NM 004010; RefSeq (protein): NP 000100; NP 003997; NP 004000; NP 004001; XP 00-1002. Location (UCSC): Chr X: 31.1 - 33.34 Mb; In Mouse: Entrez: 13405; Ensembl: ENSMU SG00000045103 ; UniProt: PI 1531; RefSeq (mRNA): \ M 007868: \\i 0013 14034; NM 0013 14035; NM_001314036; NM_001314037; RefSeq (protein): NP 001300963; NP__Q01300964; NP 001300965; NP 001300966; NP 001300967; Location (UCSC): Chr X: 82.95 - 85.21 Mb.

[00640] The DMD gene reportedly contains 79 exons distributed over 2.3 million bp of genetic real estate on the X chromosome; however, only approximately 14,000 bp (<1%) is reported to be used for translation into protein (coding sequence). It is reported that about 99.5% of the genetic sequence, the intronic sequences, is spliced out of the 2.3 million bp initial heteronuclear RNA transcript to provide a mature 14,000 bp mRNA that includes all key information for dystrophin protein production. In some embodiments, patients with DMD have mutation(s) in the DMD gene that prevent the appropriate construction of the wild-type DMD mRNA and/or the production of the wild-type dystrophin protein, and patients with DMD often show marked dystrophin deficiency in their muscle.

[00641] In some embodiments, a dystrophin transcript, e.g., mRNA, or protein encompasses those related to or produced from alternative splicing. For example, sixteen alternative transcripts of the dystrophin gene were reported following an analysis of splicing patterns of the DMD gene in skeletal muscle, brain and heart tissues. Sironi et al. 2002 FEES Letters 517: 163-166.

[00642] It is reported that dystrophin has several isoforms. In some embodiments, dystrophin refers to a specific isoform. At least three full-length dystrophin isoforms have been reported, each controlled by a tissue-specific promoter. Klamut et al 1990 Mol. Cell. Biol. 10: 193-205; Nudel et al. 1989 Nature 337: 76-78; Gorecki et al. 1992 Hum. Mol. Genet. 1: 505-510. The muscle isoform is reportedly mainly expressed in skeletal muscle but also in smooth and cardiac muscles [Bies, R.D., Phelps, S.F., Cortez, M.D., Roberts, R., Caskey, C.T. and Chamberlain, J.S. 1992 Nucleic Acids Res. 20: 1725-1731], the brain dystrophin is reportedly specific for cortical neurons but can also be detected in heart and cerebellar neurons, while the Purkinje-cell type reportedly accounts for nearly all cerebellar dystrophin [Gorecki et al. 1992 Hum. Mol. Genet. 1: 505-510] Alternative splicing reportedly provides a means for dystrophin diversification: the 3' region of the gene reportedly undergoes alternative splicing resulting in tissue-specific transcripts in brain neurons, cardiac Purkinje fibers, and smooth muscle cells [Bies et al. 1992 Nucleic Acids Res 20: 1725-1731; and Feener et al. 1989 Nature 338: 509-511] while 12 patterns of alternative splicing have been reported in the 5' region of the gene in skeletal muscle [Surono et al. 1997 Biochem. Btophys. Res. Commun. 239: 895-899]

[00643] In some embodiments, a dystrophin mRNA, gene or protein is a revertant version.

Among others, revertant dystrophins were reported in, for example: Hoffman et al. 1990 J. Neurol. Sci. 99:9-25; Klein et al. 1992 Am. I. Hum Genet. 50: 950-959; and Chelly et al. 1990 Cell 63: 1239-1348; Arahata et al. 1998 Nature 333: 861-863; Bonilla et al. 1988 Cell 54: 447-452; Farnn et al. 1992 Neur. Disord. 2: 41-45; Nicholson et al. 1989 J. Neurol. Sci. 94: 137-146: Shimizu et al. 1988 Proc. Jpn. Acad. Sci. 64: 205-208; Sicinzki et al. 1989 Science 244: 1578-1580; and Sherratt et al. Am. J. Hum. Genet 53: 1007-1015

[00644] Various mutations in the DMD gene can and/or were reported to cause muscular dystrophy.

Muscular Dystrophy

[00645] Compositions comprising one or more DMD oligonucleotides described herein can he used to treat muscular dystrophy. In some embodiments, muscular dystrophy (MD) is any of a group of muscle conditions, diseases, or disorders that results in (increasing) weakening and breakdown of skeletal muscles over time. The conditions, diseases, or disorders differ in which muscles are primarily affected, the degree of weakness, when symptoms begin, and how quickly symptoms worsen. Many MD patients will eventually become unable to walk. In many cases musuclar dystrophy is fatal. Some types are also associated with problems in other organs, including the central nervous system. In some embodiments, the muscular dystrophy is Duchenne (Duchenne’s) Muscular Dystrophy (DMD) or Becker (Becker's) Muscular Dystrophy (BMD).

[00646] In some embodiments, a symptom of Duchenne Muscular Dystrophy is muscle weakness associated with muscle wasting, with the voluntary muscles being first affected, especially those of the hips, pelvic area, thighs, shoulders, and calves. Muscle weakness can also occur later, in the anus, neck, and other areas. Calves are often enlarged. Symptoms usually appear before age six and may appear in early infancy. Other physical symptoms are: awkward manner of walking, stepping, or running (in some cases, patients tend to walk on their forefeet, because of an increased calf muscle tone), frequent falls, fatigue, difficulty with motor skills (e.g., running, hopping, jumping), lumbar hyperlordosis, possibly leading to shortening of the hip-flexor muscles, unusual overall posture and/or manner of walking, stepping, or naming, muscle contractures of Achilles tendon and hamstrings impair functionality', progressive difficulty walking, muscle fiber deformities, pseudohypertrophy (enlarging) of tongue and calf muscles, higher risk of neurobehavioral disorders (e.g., ADHD), learning disorders (e.g., dyslexia), and non-progressive weaknesses in specific cognitive skills (e.g., short-term verbal memory), which are believed to be the result of absent or dysfunctional dystrophin in the brain, eventual loss of ability to walk (usually by the age of 12), skeletal deformities (including scoliosis m some cases), and trouble getting up from lying or sitting position.

[00647] In some embodiments, Becker muscular dystrophy (BMD) is caused by mutations that give rise to shortened but in-frame transcripts resulting in the production of truncated but partially functional protein) s). Such partially functional protein(s) were reported to retain the critical amino terminal, cysteine rich and C-terminal domains but usually lack elements of the central rod domains which were reported to he of less functional significance. England et al. 1990 Nature, 343, 180-182.

[00648] In some embodiments, BMD phenotypes range from mild DMD to virtually asymptomatic, depending on the precise mutation and the level of dystrophin produced. Yin et al. 2008 Hum. Mol. Genet. 17: 3909-3918.

[00649] In some embodiments, dystrophy patients with out-of-frame mutations are generally diagnosed with the more severe Duchenne Muscular Dystrophy, and dystrophy patients with in-frame mutations are generally diagnosed with the less severe Becker Muscular Dystrophy. However, a minority of patients with in-frame deletions are diagnosed with Duchenne Muscular Dystrophy, including those with del etion mutations starting or ending in exons 50 or 51, which encode part of the hinge region, such as deletions of exons 47 to 51 , 48 to 51, and 49 to 53. Without wishing to be bound by any particular theory, the present disclosure notes that the patient-to-patient variability in disease severity despite the presence of the same exon deletion reportedly may be related to the effect of the specific deletion breakpoints on mRNA splicing efficiency and/or paterns; translation or transcription efficiency after genome rearrangement; and stability or function of the truncated protein structure. Yokota et al. 2009 Arch. Neurol. 66: 32.

Exon Skipping as a Treatment for Muscular Dystrophy

[00650] In some embodiments, a treatment for muscular dystrophy comprises the use of a DMD oligonucleotide which is capable of mediating skipping of one or more Dystrophin exons. In some embodiments, the present disclosure provides methods for treatment of muscular dystrophy comprising administering to a subject suffering therefrom or susceptible thereto an DMD oligonucleotide, or a composition comprising a DMD oligonucleotide. Particularly, among other things, the present disclosure demonstrates that chirally controlled oligonucleotide/chirally controlled oligonucleotide compositions are unexpectedly effective for modulating exon skipping compared to otherwise identical but non-chirally controlled oligonucleotide/oligonucleotide compositions. In some embodiments, the present disclosure demonstrates incorporation of one or more non-negatively charged intemucleotidie linkage can greatly improve delivery and/or overall exon skipping efficiency.

100651 In some embodiments, a treatment for muscular dystrophy employs the use of a DMD oligonucleotide, wherein the oligonucleotide is capable of providing skipping of one or more exons. Skipping of one or more (e.g , multiple) DMD exons can, for example, remove a mutated exon(s), or compensate for a mutation(s) (e.g., restoring the reading frame if the mutation is a frameshift mutation) in an exon which is not skipped. In some embodiments, a DMD oligonucleotide is capable of mediating the skipping of an exon which comprises a mutation (e.g., a frameshift, insertion, deletion, missense, or nonsense mutation, or other mutation), wherein the skipping of the exon maintains (or restores) the proper reading frame of the DMD gene, and translation produces a truncated but functional (or largely functional) DMD protein. In some embodiments, a DMD oligonucleotide compensates for an exon comprising a frameshift mutation by providing skipping of a different exon (not the one comprising the frameshift mutation), and thus restoring the reading frame of the DMD gene. In some embodiments, a patient having muscular dystrophy has a frameshift mutation in one exon of the DMD gene; and this patient is treated with a DMD oligonucleotide which does not cause skipping of the exon having the mutation, but causes skipping of a different exon, which restores the reading frame of the DMD gene, so that a functional DMD protein is produced (and, if the deleted exon is 3’ to the exon which has the frameshift mutation, this functional DMD protein will generally have an amino acid of a normal DMD protein, except for a sequence of amino acids not normally found in DMD, spanning from the frameshift mutation to the exon which is 3’ to the deleted exon).

[00652] hi some embodiments, a composition comprising a DMD oligonucleotide is useful for treatment of a Dystrophin-related disorder of the central nervous system. In some embodiments, the present disclosure pertains to a method of treatment of a Dystrophin-related disorder of the central nervous system, wherein the method comprises the step of administering a therapeutically effective amount of a DMD oligonucleotide to a patient suffering from a Dystrophin-related disorder of the central nervous system. In some embodiments, a DMD oligonucleotide is administered outside the central nervous system (as non-limiting examples, intravenously or intramuscularly) to a patient suffering from a Dystrophin-related disorder of the central nervous system, and the DMD oligonucleotide is capable of passing through the blood-brain barrier into the central nervous system. In some embodiments, a DMD oligonucleotide is administered directly into the central nervous system (as non-limiting example, via intrathecal, intraventricular, intracranial, etc., delivery).

[00653] In some embodiments, a Dystrophin-related disorder of the central nervous system, or a symptom thereof, can be any one or more of: decreased intelligence, decreased long term memory, decreased short term memory, language impairment, epilepsy, autism spectrum disorder, attention deficit hyperactivity disorder (ADHD), obsessive-compulsive disorder, learning problem, behavioral problem, a decrease in brain volume, a decrease in grey matter volume, lower white matter fractional anisotropy, higher white matter radial diffusivity, an abnormality of skull shape, or a deleterious change in the volume or structure of the hippocampus, globus pallidus, caudate putamen, hypothalamus, anterior commissure, periaqueductal gray, internal capsule, amygdala, corpus callosum, septal nucleus, nucleus aecumbens, fimbria, ventricle, or midbrain thalamus. In some embodiments, a patient exhibiting muscle- related symptoms of muscular dystrophy also exhibits symptoms of a Dystrophin-related disorder of the central nervous system.

[00654] hi some embodiments, a Dystrophin-related disorder of the central nervous system is related to, associated with and/or caused by an abnormality in the level, activity, expression and/or distribution of a gene product of the Dystrophin gene, such as full-length Dystrophin or a smaller isoform of Dystrophin, including, but not limited to, Dp260, Dpl40, Dpi 16, Dp71 or Dp4Q. In some embodiments, a DMD oligonucleotide is administered into the central nervous system of a muscular dystrophy patient in order to ameliorate one or more systems of a Dystrophin-related disorder of the central nervous system. In some embodiments, a Dystrophin -related disorder of the central nervous system is related to, associated with and/or caused by an abnormality in the level, activity, expression and/or distribution of a gene product of the Dystrophin gene, such as full-length Dystrophin or a smaller isofonn of Dystrophin, including, but not limited to, Dp260, Dp 140, Dp 116, Dp7l or Dp40. In some embodiments, administration of a DMD oligonucleotide to a patient suffering from a Dystrophin-related disorder of the central nervous system increases the level, activity, and/or expression and/or improves the distribution of a gene product of the Dystrophin gene.

[00655] In some embodiments, the present disclosure provides technologies for modulating dystrophin pre-mRNA splicing, whereby selected exons are excised to either remove nonsense mutations or restore the reading frame around frameshifting mutations from the mature mRNA. In some embodiments, a DMD oligonucleotide capable of skipping an exon is capable of restoring the reading frame.

[00656] As a non-limiting example, in a patient with Duchenne Muscular Dystrophy who has a deletion of exon 50, an out-of-frame transcript is generated in which exon 49 is spliced to exon 51. As a result, a stop codon is generated in exon 51, which prematurely aborts dystrophin synthesis. In some embodiments, the present disclosure provides oligonucleotides that can mediate slapping of exon 51, restore the open reading frame of the transcript, and allow the production of a truncated dystrophin similar to that in patients with Becker muscular dystrophy (BMD).

100657 In some embodiments, in a DMD patient, a DMD gene comprises an exon comprising a mutation, and the disorder is at least partially treated by skipping of one or more exons (e.g., the exon comprising the mutation, or an exon adjacent to the exon comprising the mutation, or a set of consecutive exons, including the exon comprising the mutation)

100658 In some embodiments, in a DMD patient, a DMD gene or transcript has a mutation in an exon(s), which is a missense or nonsense mutation and/or deletion, insertion, inversion, translocation or duplication. In some embodiments, in a DMD patient, a DMD gene or transcript has a mutation in an exon(s) which results in a frame shift, premature stop codon, or otherwise perturbation of the proper reading frame.

100659 In some embodiments, in a treatment for muscular dystrophy, an exon of DMD is skipped, wherein the exon encodes a string of amino acids not essential for DMD protein function, or whose skipping can provide a fully or partially functional DMD protein in some embodiments, in a treatment for muscular dystrophy, an exon of DMD is skipped, wherein the exon(s) skipped include an exon which comprises a mutation or is adjacent to (e.g., flanking) an exon comprising a mutation, or where multiple exons are skipped, the skipped exons optionally include an exon comprising a mutation. In some embodiments, in a treatment for muscular dystrophy, two or more exons are skipped, wherein the exons skipped include an exon which comprises a mutation or is adjacent to (e.g., flanking) an exon comprising a mutation. In some embodiments, in a treatment for muscular dystrophy, an exon comprises a frameshift mutation, and the skipping of a different exon (while leaving the exon with the frame shift mutation in place) restores the proper reading frame.

[00660] In some embodiments, m a treatment for muscular dystrophy, a DMD oligonucleotide is capable of mediating skipping of one or more DMD exons, thereby either restoring or maintaining the proper reading frame, and/or creating an artificially internally truncated DMD which provides at least partially improved or fully restored biological activity.

[00661] In some embodiments, an DMD oligonucleotide skips an exon(s) which is not exon 64 and exon 70, portions of which are reportedly important for protein function, and/or which is not first or the last exon. In some embodiments, an DMD oligonucleotide skips an exon(s), but skipping of the exon(s) does not cause deletion of one or more or all actin-binding sites in the N-terminal region.

[00662] In some embodiments, an internally truncated DMD protein produced from a dystrophin transcript with a skipped exon(s) is more functional than a terminally truncated DMD protein e.g., produced from a dystrophin transcript with an out-of-frame deletion.

[00663] In some embodiments, an internally truncated DMD protein produced from a dystrophin transcript with a skipped exon(s) is more resistant to nonsense-mediated decay, which can degrade a terminally truncated DMD protein, e.g., produced from a dystrophin transcript with an out-of-frame deletion. [00664] In some embodiments, a treatment for muscular dystrophy employs the use of a DMD oligonucleotide, wherein the oligonucleotide is capable of providing skipping of one or more exons. Skipping of one or more (e.g., multiple) DMD exons can, for example, remove a mutated exon, or compensate for a mutation (e.g., restoring from for a frame shift mutation) in an exon which is not skipped.

[00665] In some embodiments, the present disclosure encompasses the recognition that the nature and location of a DMD mutation may be utilized to design exon-skipping strategy. In some embodiments, if a DMD patient has a mutation in an exon, skipping of the mutated exon can produce tin internally truncated (internally shortened) but at least partially functional DMD protein product.

[00666] In some embodiments, a DMD patient has a mutation winch alters splicing of a DMD transcript, e.g., by inactivating a site required for splicing, or activating a cryptic site so that it becomes active for splicing, or by creating an alternative (e.g., unnatural) splice site. In some embodiments, such a mutation causes production of proteins with low or no activities. In some embodiments, splicing modulation, e.g., exon slapping, suppression of such a mutation, etc., can be employed to remove or reduce effects of such a mutation, e.g., by restoring proper splicing to produce proteins with restored activities, or producing an internally truncated dystrophin protein with improved or restored activities, etc. 100667 In some embodiments, a DMD patient has a mutation wliich is a duplication of one or several exons, and the present disclosure provides exon skipping technologies to delete the duplication and/or to restore the reading frame.

[00668] In some embodiments, a DMD patient has a mutation which causes the skipping of an exon, which in turn can cause a frameshift. In some embodiments, the present disclosure provides technologies that can pro vide skipping of an additional exon(s) to restore the reading frame. For example, deletion of exon 51 , which causes a frame shift, may be addressed by skipping of exon 50 or 52, which restores the reading frame. In some embodiments, a DMD patient has a mutation in one exon which causes a frame shift, and a deletion of a different exon(s) (e.g., a different exon, or an adjacent or flanking exon(s) immediately 5’ or 3’ to the mutated exon) restores the reading frame.

[00669] In some embodiments, restoring the reading frame can convert an out-of-frame mutation to an in-frame mutation; in some embodiments, in humans, such a change can transform severe Duchenne Muscular Dystrophy into milder Becker Muscular Dystrophy.

[00670] In some embodiments, a DMD patient or a patient suspected to have DMD is analyzed for DMD genotype prior to administration of a composition comprising a DMD oligonucleotide.

[00671] In some embodiments, a DMD patient or a patient suspected to have DMD is analyzed for DMD phenotype prior to administration of a composition comprising a DMD oligonucleotide.

[00672] In some embodiments, a DMD patient is analyzed for genotype and phenotype to determine the relationship of DMD genotype and DMD phenotype prior to administration of a composition comprising a DMD oligonucleotide.

[00673] In some embodiments, a patient is genetically verified to have dystrophy prior to administration of a composition comprising a DMD oligonucleotide.

[00674] In some embodiments, analysis of DMD genotype or genetic verification of DMD or a patient comprises determining if the patient has one or more deleterious mutations in DMD.

[00675] In some embodiments, analysis of DMD genotype or genetic verification of DMD or a patient comprises determining if the patient has one or more deleterious mutations in DMD and/or analyzing DMD splicing and/or detecting splice variants of DMD, wherein a splice variant is produced by an abnormal splicing of DMD.

[00676] In some embodiments, analysis of DMD genotype or genetic verification of DMD informs the selection of a composition comprising a DMD oligonucleotide useful for treatment.

[00677] In some embodiments, an abnormal or mutant DMD gene or a portion thereof is remo ved or copied from a patient or a patient’s edits) or tissue(s) and the abnormal or mutant DMD gene, or a portion thereof comprising the abnormality or mutation, or a copy thereof, is inserted into a cell. In some embodiments, this cell can be used to test various compositions comprising a DMD oligonucleotide to predict if such a composition would be useful as a treatment for the patient. In some embodiments, the cell is a myoblast or myotubule.

[00678] In some embodiments, an individual or patient can produce, prior to treatment with a

DMD oligonucleotide, one or more splice variants of DMD, often each variant being produced at a very ' low level. In some embodiments, a method such as that described in Example 20 can be used to detect low levels of splice variants being produced a patient prior to, during or after administration of a DMD oligonucleotide .

[00679] In some embodiments, a patient and/or the tissues thereof are analyzed for production of various splicing variants of a DMD gene prior to administration of a composition comprising a DMD oligonucleotide.

[00680] In some embodiments, the present disclosure provides methods for designing a DMD oligonucleotide (e.g , an oligonucleotide capable of mediating skipping of one or more exons of DMD). In some embodiments, the present disclosure utilizes rationale design described herein and optionally sequence walks to design oligonucleotides, e.g., for testing exon skipping in one or more assays and/or conditions. In some embodiments, an efficacious oligonucleotide is developed following rational design, including using various information of a given biological system.

[00681] In some embodiments, in a method for developing DMD oligonucleotides, oligonucleotides are designed to anneal to one or more potential splicing-related motifs and then tested for their ability to mediate exon skipping. In some embodiments, splicing-related motifs include, but are not limited to, any one or more of: an acceptor, exon recognition sequence (ERS), exonic splice enhancer (ESE) site, splicing enhancer sequence (SES), branch point sequence, and donor splice site of a target exon. Certain sequences that may be involved in splicing were reported in, for example: Disset et al. 2006 Human Mol. Gen. 15: 999-1013.

[00682] In some embodiments, software packages, such as RESCUE-ESE, ESEfmder, and the

PESX server, may be utilized to predict putative ESE sites (Fairbrother et al. 2002 Science 297: 1007- 1013; Cartegni et al. 2003 Nat. Struct. Biol. 120-125; Zhang and Chasin 2004 Gen. Dev 18: 1241-1250; Smith et al. 2006 Hum. Mol. Genet. 15: 2490-2508).

[00683] In some embodiments, a DMD oligonucleotide which targets or interacts with an acceptor, exon recognition sequence (ERS), exonic splice enhancer (ESE) site, or donor splice site of a DMD exon does not interact or significantly interact with a sequence in another (e.g., off-target) gene.

100684 In some embodiments, in a rational approach to DMD oligonucleotide design, oligonucleotides are designed with consideration of secondary structures of dystrophin transcripts, e.g., mRNA. Designed oligonucleotide can then be assessed for exon skipping. A number of effective DMD oligonucleotides have been designed using rational approaches described in the present disclosure.

[006851 In some embodiments, alternatively or additionally, sequence walk, e.g., of an exon sequence can be performed to search for efficacious DMD oligonucleotide sequences.

[00686] In some embodiments, provided methods comprise sequence walking. In some embodiments, a set of overlapping oligonucleotides is generated. In some embodiments, oligonucleotides in a set have the same length, and the 5’ ends of the oligonucleotides in the set are evenly spaced apart. In some embodiments, a set of overlapping oligonucleotides encompasses an entire exon or a portion) s) thereof. The 5’ ends of the oligonucleotides in a walk can be evenly spaced at a suitable distance, e.g., 1 base apart, 2 bases apart, 3 bases apart, etc. Among other things, the present disclosure demonstrates that sequences can be optimized and in combination with chemistry and/or stereochemistry technologies of the present disclosure, highly effective oligonucleotides (and compositions and methods of use thereof) can he prepared.

Example Technologies for Assessing Oligonucleotides and Oligonucleotide Compositions

[00687] Various technologies for assessing properties and/or activities of oligonucleotides can be utilized in accordance with the present disclosure, e.g., US 20170037399, WO 2017/015555, WO 2017/015575, WO 2017/192664, WO 2017/062862, WO 2017/192679, WO 2017/210647, etc.

[00688] For example, DMD oligonucleotides can be evaluated for their ability to mediate exon skipping in various assays, including in vitro and in vivo assays, in accordance with the present disclosure. In vitro assays can be performed in various test cells described herein or known in the art, including but not limited to, 148-50 Patient-Derived Myoblast Cells. In vivo tests can be performed in test animals described herein or known in the art, including but not limited to, a mouse, rat, cat, pig, dog, monkey, or non-human primate.

[00689] As non-limiting examples, a number of assays are described below' for assessing properties/activities of DMD oligonucleotides. Various other suitable assays are available and may be utilized to assess oligonucleotide properties/activities, including those of oligonucleotides not designed for exon skipping (e.g , for oligonucleotides that may involve RNase H for reducing levels of target transcripts, assays described in US 20170037399, WO 2017/015555, WO 2017/015575, WO 2017/192664, WO 2017/192679, WO 2017/210647, etc.).

[00690] A DMD oligonucleotide can be evaluated for its ability to mediate skipping of an exon in the Dystrophin RNA, which can be tested, as non-limiting examples, using nested PCR, qRT-PCR, and/or sequencing.

[00691] A DMD oligonucleotide can be evaluated for its ability to mediate protein restoration

(e.g , production of an internally truncated protein lacking the amino acids corresponding to the codons encoded in the skipped exon, which has improved functions compared to proteins (if any) produced prior to exon skipping), which can be evaluated by a number of methods for protein detection and/or quantification, such as western blot, immunostaming, etc. Antibodies to dystrophin are commercially available or if desired, can be developed for desired purposes.

[00692] A DMD oligonucleotide can be evaluated for its ability to mediate production of a stable restored protein. Stability of restored protein can be tested, in non-limiting examples, in assays for serum and tissue stability.

[00693] A DMD oligonucleotide can be evaluated for its ability to bind protein, such as albumin.

Example related technologies include those described, e.g , in WO 2017/015555, WO 2017/015575, etc.

[00694] A DMD oligonucleotide can be evaluated for immuno activity, e.g., through assays for cytokine activation, complement activation, TLR9 activity, etc. Example related technologies include those described, e.g., in WO 2017/015555, WO 2017/015575, WO 2017/192679, WO 2017/210647, etc, [00695] In some embodiments, efficacy of a DMD oligonucleotide can be tested, e.g., in in silico analysis and prediction, a cell-free extract, a cell transfected with artificial constructs, an animal such as a mouse with a human Dystrophin transgene or portion thereof, normal and dystrophic human myogenic cell lines, and/or clinical trials. It may be desirable to utilize more than one assay, as normal and dystrophic human myogenic cell lines may sometimes produce different efficacy results under certain conditions (Mitrpant et al. 2009 Mol. Ther. 17: 1418). [00696] In some embodiments, DMD oligonucleotides can be tested in vitro in cells. In some embodiments, testing in vitro in cells involves gymnotic delivery of the oiigonueleotide(s), or delivery using a delivery agent or transfectant, many of which are known in the art and may be utilized in accordance with the present disclosure.

[00697] In some embodiments, DMD oligonucleotides can be tested in vitro in normal human skeletal muscle cells (hSkMCs). See, for example, Arechavala et a!. 2007 Hum. Gene Ther. 18: 798-810.

[00698] In some embodiments, DMD oligonucleotides can be tested in a muscle explant from a

DMD patient. Muscle explants from DMD patients are reported in, for example, Fletcher et al. 2006 J. Gene Med. 8: 207-216; McClorey et al. 2006 Neur. Dis. 16: 583-590: and Arechavala et al. 2007 Hum. Gene Ther. 18: 798-810.

[00699] In some embodiments, cells are or comprise cultured muscle cells from DMD patients.

See, for example: Aartsma-Rus et al. 2003 Hum. Mol. Genet. 8: 907-914.

[00700] In some embodiments, an individual DMD oligonucleotide may demonstrate experiment- to-experiment variability in its ability to skip an exon under certain circumstances. In some embodiments, an individual DMD oligonucleotide can demonstrate variability in its ability to skip an exon(s) depending on which cells are used, the growth conditions, and other experimental factors. To control variations, typically oligonucleotides to be tested and control oligonucleotides are assayed under the same or substantially the same conditions.

[00701] In vitro experiments also include those conducted with patient-derived myoblasts.

Certain results from such experiments were described herein. In certain such experiments, cells were cultured in skeletal growth media to keep them in a dividing / immature myoblast state. Hie media as then changed to‘differentiation’ media (containing insulin and 2% horse serum) concurrent with spiking oligonucleotides in the media for dosing. The cells differentiated into myotubes as they were getting dosed for a suitable period of time, e.g., a total of 4d for RNA experiments and 6d for protein experiments (such conditions referenced as‘0d pre-differentiation’ (Od + 4d for RNA, Od + 6d for protein)).

[00702] Without wishing to be bound by any particular theory, the present disclosure notes that it may be desirable to know if DMD oligonucleotides are able to enter mature myotubes and induce skipping in these cells as well as‘immature’ cells. In some embodiments, the present disclosure provided assays to test effects of DMD oligonucleotides in myotubes. In some embodiments, a dosing schedule different from the‘0d pre-differentiation’ was used, wherein the myoblasts were pre-differentiated into myotubes in differentiation media for several days (4d or 7d or 1 Od) and then DMD oligonucleotides were administered. Certain related protocols are described in Example 19.

100703] In some embodiments, the present disclosure demonstrated that, in the pre-differentiation experiments, DMD oligonucleotides (excluding those which are PMOs) usually give about the same level of RNA skipping and dystrophin protein restoration, regardless of the number of days cells were cultured in differentiation media prior to dosing. In some embodiments, the present disclosure provides oligonucleotides that may be able to enter and be active in myoblasts and in myotubes. In some embodiments, a DMD oligonucleotide is tested in vitro in D45-52 DMD patient cells (also designated D45-52 or de!45-52) or D52 DMD patient cells (also designated D52 or de!52) with 0, 4 or 7 days of pre differentiation.

[00704] In some embodiments, DMD oligonucleotides can be tested in any one or more of various animal models, including non-mammalian and mammalian models; including, as non-limiting examples, Caenorhabditis, Drosophila, zebrafish, mouse, rat, cat, dog and pig. See, for example, a review m McGreevey et ai. 2015 Dis. Mod Mech. 8: 195-213.

[00705] Example use of mdx mice is reported in, for example: Lu et al 2003 Nat. Med. 9: 1009;

Jearawiriyapaisam et al. 2008 Mol. Then, 16, 1624-1629; Yin et al 2008 Hum. Mol. Genet., 17, 3909- 3918; Wu et al. 2009 Mol. Then, 17, 864-871; Wu et al. 2008 Proc. Natl Acad. Sen USA, 105, 14814 14819; Mann et al. 2001 Proc. Nat. Acad. Sen USA 98: 42-47; and Gebski et al. 2003 Hum. Mol. Gen. 12: 1801-1811

[00706] Efficacy of DMD oligonucleotides can be tested in dogs, such as the Golden Retriever

Muscular Dystrophy (GRMD) animal model. Lu et al. 2005 Proc. Natl. Acad. Sei. U S A 102: 198-203; Alter et al. 2006 Nat. Med. 12: 175-7; McClorey et al. 2006 Gene Ther. 13:1373-81; and Yokota et al. 2012 Nucl. Acid Ther. 22: 306.

[00707] A DMD oligonucleotide can be evaluated in vivo in a test animal for efficient deliver} ' to various tissues (e.g., skeletal, heart and/or diaphragm muscle); this can be tested, in non-limiting examples, by hybridization ELISA and tests for distribution in animal tissue.

[00708] A DMD oligonucleotide can be evaluated in vivo in a test animal for plasma PK; this can be tested, as non-limiting examples, by assaying for AUC (area under the curve) and half-life.

100709] In some embodiments, DMD oligonucleotides can be tested in vivo, via an intramuscular administration a muscle of a test animal.

[00710] In some embodiments, DMD oligonucleotides can be tested in vivo, via an intramuscular administration into the gastrocnemius muscle of a test animal

[00711] In some embodiments, DMD oligonucleotides can be tested in vivo, via an intramuscular administration into the gastrocnemius muscle of a mouse.

[00712] In some embodiments, DMD oligonucleotides can be tested in vivo, via an intramuscular administration into the gastrocnemius muscle of a mouse model transgenic for the entire human dystrophin locus. See, for example: Bremmer-Bout et al. 2004 Mol. Ther. 10, 232-240. [00713] Additional tests which can be performed to evaluate the efficacy of DMO oligonucleotides include centrally nucleated fiber counts and dystrophin-positive fiber counts, and functional grip strength analysis. See, as non-limiting examples, experimental protocols reported in: Yin et al. 2009 Hum. Mol. Genet. 18: 4405-4414.

[00714] Additional methods of testing DMD oligonucleotides include, as non-limiting example, methods reported in: Kinali et al. 2009 Lancet 8: 918; Be non i et al. 2.003 Hum. Mol. Gen. 12: 1087— 1099.

Certain Embodiments of Oligonucleotides and Compositions Thereof

[00715] Among other things, the present disclosure provides oligonucleotides, and compositions and methods of use thereof, useful for targeting various genes, including products encoded thereby and/or conditions, diseases and/or disorders associated therewith. In some embodiments, the present disclosure provides oligonucleotides, and compositions and methods of use thereof, for DMD. In some embodiments, the present disclosure provides a DMD oligonucleotide, wherein the base sequence of the DMD oligonucleotide is or comprises at least 15 contiguous bases of the sequence of any DMD oligonucleotide listed herein. In some embodiments, the present disclosure provides a DMD oligonucleotide, wherein the base sequence of the DMD oligonucleotide is or comprises at least 15 contiguous bases of the sequence of any DMD oligonucleotide listed herein, and wherein the DMD oligonucleotide is less than about 50 bases long. In some embodiments, the present disclosure provides an oligonucleotide or an oligonucleotide composition which comprises a non-negatively charged internucleotidic linkage.

[00716] hi some embodiments, the present disclosure provides a chirally controlled composition of a DMD oligonucleotide (a plurality of DMD oligonucleotides), wherein the base sequence of the DMD oligonucleotide is or comprises at least 15 contiguous bases of the sequence of any DMD oligonucleotide listed herein. In some embodiments, the present disclosure provides a chirally controlled composition of a DMD oligonucleotide, wherein the base sequence of the DMD oligonucleotide is or comprises at least 15 contiguous bases of the sequence of any DMD oligonucleotide listed herein, and wherein the DMD oligonucleotide is less than about 50 bases long.

|00717| In some embodiments, the present disclosure provides a chirally controlled oligonucleotide having a sequence consisting of or comprising a sequence or a 15 base portion thereof found in any oligonucleotide listed in Table Al, wherein one or more U may be optionally and independently replaced with T or vice versa.

|00718| In some embodiments, the present disclosure provides a chirally controlled oligonucleotide comprising a sequence of UCAAGGAAGAUGGCAUUUCU, CUCCGGUUCUGAAGGUGUUC, or UUCUGAAGGUGUUCUUGUAC, or a portion thereof at least 15 bases long, wherein each U can be optionally and independently replaced by T, wherein at least one interaucleotidic linkage is a chiraliy controlled intemucleotidic linkage. In some embodiments, the present disclosure provides a chiraliy controlled oligonucleotide comprising a sequence of U C AAGGA AGAU GGC A U UU C U, CUCCGGUUCUGAAGGUGUUC, or

UUCUGAAGGUGUUCUUGUAC, or a portion thereof at least 15 bases long, wherein each U can be optionally and independently replaced by T, wherein at least one chiraliy controlled intemucleotidic linkage has the structure of formula I, I-a, I-b, I-c, I-n-1, 1-n-2, I-n-3, 1-n-4, II, II-a-1, II-a-2, II-b-1, II- b-2, II-c-1, II-c-2, II-d-1, II-d-2, III, or a salt form thereof. In some embodiments, the present disclosure provides a chiraliy controlled oligonucleotide comprising a sequence of

UCAAGGAAGAUGGCAUUUCU, CUCCGGUUCUGAAGGUGUUC, or

UUCUGAAGGUGUUCUUGUAC, or a portion thereof at least 15 bases long, wherein each U can be optionally and independently replaced by T, wherein at least one chiraliy controlled intemucleotidic linkage has tire structure of formula I, I-a, I-b, I-c, I-n-1, 1-n-2, I-n-3, 1-n-4, II, II-a-1, II-a-2, li-b-1, II- b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof. In some embodiments, the present disclosure provides a chiraliy controlled oligonucleotide comprising a sequence of

UCAAGGAAGAUGGCAUUUCU, CUCCGGUUCUGAAGGUGUUC, or

UUCUGAAGGUGUUCUUGUAC, or a portion thereof at least 15 bases long, wherein each U can be optionally and independently replaced by T, wherein each intemucleotidic linkage has the structure of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1 , II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof In some embodiments, the present disclosure provides a chiraily controlled oligonucleotide comprising a sequence of UCAAGGAAGAUGGCAUUUCU,

CUCCGGUUCUGAAGGUGUUC, or UUCUGAAGGUGUUCUUGUAC, or a portion thereof at least 15 bases long, wherein each U can be optionally and independently replaced by T, wherein at least one intemucleotidic linkage has the structure of formula I-c or a salt form thereof. In some embodiments, the present disclosure provides a chiraliy controlled oligonucleotide comprising a sequence of UCAAGGAAGAUGGCAUUUCU, CUCCGGUUCUGAAGGUGUUC, or

UUCUGAAGGUGUUCUUGUAC, or a portion thereof at least 15 bases long, wherein each U can be optionally and independently replaced by T, wherein at least one intemucleotidic linkage has the structure of formula I-c or a salt form thereof, and at least one intemucleotidic linkage is a non-negatively charged intemucleotidic linkage. In some embodiments, the present disclosure provides a chiraily controlled oligonucleotide comprising a sequence of UCAAGGAAGAUGGCAUUUCU,

CUCCGGUUCUGAAGGUGUUC, or UUCUGAAGGUGUUCUUGUAC, or a portion thereof at least 15 bases long, wherein each U can be optionally and independently replaced by T, wherein at least one internucleotidic linkage is a chirally controlled phosphorothioate interaucleotidic linkage, and at least one imtemucleotidic linkage is a non-negatively charged internucleotidic linkage having the structure of formula I-n-1, I-n-2, 1-n-3, 1-n-4, II, II-a-1, II-a-2, II-b-1 , II-b-2, II-c-1 , II-c-2, II-d-1, II-d-2, or a salt form thereof. In some embodiments, the present disclosure provides a chirally controlled oligonucleotide comprising a sequence of UCAAGGAAGAUGGCAUUUCU, CUCCGGUUCUGAAGGUGUUC, or UUCUGAAGGUGUUCUUGUAC, or a portion thereof at least 15 bases long, wherein each U can be optionally and independently replaced by T, wherein each internucleotidic linkage is a phosphodiester.

[00719] In some embodiments, an oligonucleotide comprises one or more internucleotidic linkages which comprise a phosphorus modification prone to“autorelease ,, under certain conditions. That is, under certain conditions, a particular phosphorus modification is designed such that it seif-cleaves from the oligonucleotide to provide, e.g., a phosphate diester such as those found in naturally occurring DNA and RNA. In some embodiments, such a phosphorus modification has a structure of O L R ! . wherein each of L and R 1 is independently as described in the present disclosure.

[00720] hi some embodiments, a provided oligonucleotide of the present disclosure comprises chemical modifications and/or stereochemistry that delivers desirable properties, e.g., deliver} to target cells/tissues/organs, pharmacodynamics, pharmacokinetics, etc

[00721] In some embodiments, an oligonucleotide comprises a modification at a linkage phosphorus which can be transformed to a natural phosphate linkage by one or more esterases, nucleases, and/or cytochrome P450 enzymes, including but not limited to: CYP1 Al, CYP1A2, CYPIB!, CYP2A6, CYP2A7, CYP2AI3, CYP2B6, CYP2C8, CYP2C9, CYP2C18, CYP2C19, CYP2D6, CYP2E1, CYP2F1, CYP2J2, CYP2R1, CYP2S1, CYP2U1, CYP2W1, CYP3A4, CYP3A5, CYP3A7, CYP3A43, CYP4A11, CYP4A22, CYP4B1, CYP4F2, CYP4F3, CYP4F8, CYP4F11, CYP4F12, CYP4F22, CYP4V2, CYP4X1, CYP4Z1, CYP5A1, CYP7A1, CYP7B1, CYP8A1 (prostacyclin synthase), CYP8B 1 (bile acid biosynthesis), CYP1 1 A1 , CYP11B1 , CYP11B2, CYP17A 1, CYP19AI , CYP20A1, CYP21A2, CYP24A1, CYP26A1, CYP26B1, CYP26C1, CYP27A1 (bile acid biosynthesis), CYP27B1 (vitamin D3 1 -alpha hydroxylase, activates vitamin D3), CYP27C1 (unknown function), CYP39A1, CYP46A1, and CYP51A1 (lanosterol 14-alpha demethylase).

[00722] In some embodiments, an oligonucleotide comprises a modification at a linkage phosphorus that is a pro-drug moiety, e.g., a P-modification moiety facilitates delivery of an oligonucleotide to a desired location prior to removal. For instance, in some embodiments, a P- modification moiety results from PEGyiation at the linkage phosphorus. One of skill in the relevant arts will appreciate that various PEG chain lengths are useful and that the selection of chain length will be determined in part by the result that is sought to be achieved by PEGyiation. For instance, in some embodiments, PEGyiation is effected in order to reduce RES uptake and extend in vivo circulation lifetime of an oligonucleotide.

[00723] In some embodiments, a PEGylation reagent for use in accordance with the present disclosure is of a molecular weight of about 300 g/mol to about 100,000 g/mol. In some embodiments, a PEGylation reagent is of a molecular weight of about 300 g/mol to about 10,000 g/mol. In some embodiments, a PEGylation reagent is of a molecular weight of about 300 g/mol to about 5,000 g/mol. In some embodiments, a PEGylation reagent is of a molecular weight of about 500 g/mol. In some embodiments, a PEGylation reagent of a molecular weight of about 1000 g/mol. In some embodiments, a PEGylation reagent is of a molecular weight of about 3000 g/mol. In some embodiments, a PEGylation reagent is of a molecular weight of about 5000 g/mol.

[00724] In certain embodiments, a PEGylation reagent is PEG500. In certain embodiments, a

PEGylation reagent is PEG1000. In certain embodiments, a PEGylation reagent is PEG3000. In certain embodiments, a PEGylation reagent is PEG 5000.

100725 In some embodiments, an oligonucleotide comprises a P-modification moiety that acts as a PK enhancer, e.g., lipids, PEGyiated lipids, etc.

[00726] In some embodiments, oligonucleotides of the present disclosure, e.g., DMD oligonucleotides, comprise a P-modification moiety that promotes cell entry and/or endosomal escape, such as a membrane-disruptive lipid or peptide.

[00727] hi some embodiments, an oligonucleotide comprises a P-modification moiety that acts as a targeting moiety. In some embodiments, a P-modification moiety is or comprises a targeting moiety. In some embodiments, a target moiety is an entity that is associates with a payload of interest (e.g.. with an oligonucleotide or oligonucleotide composition) and also interacts with a target site of interest so that the payload of interest is targeted to the target site of interest when associated with the targeting moiety to a materially greater extent than is observed under otherwise comparable conditions when the payload of interest is not associated with the targeting moiety. A targeting moiety may be, or comprise, any of a variety of chemical moieties, including, for example, small molecule moieties, nucleic acids, polypeptides, carbohydrates, etc. Targeting moieties are described, e.g., in Adarsh et al.,“Organelle Specific Targeted Drag Delivery - A Review,” International Journal of Research in Pharmaceutical and Biomedical Sciences, 201 1 , p. 895.

[00728] Examples of such targeting moieties include, but are not limited to, proteins (e.g.

Transferrin), oligopeptides (e.g., cyclic and acyclic RGD-containmg oligopeptides), antibodies (monoclonal and polyclonal antibodies, e.g. IgG, IgA, IgM, IgD, IgE antibodies), sugars / carbohydrates (e.g., monosaccharides and/or oligosaccharides (mannose, mannose-6-phosphate, galactose, and the like)), vitamins (e.g., folate), or other small biomolecules. In some embodiments, a targeting moiety is a steroid molecule (e.g., bile acids including cholic acid, deoxycholic acid, dehydrocholic acid; cortisone; digoxigenin; testosterone; cholesterol; cationic steroids such as cortisone having a trimethylaminomethyl hydrazide group attached via a double bond at the 3-position of the cortisone ring, etc). In some embodiments, a targeting moiety is a lipophilic molecule (e.g., a!icvclic hydrocarbons, saturated and unsaturated fatty acids, waxes, teipenes, and polyalicyclic hydrocarbons such as adamantine and buckminsterfuilerenes). In some embodiments, a lipophilic molecule is a terpenoid such as vitamin A, retinoic acid, retinal, or dehydroretinal. In some embodiments, a targeting moiety is a peptide.

[00729] In some embodiments, a P-modifieation moiety is a targeting moiety having the structure of X-L-R 1 wherein each of X, L, and R 5 is independently as described in the present disclosure.

100730 In some embodiments, a P-modification moiety facilitates cell specific delivery.

[00731] In some embodiments, a P-modification moiety may perform one or more than one functions. For instance, in some embodiments, a P-modification moiety acts as a PK enhancer and a targeting ligand. In some embodiments, a P-modification moiety acts as a pro-drug and an endosomal escape agent. Numerous other such combinations are possible and are included in the present disclosure.

Certain Examples of Oligonucleotides and Compositions

[00732] In some embodiments, the present disclosure provides oligonucleotides and/or oligonucleotide compositions that are useful for various puiposes, e.g., modulating skipping, reducing levels of transcripts, improving levels of beneficial proteins, treating conditions, diseases and disorders, etc. In some embodiments, the present disclosure provides oligonucleotide compositions with improved properties, e.g., increased activities, reduced toxicides, etc. Among other things, oligonucleotides of the present disclosure comprise chemical modifications, stereochemistry, and/or combinations thereof which can improve various properties and activities of oligonucleotides. Non-limiting examples are listed in Table Al. In some embodiments, an oligonucleotide type is a type as defined by the base sequence, pattern of backbone linkages, pattern of backbone chiral centers and pattern of backbone phosphorus modifications of an oligonucleotide in Table Al, wherein the oligonucleotide comprises at least one chirally controlled mtemucleotidic linkage (at least one R or S in“Stereochemistry/Linkage”). In some embodiments, a plurality of oligonucleotides of a particular oligonucleotide type is a plurality of an oligonucleotide in Table Al (e.g., a plurality of oligonucleotides is a plurality of \W~1095) In some embodiments, a plurality of oligonucleotides in a chirally controlled oligonucleotide composition is a plurality of an oligonucleotide Table Al (e.g., a plurality of oligonucleotides is a plurality of WV- 1095), wherein the oligonucleotide comprises at least one chirally controlled intemucleotidic linkage (at least one R or S in“Stereochemistry/Linkage”).

[00733] Table .41 lists non-limiting examples of DMD oligonucleotides .411 of the oligonucleotides in Table 41 are DMD oligonucleotides, except for WV-12915, WV-12914, WV-12913, WV-12912, WV-12911, WV-12910, WV-12909, WV-12908, WV-12907, WV-12906, WV-12905, WV- 12904, WV-15887, WV-24100, WV-24101, WV-24102, WV-24103, WV-24104, WV-24105, WV- 24106, WV -24107, WV-24108, WV-24109, WV-241 10, WV-XBD108, WV-XBD 109, WV-XBD 1 10, WV-XKCD1Q8, WV-XKCD 109, WV-XKCD 110, which all target Malat-1, which is a gene target different than DMD.

100734 In some embodiments, the present disclosure pertains to an oligonucleotide or oligonucleotide composition, wherein the base sequence of the oligonucleotide comprises at least 15 contiguous bases, with 1-3 mismatches, of the base sequence of a DMD oligonucleotide disclosed in Table Al . In some embodiments, the present disclosure pertains to an oligonucleotide or oligonucleotide composition, wherein the base sequence of the oligonucleotide comprises at least 15 contiguous bases of the base sequence of a DMD oligonucleotide disclosed in Table Al In some embodiments, the present disclosure pertains to an oligonucleotide or oligonucleotide composition, wiierein the base sequence of the oligonucleotide comprises the base sequence of a DMD oligonucleotide disclosed in Table Al. In some embodiments, the present disclosure pertains to an oligonucleotide or oligonucleotide composition, wherein the base sequence of the oligonucleotide is the base sequence of a DMD oligonucleotide disclosed in Table Al

[00735] In some embodiments, the present disclosure pertains to an oligonucleotide or oligonucleotide composition, wherein the base sequence of the oligonucleotide comprises at least 15 contiguous bases, with 1-3 mismatches, of the base sequence of a DMD oligonucleotide disclosed in Table Al, or wherein the base sequence of the oligonucleotide comprises at least 15 contiguous bases of the base sequence of a DMD oligonucleotide disclosed in Table Al, or wherein the base sequence of the oligonucleotide comprises the base sequence of a DMD oligonucleotide disclosed in Table Al , or wherein the base sequence of the oligonucleotide is the base sequence of a DMD oligonucleotide disclosed m Table Al; and wherein the oligonucleotide is stereorandom (e.g., not chirally controlled), or the oligonucleotide is chirally controlled, and/or the oligonucleotide comprises at least one intemucleotidic linkage which is chirally controlled, and/or the oligonucleotide optionally comprises a sugar modification which is a LNA, and/or the oligonucleotide comprises a sugar which is a natural deoxyribose, a 2’-OMe or a 2’-MOE. In some embodiments, the present disclosure pertains to an oligonucleotide capable of mediating skipping of a DMD exon, wherein the oligonucleotide comprises at least one LNA.

[00736] In the following table ID indicates identification or oligonucleotide number; and

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In Table A1 (including Table AL L, Table A1.2, Table A1.3, etc.): d vi

o

Spaces in Table A1 are utilized for formatting and readability, e.g., OXXXXX XXXXX XXXXX XXXX illustrates the same stereochemistry as s OXXXXXXXXXXXXXXXXXXX; * S and *S both indicate phosphorothioate intemucleotidic linkage wherein the linkage phosphorus has S'p O configuration; etc. -4

All oligonucleotides listed in Tables A1 are single-stranded. As described in the present application, they may be used as a single strand, or as a § strand to form complexes with one or more other strands.

Some sequences, due to their length, are divided into multiple lines.

ID: Identification number for an oligonucleotide.

WV-8806, WV-13405. WV-13406 and WV-13407 are fully PMO (morpholino oligonucleotides; [all PMO] in Table). 3

O

O

O

O

00

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n H m bo o o bO

O

Abbreviations in Tables:

m5Ceo: 5 -Methyl 2'-Methoxyethyl

SMS: S -^SVCH modification of sugar moieties;

SMSfC: 2’-F-5’ -(^-methyl C (in oligonucleotides, , wherein in BA is nucleobase C and R 2S is -F, and the 5’ and 3’ positions independently connect to -QH, intemucleotidic linkages,

linkers/linkages-H, linkers/linkages-Mod, etc. Nucleoside form i wherein in BA is nucleobase C and R 2s is -F);

C6: C6 amino linker (L001, ---NH-(CH 2 ) 6 -- wherein -NH- is connected to Mod (e.g., through C(O) in

Mod) or -H, and (CH 2 ) 6 - is connected to the 5’-end (or 3’-end if indicated) of oligonucleotide chain through, e.g., phosphodiester (-0-P(0)(0H)-0-. May exist as a salt form. May be illustrated in the Tables as O or PO), phosphorothioate (-0-P(0)(SH)-0-. May exist as a salt form. May be illustrated in the Tables as * if the phosphorothioate not chirally con trolled; *S, S, or Sp, if chirally controlled and has an Sp configuration, and *R, R, or Rp. if chirally controlled and has an Rp configuration), or phosphorodithioate (-0-P(S)(SH)-0-. May exist as a salt form. May be illustrated in the Tables as PS2 or : or D) linkage. May also be referred to as C6 linker or C6 amine linker);

: or D: Phosphodithioate (Phosphorodithioate), represented by D or a colon ( : );

nOO 1 : non-negative ly charged linkage (which is stereorandom unless otherwise indicated

(e.g, as nOOIR, or nOOl S));

n002: non-negatively charged linkage (which is stereorandom unless otherwise indicated (e.g., as n002R, or n002S)); n003: non-negative ly charged linkage (which is stereorandom unless otherwise indicated (e.g., as n003R, or n003S));

n004: non-negative ly charged linkage (which is stereorandom unless otherwise indicated (e.g., as n004R, or n004S));

n005: non-negative ly charged linkage (which is stereorandom unless otherwise indicated (e.g., as n005R, or

n006: non-negative ly charged linkage (which is stereorandom unless otherwise indicated (e.g., as n006R, or n006S));

n007 : non-negative ly charged linkage (w'hich is stereorandom at linkage phosphorus unless otherwise indicated (e.g., as n007R, or n007S));

n008: non-negatively charged linkage (wdiich is stereorandom unless otherwise indicated (e.g., as m008R, or nOOBS));

n009: non-negatively charged linkage (which is stereorandom unless otherwise indicated (e.g , as n009R, or n009S)); n010: non-negatively charged linkage (winch is stereorandom unless otherwise indicated (e.g., as nO!OR, or nOlOS));

nOOIR: nOOl being ehiraiiy controlled and having the Rp configuration;

n002R: n002 being chira!iy controlled and having the Rp configuration;

n003R: n003 being ehiraiiy controlled and having the Rp configuration;

n004R: n004 being ehiraiiy controlled and having the Rp configuration;

n005R: n005 being ehiraiiy controlled and having the Rp configuration;

n006R: n006 being ehiraiiy controlled and having the Rp configuration;

n007R: n007 being ehiraiiy controlled and having the Rp configuration;

n008R: n008 being ehiraiiy controlled and having the Rp configuration;

n009R: n009 being ehiraiiy controlled and having the Rp configuration;

nOfOR: nOl O being ehiraiiy controlled and having the Rp configuration;

nOOlS: nOOl being ehiraiiy controlled and having the Sp configuration;

n002S: n002 being ehiraiiy controlled and having the Sp configuration;

n003S: n003 being ehiraiiy controlled and having the Sp configuration;

n004S: n004 being ehiraiiy controlled and having the Sp configuration;

nOQSS: n005 being ehiraiiy controlled and having the Sp configuration;

n006S: n006 being ehiraiiy controlled and having the Sp configuration;

n007S: n007 being ehiraiiy controlled and having the Sp configuration;

n008S: n008 being ehiraiiy controlled and having the Sp configuration;

n009S: n009 being ehiraiiy controlled and having the Sp configuration;

nOlOS: nOlO being ehiraiiy controlled and having the Sp configuration;

nO, nX: in Linkage / Stereochemistry, nO or nX indicates a stereorandom nOOl;

nR: in Linkage / Stereochemistry, nR indicates a linkage, e.g , nOOl, n002, n003, n004, n005, n006, n007, n008, n009, etc. , being ehiraiiy controlled and having the Rp configuration (e.g. , for nOO 1 , nOO 1R in Description);

nS: m Linkage / Stereochemistry, nS indicates a linkage, e.g., nOOl, n002, n003, n004, n005, n006, n007, n008, n009, etc., being ehiraiiy controlled and having the Sp configuration (e.g., for nOOl , nOOlR in Description); BrfU: a nucleoside unit wherein the nucleobase wherein the sugar has a 2’-F

(f) modification

BrsnU: a nucleoside unit wherein the nucleobase wherein the sugar has a 2’

OMe (m) modification

BrdU: a nucleoside unit wherein the nucleobase wherein the sugar is 2-

deoxyribose (as widely found in natural DNA; 2 , -deoxy (d)) ( ^ );

L004: linker having the structure of -NH(CH 2 )4CH(CH 2 OH)CH 2- , wherein -NH- is connected to Mod (e.g., through -C(0) ~ in Mod) or -H, and the -CH 2- connecting site is connected to a linkage, e.g., phosphodiester (-0-P(0)(0H)-0-. May exist as a salt form. May be illustrated in the Tables as O or PO), phosphorothioate (-0-P(0)(SH)-0-. May exist as a salt form. May be illustrated in the Tables as * if the phosphorothioate not chirally controlled; *S, S, or Ap, if chiral!y controlled and has an 5p configuration, and *R, R, or Rp, if chirally controlled and has an Rp configuration), or phosphorodithioate ( 0-P(S)(SH) ~ 0-. May exist as a salt form. May be illustrated in the Tables as PS2 or : or D) linkage, at the 5’- or 3’ -end of an oligonucleotide chain as indicated. For example, an asterisk immediately preceding a L004 (e.g., *L004) indicates that the linkage is a phosphorothioate linkage, and the absence of the indication of any other linkage immediately preceding L004 indicates that the linkage is a phosphodiester linkage. For example, in WV-9858, which terminates in fUL004, the linker L004 is connected (via the ~-CH 2 site) to the phosphodiester linkage at the 3’ position at the 3’ -terminal sugar (which is 2’-F and connected to the nucleobase U), and the L004 linker is connected via ~ NH- to -H; similarly, in WV-10886, WV-10887, and WV-10888, the L004 linker is connected (via the -CH 2 - site) to the phosphodiester linkage at the 3’ position of the 3’-terminal sugar, and the L004 is connected via XI i to Modi) 12 (WV-10886), Mod085 (WV-10887) or Mod086 (WV-10888);

LOOS: linker having the structure of ~NH(CH 2 ) 5 C(0)N(CH 2 CH 2 0H)CH 2 CH 2 --, wherein -NH- is connected to Mod (e.g., through -C(O)- in Mod) or -H, and the -CH 2 ~ connecting site is connected to a linkage, e.g., phosphodiester (-0-P(0)(0H)-0-. May exist as a salt form. May be illustrated in the Tables as O or PO), phosphorothioate (-0-P(0)(SH)-0-. May exist as a salt form. May be illustrated in the Tables as * if the phosphorothioate not chirally controlled; *S, S, or <Sp, if chirally controlled and has an 5p configuration, and *R, R, or Rp, if chirally controlled and has an Rp configuration), or phosphorodithioate (-0-P(S)(SH)-0-. May exist as a salt form. May be illustrated in the Tables as PS2 or : or D) linkage, at the 5’- or 3’-end of an oligonucleotide chain as indicated. For example, an asterisk immediately preceding a LG05 (e.g., *L005) indicates that the linkage is a phosphorothioate linkage, and the absence of the indication of any other linkage immediately preceding L005 indicates that the linkage is a phosphodiester linkage. For example, in WV -12571 , LOOS is connected to -H (no Mod following LOOS; via the -NH- site) and the phosphodiester linkage at the 3’ position of the 3’-terminal sugar (via the— CH 2— site); and in WV-12572, LOOS is connected to Mod020 (via the -NH- site) and the phosphodiester linkage at the 3’ position of the 3 -terminal sugar (via the -CH 2- site);

LOO 1 LOOS: linker having the structure of

-NH(CH 2 ) 5 C(0)N(CH 2 CH 2- 0-P(0)(0H)-0-(CH 2 ) 6 NH-)CH 2 CH 2- , wherein each of the two -NTT- is independently connected to Mod (e.g., through -C(O)-) or -IT, and the -CH 2- connecting site is connected to a linkage, e.g., phosphodiester (-0-P(Q)(QH)-Q-. May exist as a salt form. May be illustrated in the Tables as O or PO), phosphorothioate (-0-P(0)(SH)-0-. May exist as a salt form.

May be illustrated in the Tables as * if the phosphorothioate not chirally controlled; *S, S, or Sip, if chirally controlled and has an Sp configuration, and *R, R, or Rp, if chirally controlled and has an Rp configuration), or phosphorodithioate (-0-P(S)(SH)-0-. May exist as a salt form. May be illustrated in the Tables as PS2 or : or D) linkage at the S’- or 3’-end of an oligonucleotide chain as indicated. eo: 2’-MOE (2 -OCH 2 CH 2 OCH 3 ) modification on the preceding nucleoside (e.g., Aeo ( , wherein BA is nucleobase A));

F, f: 2’-F modification on the following nucleoside (e.g., fA ( wherein BA is nudeobase

A)); m: 2’-OMe modification on the following nucleoside (e.g., ni.4 ( , wherein BA is nucleobase A));

r: 2’ -OH on the following nucleoside (e.g., rA wdierein BA is nucleobase A, as existed in natural RNA));

L012: intemucleotidic linkage having the structure of-0-P(0)[0(CH 2 ) 2 0(CH 2 ) 2 0(CH 2 ) 2 0H]-0-. May be illustrated as 00 in the Tables;

*, PS: Phosphorothioate;

PS2, : D: phosphorodithioate (e.g , WV-3078, wherein a colon (:) indicates a phosphorodithioate):

*R, R, Rp: Phosphorothioate in Rp conformation;

*S, S, Sp: Phosphorothioate in Ap conformation;

X: Phosphorothioate stereorandom;

NA: Not Applicable;

O, PO: phosphodiester (phosphate). When no intemucleotidic linkage is specified between two nucleoside units, the intemucleotidic linkage is a phosphodiester linkage (natural phosphate linkage). When used to indicate linkage between Mod and a linker, e.g., L001, O may indicate -C(O)- (connecting Mod and L001 , for example:

ModO 13L00 ifU* SfC* SfA* SfA * SfC* SfC* SmAf A* SmGmA* SfU* SniGmGfC* SfA * SfU* SfU* SfU* SfC

*SfU (Description), OOSSSSSSOSOSSOOSSSSSS (Linkage/Stereochemistry). Note the second O in OOSSSSSSOSOSSOOSSSSSS (Linkage/Stereochemistry) represents phosphodiester linkage connecting L001 and the 5 -Q- of the 5’ -terminal sugar of the oligonucleotide chain (see illustrations below.

Alternatively, the -O - may be considered part of the phosphodiester linkage (or another type of linkage such as a phosphorothioate linkage), in which case the phosphodiester linkage (or another type of linkage such as phosphorothioate linkage) is connected to tire 5" position of the 5’-terminal sugar of the oligonucleotide chain). In some instances,“O” for -C(O)- (connecting Mod and L001) is omitted (e.g., for

Modi) 13L00 IfU* SfC* SfA* SfA* SfC* SfC* Sm.AfA* SmGmA* SfU* SmGmGfC* SfA* SfU* SfU* SfU* SfC *SfU,‘ Linkage/Stereochemistry” OSSSSSSOSOSSOOSSSSSS);

Various Mods:

ModOO! (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Laurie (in Mod013), Myristic ( Mod014), Palmitic (in Mod005), Stearic (in Mod0l5), Oleic (in ModOl 6), Linoleic (in Modi) 17), alpha-Linoleinc (in ModOl 8), gamma-Linolenic (in Modi) 19), DMA (in Mod006), Turbinaric (in Mod020), Dilinoieic (in Mod02l), TriGlcNAc (in Mod024), TrialphaMannose (in Mod026), MonoSulfonamide (in Mod 027), Tri Sulfonamide (in Mod029), Laurie (in Mod030), Myristic (in Mod031 ), Palmitic (in Mod032), and Stearic (in Mod033): Laurie acid (for Mod013), Myristic acid (for Mod014), Palmitic acid (for Mod005), Stearic acid (for Mod015), Oleic acid (for Mod016), Linoleic acid (for Mod0l7), alpha-Linolenic acid (for ModOl 8), gamma-Linolenic acid (for ModOl 9), docosahexaenoic acid (for Mod006), Turbinaric acid (for Mod020), alcohol for Dilinoleyl (for Mod021 ), acid for TriGlcNAc (for Mod024), acid for TrialphaMannose (for Mod026), acid for

MonoSulfonamide (for Mod 027), acid for Tri Sulfonamide (for Mod029), Lauryl alcohol (for Mod030), Myristyl alcohol (for Mod031), Palmityl alcohol (for Mod032), and Stearyl alcohol (for Mod033), respectively, conjugated to oligonucleotide chains, e.g., through an amide group, a linker (e.g., C6 amino linker, (LOO 1)), and/or a linkage group (e.g., phosphodiester linkage (PO), phosphorothioate linkage (PS), etc.): e.g., ModOl 3 (Laurie acid with C6 amino linker and PO or PS), ModOl 4 (Myristic acid with C6 amino linker and PO or PS), ModOOS (Palmitic acid with C6 amino linker and PO or PS), ModOl (Stearic acid with C6 amino linker and PO or PS), Mod0 l6 (Oleic acid with C6 amino linker and PO or PS), Mod017 (Linoleic acid with C6 amino linker and PO or PS), ModOlS (alpha-Linolenic acid with C6 amino linker and PO or PS), Mod019 (gamma-Linolenic acid with C6 amino linker and PO or PS), Mod006 (DHA with C6 amino linker and PO or PS), Mod020 (Turbinaric acid with C6 amino linker and PO or PS), Mod02 l (alcohol (see below 7 ) with PO or PS), Mod024 (acid (see below) with C6 amino linker and PO or PS), Mod026 (acid (see below) with C6 amino linker and PO or PS), Mod027 (acid (see below) with C6 amino linker and PO or PS), Mod029 (acid (see below 7 ) with C6 amino linker and PO or PS), Mod030 (Lauryl alcohol with PO or PS), Mod031 (Myristyl alcohol with PO or PS), Mod032 (Palmityl alcohol with PO or PS), and Mod033 (Stearyl alcohol with PO or PS), with PO or PS for each oligonucleotide indicated in Table Al. For example, WV-3557 Steary alcohol conj ugated to

oligonucleotide chain of WV-3473 via PS:

Mod033*fU* SfC* SfA * SfA * SfG* SfG* Sm AfA * SmGmA* SfU* SmGmGfC* Sf A* SfU* SfU* SfU* SfC* Sf

U (Description), XSSSSSSOSOSSOOSSSSSS (Stereochemistry); and

WV-4106 Stearic acid conjugated to oligonucleotide chain of WV-3473 via amide group, C6, and PS:

ModOISLOOl* Li* SfC * S£4* SfA* SfG* SfG* SmAfA* SmGmA* SfU* SmGmGfC* SfA* SfU* SfU * SfU * Sf

C*SfU (Description), XSSSSSSOSOSSOOSSSSSS (Stereochemistiy) . Certain moieties for conjugation, and example reagents (many of which were previously known and are commercially available or can be readily prepared using known technologies in accordance with the present disclosure, e.g., Laurie acid (for ModOlS), Myristic acid (for Mod0l4), Palmitic acid (for Mod0G5), Stearic acid (for Mod015), Oleic acid (for Mod0l 6), Linoleic acid (for Mod017), alpha-Linolenic acid (for ModOlS), gamma-Linolenic acid (for Mod019), docosahexaenoic acid (for Mod006), Turbinaric acid (for Mod020), alcohol for Dilinoleyl (for Mod021), Lauryl alcohol (for Mod030), Myristyl alcohol (for Mod03 l), Palmityl alcohol (for Mod032), Stearyl alcohol (for Mod033), etc.) are listed below. Certain example moieties (e.g., lipid moieties, targeting moiety, etc.) and/or example preparation reagents (e.g., acids, alcohols, etc.) for conjugation to oligonucleotide chains include the below with a non-limiting example of a linker:

Mod005 (with -C(0) ~ connecting to, e.g., -NH- of a linker such as L001) and Palmitic acid:

ModOOSLOOl (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

Mod006 (with -C(O)- connecting to, e.g., -NH- of a linker such as L00I) and DHA:

Mod006L001 (with PO or PS connecting to 5’-0- of an oligonucleotide chain): X = O or S

Mod009 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001 ): H- of a linker such as LOO 1 )

Mod013 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001) and Laurie acid:

Mod013LQ01 (with PO or PS connecting to 5 -0- of an oligonucleotide chain):

Mod014 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001 ) and Myristic acid:

Mod014L001 (with PO or PS connecting to 5’-Q- of an oligonucleotide chain):

Mod()15 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001) and Stearic acid:

Mod0i5L,00i (with PO or PS connecting to 5’-Q- of an oligonucleotide chain):

Mod016 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001) and Oleic acid:

Mod016L001 (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

X = O or S

Mod017 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001) and Linoleic acid:

Mod 017L001 (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

X= O or S

Mod018 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001) and alpha-Linolenic acid:

ModOlBLOOl (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

X = O or S

Mod019 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001) and gamma-Linolenic acid:

Mod0i9L,00i (with PO or PS connecting to 5’-Q- of an oligonucleotide chain):

Mod020 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001) and Turbinaric acid:

Mod020L001 (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

Mod021 (with PO or PS connecting to 5’-0- of an oligonucleotide chain) and alcohol:

Mod024 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001) and acid:

Mod024L001 (with PC) or PS connecting to 5 -O- of an oligonucleotide chain):

Mod026 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001) and acid:

Mod026L001 (with PO or PS connecting to 5’-0- of an oligonucleotide chain): Mod027 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001) and acid:

Mod027L001 (with PO or PS connecting to 5 {) of an oligonucleotide chain):

Mod028 (with -C(O)- connecting to, e.g , -NH- of a linker such as L001):

Mod029 (with -C(O)- connecting to, e.g., -NH- of a linker such as LOOI) and acid:

Mod029L00l (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

Mod030 (with PO or PS connecting to 5 -Q- of an oligonucleotide chain) and Lauryl alcohol:

Mod031 (with PO or PS connecting to 5 -0- of an oligonucleotide chain) and Myristyi alcohol:

Mod032 (with PO or PS connecting to 5 -0- of an oligonucleotide chain) and PaJmityl alcohol:

Mod033 (with PO or PS connecting to 5’-0- of an oligonucleotide chain) and Stearyl alcohol:

Mod053 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Mod070 (with -C(O)- connecting to, e.g., -NH- of a tinker such as L001):

Mod07 ! (with -C(O)- connecting to, e.g., -NH- of a linker such as L001)

Mod086 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001 ):

Mod092 (with -C(O)- connecting to, e.g., -NH- of a linker such as L,001):

Mod093 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001 ):

Mod007 (with -C(O)- connecting to, e.g., -NH- of a linker such as

Mod050 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Mod043 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Mod057 (with -C(O)- connecting to, -NH- of a linker such as L001)

Mod058 (with -C(O)- connecting to, e.g , -NH- of a linker such as L001):

Mod059 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001): Mod066 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Mod074 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Mod085 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Mod091L00l (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

(e.g., in WV-11 1 14, X = O (PO) and connecting to 5’-0- of the oligonucleotide chain) Mod097 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Mod098 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Mod099 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001)

Mod 100 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Modl02 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Modi 03 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Mod 104 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Mod 105 (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Mod 106 (with PO or PS connecting to 5 -Q- of an oligonucleotide chain):

(e.g., in WV-15844, X = O (PO) and connecting to 5 -0- of the oligonucleotide chain)

Mod 107 (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

(e.g., in WV-15845 and WV-16011 , X = O (PO) and connecting to 5’-Q~ of the oligonucleotide chain) ModlOB (with -C(O)- connecting to, e.g., -NH- of a linker such as L001):

Modl09L001 (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

Modi 10L001 (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

(e.g., mWV-19793,X = 0)

Modi 11:

Modi 1 1L001 (with PO or PS connecting to 5’-0- of an oligonucleotide chain)

Modi 13L001 (with PO or PS connecting to 5 () of an oligonucleotide chain):

-19796, X = O)

Modi 14:

Modi 14L001 (with PO or PS connecting to 5’-0- of an oligonucleotide chain);

Modi 15L001 (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

(e.g., in WV-19798, X = O)

Modi 18:

Modi 18L001 (with RO or PS connecting to 5’-0- of an oligonucleotide chain):

Modi 19L001 (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

Modl20L00l (with PO or PS connecting to 5’-0- of an oligonucleotide chain):

L009n001L009n001L009n001L009: connected to the 5’ -position of the 5’ terminal sugar of an oligonucleotide chain (e.g., for WV -23576 and WV -23578, sugar of fU) through a phosphodiester:

L009n001L009n001L009n001 : connected to the S’-position of the 5’ terminal sugar of an oligonucleotide chain (e.g., for WV -23577 and WV-23579, sugar of fU) through nOOl :

L010n001L0l0n001L010n001L009: connected to the 5’ -position of the 5’ terminal sugar of an oligonucleotide chain (e.g., for WV -23936 and WV-23938, sugar of fU) through a phosphodiester:

LOlOnOOlLOlOnOOlLOlOnOOl : connected to the 5’ -position of the 5’ terminal sugar of an oligonucleotide chain (e.g., for WV -23937 and WV-23939, sugar of fU) through nOOl :

[00737] In some embodiments, some functional groups are optionally protected, e.g., for Mod024 and/or Mod 026, the hydroxyl groups are optionally protected as AcO-, before and/or during conjugation to oligonucleotide chains, and the functional groups, e.g., hydroxyl groups, can be deprotected, for example, during oligonucleotide cleavage and/or deprotection:

[00738] Applicant notes that presented in Table Al are example ways of presenting structures of provided oligonucleotides, for example, WV-3546

(Mod020L00 lfU* SfC* SfA* SfA* SfG* SfG* SmAfA* SmGmA* SfU* SmGmGfC* SfA* SfU* SfU* SfU* Sf

C*SfU) can be presented as a lipid moiety (Mod020, ) connected via -C(O)- (OOSSSSSSOSOSSOOSSSSSS, which “O” may be omitted as in Table Al ) to the -NH- of -NH-(CH 2 ) 6 _ , wherein the -(CH 2 ) 6 ~ is connected to the 5 '-end of the oligonucleotide chain via a phosphodiester linkage (OOSSSSSSOSOSSOOSSSSSS). One having ordinary skill in the art understands that a provided oligonucleotide can be presented as combinations of lipid, linker and oligonucleotide chain units in many different ways, wherein in each way the combination of the units provides the same oligonucleotide. For example, WV-3546, can be considered to have a structure of and have a lipid moiety R^ of connected to its oligonucleotide chain (A c ) unit through a linker L LD having the structure of -C(0)-NH-(CH 2 ) 6 -0P(=0)(0H)-0-, wherein -C(O)- is connected to R lD , and -O- is connected to A c (as 5’-0- of the oligonucleotide chain); one of the many

alternative ways is that

---NH---(CH2)6 OP(=O)(OH)---()---, wherein -NH- is connected to R LD , and O is connected to A c (as 5’ Q of the oligonucleotide chain).

[00739] In some embodiments, each phosphorothioate intemucleotidic linkage of an oligonucleotide is independently a chirally controlled intemucleotidic linkage. In some embodiments, a provided oligonucleotide composition is a chirally controlled oligonucleotide composition of an oligonucleotide type listed Table Al, wherein each phosphorothioate intemucleotidic linkage of the oligonucleotide is independently a chirally controlled intemucleotidic linkage.

100740| In some embodiments, the present disclosure provides compositions comprising or consisting of a plurality of provided oligonucleotides (e.g., chirally controlled oligonucleotide compositions) hi some embodiments, ail oligonucleotides of the plurality are of the same type, i.e., all have the same base sequence, pattern of backbone linkages, patern of backbone chiral centers, and pattern of backbone phosphorus modifications. In some embodiments, all oligonucleotides of the same type are structural identical. In some embodiments, provided compositions comprise oligonucleotides of a plurality of oligonucleotides types, typically in controlled amounts. In some embodiments, a provided chirally controlled oligonucleotide composition comprises a combination of two or more provided oligonucleotide types.

[00741] In some embodiments, an oligonucleotide composition of the present disclosure is a chirally controlled oligonucleotide composition, wherein the sequence of the oligonucleotides of its plurality comprises or consists of a base sequence listed in Table Al.

[00742] In some experiments, provided oligonucleotides can provide surprisingly high activities, e.g., when compared to those of Drisapersen and/or Eteplirsen. For example, chirally controlled oligonucleotide compositions of WV-887, WV-892, WV-896, WV-1714, WV-2444, WV-2445, WV- 2526, WV-2527, WV-2528, and WV-2530, and many others, each showed a superior capability, in some embodiments many fold higher, to mediate skipping of an exon in dystrophin, compared to Drisapersen and/or Eteplirsen. Certain data are provided in the present disclosure as examples.

100743| In some embodiments, the present disclosure pertains to a composition comprising a chiraily controlled oligonucleotide selected from any DMD oligonucleotide listed herein, or any DMD oligonucleotide having a base sequence comprising at least 15 consecutive bases of any DMD oligonucleotide listed herein.

[00744] In some embodiments, a provided oligonucleotide is no more than 25 bases long. In some embodiments, a provided oligonucleotide is no more than 25 to 60 bases long. In some embodiments, a U can be replaced with T, or vice versa.

[00745] In some embodiments, when assaying example oligonucleotides in mice, oligonucleotides (e.g., WV-3473, WV-3545, WV-3546, WV-942, etc.) are intravenous injected via tail vein in male C57BL/lOScSndmdmdx mice (4-5 weeks old), at tested amounts, e.g., 10 mg/kg, 30 mg/kg, etc. In some embodiments, tissues are harvested at tested times, e.g., on Day, e.g., 2, 7 and/or 14, etc., after injection, in some embodiments, fresh-frozen in liquid nitrogen and stored in -80 °C until analysis.

[00746] Various assays can be used to assess oligonucleotide levels in accordance with the present disclosure. In some embodiments, hybrid-ELISA is used to quantify oligonucleotide levels in tissues using test article serial dilution as standard curve: for example, in an example procedure, maleic anhydride activated 96-well plate (Pierce 15110) was coated with 50 mΐ of capture probe at 500 nM in 2.5% NaHCOS (Gibco, 25080-094) for 2 hours at 37 °C. The plate was then washed 3 times with PBST (PBS + 0.1% Tween-20), and blocked with 5% fat free milk-PBST at 37 °C for 1 hour. Test article oligonucleotide was serial diluted into matrix. This standard together with original samples were diluted with lysis buffer (4 M Guanidine; 0.33% N-Lauryl Sarcosine; 25 mM Sodium Citrate; 10 mM DTT) so that oligonucleotide amount in all samples is less than 100 ng/mL. 20 mΐ of diluted samples were mixed with 180 mΐ of 333 nM detection probe diluted in PBST, then denatured in PCR machine (65 °C, 10 min, 95 °C, 15 min, 4 C ). 50 mΐ of denatured samples were distributed in blocked ELISA plate in triplicates, and incubated overnight at 4 °C. After 3 washes of PBST, 1:2000 streptavidin-AP in PBST was added, 50 mΐ per well and incubated at room temperature for I hour. After extensive wash with PBST, 100 mΐ of AttoPhos (Promega Si 000) was added, incubated at room temperature in dark for 10 min and read on plate reader (Molecular Device, M5) fluorescence channel: Ex435 nm, Em555 nm. Oligonucleotides in samples were calculated according to standard curve by 4-parameter regression.

[00747] In some embodiments, provided oligonucleotides are stable in both plasma and tissue homogenates. Additional Embodiments and Examples of Oligonucleotides and Compositions, including Dystrophin (DMD) Oligonucleotides and Compositions

|00748] Among other things, the present disclosure provides oligonucleotides, compositions, and methods for, modulating splicing, reducing target levels, treating various conditions, disorders, diseases, etc. For example, in some embodiments, the present disclosure provides dystrophin (DMD) oligonucleotides and/or DMD oligonucleotide compositions that are useful for various purposes. In some embodiments, a DMD oligonucleotide and/or composition is capable of mediating skipping of exon 23 in the mouse DMD gene. In some embodiments, a DMD oligonucleotide and/or composition is capable of mediating skipping of exon 44 in the human or mouse DMD gene. In some embodiments, a DMD oligonucleotide and/or composition is capable of mediating skipping of exon 46 in the human or mouse DMD gene. In some embodiments, a DMD oligonucleotide and/or composition is capable of mediating skipping of exon 47 in the human or mouse DMD gene. In some embodiments, a DMD oligonucleotide and/or composition is capable of mediating skipping of exon 51 in the human or mouse DMD gene. In some embodiments, a DMD oligonucleotide and/or composition is capable of mediating skipping of exon 52 in the human or mouse DMD gene. In some embodiments, a DMD oligonucleotide and/or composition is capable of mediating skipping of exon 53 in the human or mouse DMD gene. In some embodiments, a DMD oligonucleotide and/or composition is capable of mediating skipping of exon 54 in the human or mouse DMD gene. In some embodiments, a DMD oligonucleotide and/or composition is capable of mediating skipping of exon 55 in the human or mouse DMD gene.

[00749] In some embodiments, a DMD oligonucleotide and/or composition is capable of mediating skipping of multiple exons in the human or mouse DMD gene.

[00750] In some embodiments, a provided oligonucleotide, e.g., a DMD oligonucleotide, comprises a modification. In some embodiments, a DMD oligonucleotide comprises a sugar modification. In some embodiments, a DMD oligonucleotide comprises a sugar modification at the 2 position. In some embodiments, a DMD oligonucleotide comprises a sugar modification at the T position selected from 2’-F, 2 -QMe and 2’-MOE.

[00751] In some embodiments, a DMD oligonucleotide comprises a 2’-F, 2’-OMe and/or T-

MOE. In some embodiments, a DMD oligonucleotide comprises a 2 -F. In some embodiments, in a DMD oligonucleotide, each sugar comprises a 2 -F.

[00752] In some embodiments, a DMD oligonucleotide comprises a 2’-OMe. In some embodiments, in a DMD oligonucleotide, each sugar comprises a 2’~QMe. In some embodiments, a DMD oligonucleotide comprises a 2’-MOE. In some embodiments, in a DMD oligonucleotide, each sugar comprises a 2’-MOE. [00753] In some embodiments, a provided oligonucleotide, e.g., a DMD oligonucleotide comprises a 2’-QMe and a 2’-F. in some embodiments, a provided oligonucleotide, e.g., a DMD oligonucleotide, comprises a patern of 2’ sugar modifications, wherein the patern comprises a sequence selected from: fin, mf, ffhi, fffm, ffffin, fffffm, ffffffm, fffffffm, ffffffffin, fffffffffhi, mf, mff mfff, mffff, mffSTf. mffffff, mfffffff, mfffffff, finf, fmmf, finmmf, finmmmf, fmmmmmf, fmmmmmmf, fmmmmmmmf, fmmmmmmmmf, fmmmmmmmmmf, ffffffhimmmmmmmffffff, fffffmmnunmmmmnnnfffff, ffffmmmmmmmmmmmmffff, fffmmmmmmmmmminmmmfff, ffinminnimmmmmmmmnnnnimff, finnimmmmmmmmnnnnimmmmmf, ffffffffffinnimmmmmmmm, fffffmmmmmrnmrnffffff, ffffmmrnmmmmmmmfffff, fffirimmmmmmmmmrnmffff, flinmmmmmmmmmmmmmfff, fmmmmmmmmmmmmmmmmff, mmmmmmmmmmmmmmmmmmf, fffffffffinmmmmmmmmm, ffffinmmmmmmmffffff, fffinmmmmmmmmmfffff, ffhnnnimmmmmmmmmffff, fmmminnimmmmmmmmmfff, inmmmmmmmnnnmmmmmmff, mmmmmmmmmmmmmmmmmf, ffffffffmrnmmmmmmmm, fffmmrnmmmmmffffff, ftmmmmmmmmmmfffff, fmmmmmmmmmmmmffff, mmmmmmmmmmmmmmfff, mmmmmmmmmmmmmmmff, mmmmmmmmmmmmmmmmf, fffffffmmmmmmmmmm, ffinnnnmmmmmffffff, fhunnimmmmmmmfffff, mmmmmnnnmmmmmffff, mmmmmmnnnmmmmmfff, mmmnnnnnnmmmmmmmff mmmnnnmmmmmmmminnif, ffffffinnnnmmmmmmm, finmrnmmmmmffffff, mmmmmmmmmmfffff, mmmmmmmmmmmffff, mmmmmmrnmmmmmfff, mmmmmmmmmmmmmff, mmmmmmmmmmmmmmf, fffffmmmmmmmmmm, mmmmmmmmffffff, mmmmmmmmmfffff, mmmmmmmmmmffff, mmmmmmmmmmmfff, mmmmmmmmmmmmff, mmmmmmnnnnnnmmmf, ffffinmmnnnmmmmm, ffffffmmmnimmmmfffff, fffffinmmmmmmmnnnffff, ffffirimmmmmmmrnmmmfff, fffmrnmmmmmmmmmmmmff, ffmmmmmmmrnmmmmmmmmf, fmmmmmmmmmmmmmmmmmm, ffffffffffinmmmmmmmm, ffffffmmmmmmmmffff, ffffimmmmmmmmmmfff, ffffhimmmmmmmmmmmff, fffinmmmmmmmmmmmmmf ffinnnnmmmmmmmmmnnnnim, fmmminnnnmmmmmmmminnnn, ffffffffffinmmmmmmm, ffffffmmmrnmrnmmfff, fffffmmmmmmmrnmmff, ffffinmmmmmmmmmmmf, fffinmmmmmmmmmmmmm, ffmmmmmmmmmmmmmmm, ftnmmmmmmmmmmmmmmm, ffffffffffinmmmmmm, ffffffhimmmmmmmff, fffffmmmmmmmmmmf, ffffmmmmmmmmmmmm, fffnimmmmmmmmminnnn, ffinnnnmmmmmmmmmmin, finmmminnimmmmmmmmm, ffffffffffinmmmmm, ffffffmmmmmmmmf, fffffmmmmmmmmmm, ffffmmmmmmmmmmm, fftmmmmmmmmmmmm, flinmmmmmmmmmmmm, fmmmmmmmmmmmmmm, ffffffffffmmmmm, ffffffmmmmmmmm, fffffinmmmmmmmm, ffffhnnmmmmmmmm, fffhimmmmmmmmmm, ffinnimmmmmmmmnnn, fhnnmmnimmmmmmmm, ffffffffffinmmm, ffffffinmmmmmm, fffffmmmmmmmm, ffffinmmmmmmmm, fffmmmmmmmmmm, ftmmmmmmmmmmm, fmmmrnmmmmmmmm, ffffffffffmmm, ffffffmmrnmmm, fffffmmmmmmm, ffffmmmmmmrnm, fffmmmmmmmmm, ffmmmmmmmmmm, fmmmmmmmmmmm, ffffffffffmm, ffffffmmmmui, fffffirimmmmm , ffffmmmmmmm, fffmmmmmmmm, fimmmmmmmmm, fmmmmmmmmmm, ffffffffffm, nimmmmmmmmmffffffffff, ffffffinmmmmmmmmmmrnmrn, mmmmmmrnmmmmmmmffffff, ffinmmmmmmmfrnmfmfffff, mmffffffffmffmfmmmmrn, mfmfmfmfmfmfmfmfmfmf, mmmmmmffffffftmmmmmm, ffffffmm mmmmm mffffff mfmmffmmfmmffifnmmmfm, fmffinmffmffinmmffffinf, I ' m if. mffin, finffin, mfmmf, fmmf, fmffmm, mfmmff, mmff, fmmff, mmffm, fhiffmmf, mfmmfim, mfmm, mfmmf, mfmmff, fmffinmf. mfmmffm, mmffm, ffrnmf, fmfff, mfffin, fmfffm, fmfffmm, rnfinmfff, mmfffi, fmmfff, mmfffin, fmfffrnmf, mfmmfffm, mfmm, mfmmf, mfmmfff, tmfffmmf, mfmmfffm, mmfffin, ffffnmf, mfinmmf, fmmmf, finffinmm, mfmmmff, mmmff, finmmff mmmffm, fmffmmmf, mfmmmffm, mfmmm, mfinmmf, mfmmmff, fmffmmmf, mfmmmffm, mmmffm, fffnmmf, or any portion thereof comprising at least five consecutive modifications, wherein f is 2’-F and m is 2’-0Me.

In some embodiments, a provided oligonucleotide, e.g., a DMD oligonucleotide, comprises a patern which comprises any of: O, 00, OOO, 0000, 00000, 000000, 0000000,

00000000, 000000000, 0000000000, 00000000000, s, ss, sss, ssss, sssss,

SSSSSS, SSSSSSS, SSSSSSSS, SSSSSSSSS, SSSSSSSSSS, SSSSSSSSSSS, X, XX, XXX, xxxx, xxxxx. xxxxxx. xxxxxxx. xxxxxxxx, xxxxxxxxx, xxxxxxxxxx,

XXXXXXXXXXX, R, RR, RRR, RRRR, RRRRR, RRRRRR, RRRRRRR, RRRRRRRR. RRRRRRRRR. RRRRRRRRRR, RRRRRRRRRRR, OSOOO, OSOO, OSO, SOOO, 0X000, 0X00, 0X0, XOO, ROOOR, ROROR, ROROR, ROORR, RROOR, ROOR, OOR, RRROR, RRRO, RROR, ROR, SOOOR, ROOOS, ROOO, ROO, RO, OOOS, SOOOS, SOOO, SOOSS, SOSOS, SOSO, OSOS,

SOS, SSOOS, SSOO, SSO, SOO, SSSOS, SSSO, SOS, xooox, xooo, xoo, o, ooox, oox, ox, SOOOS, SOOO, SOO, so, ooos, oos, xxxxxxx xxxxxx . xxxxxx xxxxxx. xxxxxxxxxx, xxxxxxxxxx, xxxxxxxxx, xxxxxxxx, xxxxxxx, xxxxxx, XXXXX, XXXX, SSSSRSSRSS, SSSSRSSRS, SSSSRSSR, SSSSRSS, SSSSRS, SSSS, SSS, SSSRSSRSS, SSRSSRSS, SRSSRSS, RSSRSS, SSRSS, SSRS, SSSRSSRSSS, SSRSSRSSS, SSSRSSRSS, SSRSSRSSSS, SRSSRSSSS, SSRSSRSSS, SSR SSSSSSS. SR SSSSSSS. SSRSSSSSS, SSSSSSRSSS, SSSSSRSSS, SSSSSSRSS, SSO, SOS, 0S0, 0SS0, SSOS, SSOSS, SSOSSO, SSOSSOS, SSOSSOSS, XO, XXO, XOX, XXOX, XXOXX, XXXOXX, XXXOX, xxoxx, CCCOCCC, XXOXXO, XXOXX, XXOXXOX, or CCOCCOCC, or any portion thereof comprising at least 5 consecutive intemucleotidic linkages, wherein X is a stereorandom phosphorothioate linkage, S is a phosphorothioate linkage of the Sp configuration, and R is a phosphorothioate linkage of the Rp configuration. Various oligonucleotides, including DMD oligonucleotides, having these modifications and patterns thereof, or portions thereof, are described in the present disclosure, including those listed in Table A 1

[00756] In some embodiments, a DMD oligonucleotide comprises a non-negatively charged intemucleotidic linkage. Non-limiting examples of such an oligonucleotide include, inter alia: WV- 11237, WV-l 1238, WV-11239, WV-11340, WV-11341, WV-11342, WV-11343, WY-11344, WV-

11345, WV-l 1346, WV-l 1347, WV-12123, WV-12124, WV-12125, WV-12126, WV-12127, WV-

12128, WV-12129, WV-12130, WV-12131, WV-12132, WV-12133, WV-12134, WV-12135, WV-

12136, WV- 12553, WV-12554, WV-12555, WV-12556, WV-12557, WV-12558, WV-12559, WV-

12872, WV-12873, WV-12876, WV-12877, WV-12878, WV-12879, WV-12880, WV-12881, WV-

12882, WV-l 2883, WV-12884, WV-12885, WV-12887, WV-12888, WV-13408, WV-13409, WV-

13594, WV-13593, WV-13596, WV-13597, WV-13812, WV-13813, WV-13814, WV-13815, WV-

13816, WV-13817, WV-13820, WV-13821, WV-13822, WV-13823, WV-13824, WV-13825, WV-

13857, WV-l 3858, WV-l 3859, V-13860, WV-13861, WV-13862, WV-13863, WV-13864, WV-

13865, WV-14342, WV-14343, WV-14344, WV-14345, WV-14522, WV-14523, WV-l 4525, WV-

14526, WV-14528, WV-14529, WV-l 4530, WV-14532, WV-l 4533, WV-14565, WV-l 4566, WV-

14773, WV-14774, WV-14776, WV-14777, WV-14778, WV-14779, WV-14790, WV-14791, WV-

15052, WV-l 5053, W-15143, WV-15322, V-15323, WV-15324, WV-15325, WV-15326, WV- 15327, WV-l 5328, /V- 15329. WV-15330, V-15331, WV-15332, WV-15333, WV-15334, WV- 15335, WV-15336, WV-15337, WV-15338, WV-15366, WV-15369, WV-15589, WV-15647, WV-

15844, WV-15845, WV-15846, WV-15850, WV-l 5851, WV-15852, WV-l 5853, WV-15854, WV-

15855, WV-15856, WV-15857, WV-15858, WV-15859, WV-15860, WV-15861, WV-15862, WV-

15912, WV-15913, WV-15928, /V- 15929, WV-15930, WV-15931, WV-15932, WV-15933, WV-

15934, WV-l 5935, WV-15937, WV-15939, WV-15940, WV-15941, WV-15942, WV-15943, WV-

15944, WV-l 5945, WV-15946, WV-l 5947, WV-15948, WV-l 5949, WV-15962, WV-l 5963, WV-

15964, WV-l 5965 WV-15966, WV-15967, WV-15968, WV-15969, WV-15970, WV-15971, WV-

15972, WV-l 5973, WV-16004, WV-16005, /V- 16010, WV-16011, WV-16366, WV-16368, WV- 16369, WV-16371, WV-16372, WV-16499, WV-16505, WV-16506, WV-16507, WV-17765, WV-

17774, WV-17775, WV-17801, WV-17802, WV-l 7803, WV-17831 , WV-17832, WV-17833, WV-

17834 WV-17838. WV-17839, WV-17840. WV-17841, WV-17842 WV- 17843, WV-17854, WV-

17855, WV-17856, WV-1785 W-17858. WV-17859, WV-17860. WV-17861, WV-17862. WV-

17863, WV-17864, WV-17865, WV-17866, WV-17881, WV-17882, WV-17883, WV-l 8853, WV-

18854, WV-l 8855, WV-18856, WV-l 8857, WV-18858, WV-l 8859, WV-18860, WV-l 8861, WV-

18862 WV-18863 WV-18864. WV-18865, WV-18866. WV-18867, WV-18868. WV-l 8869, WV- 18870, WV-18871, WV-18872, WV-18873, WV-18874, WV- 18875, WV-18876, WV-18877, wv-

18878, WV-18879, WV-18880, WV-18881, WV-18882, WV-18883, WV-18884, WV-18885, wv-

18886, WV-18887, WV-18888, WV-18889, WV-18890, WV-18891, WV-18892, WV-18893, wv-

18894, WV-18893, WV'- 18896, WV-18897, WV-l 8898, WV -18899, WV-18900, WV-18901 , wv-

18902, WV-18903, WV- 18904, WV-18905, WV-18906, WV- 18907, WV-18908, WV-18909, wv-

18910, WV-18911, WV-18912, WV-18913, WV-l 8914, WV-18915, WV-18916, WV-18917, wv-

18918, WV-18919, WV- 18920, WV-18921, WV-l 8922, WV-18923, WV-18924, WV-18925, wv-

18926, WV-18927, WV- 18928, WV-18929, WV-l 8930, WV- 18931, WV-18932, WV-18933, wv-

18934, WV-18935, WV-18936, WV-18937, WV-18938, WV-18939, WV-18940, WV-18941, wv-

18942, WV- 18944, WV-18945, WV-19790, WV-l 9791, WV- 19792, WV-19793, WV-19794, wv-

19795, WV- 19796, WV- 19797, WV-19798, WV-19803, WV- 19804, WV-19805, WV-19806, wv-

19886, WV-19887, WV-19888, WV-19889, WV-l 9890, WV- 19891 , WV-19892, WV -19893, wv-

19894, WV-19895, WV- 19896, WV-19897, WV-19898, WV- 19899, WV-19900, WV- 19901 , wv-

19902, WV-19903, WV- 19904, WV-19905, WV-19906, WV- 19907, WV-19908, WV- 19909, wv-

19910, WV-19911, WV-19912, WV-19913, WV-19914, WV-19915, WV-19916, WV-19917, wv-

19918, WV-19919, WV- 19920, WV-19921, WV-l 9922, WV-19923, WV-19924, WV- 19925, wv-

19926, WV-19927, WV- 19928, WV-19929, WV-l 9930, WV- 19931, WV-19932, WV- 19933, wv-

19934, WV-19935, WV-19936, WV-19937, WV-19938, WV-19939, WV-19940, WV- 19941, wv-

19942, WV-19943, WV- 19944, WV-19945, wv-l 9946, WV- 19947, WV-19948, WV-19949, wv-

19950, WV- 19951, WV- 19952, WV-19953, WV-19954, WV-19955, WV-19956, WV-19957, wv-

19958, WV-19959, WV- 19960, WV- 19961 , WV-19962, WV- 19963, WV-19964, WV- 19965, wv-

19966, WV- 19967, WV- 19968, WV- 19969, WV-19970, WV- 19971, WV-19972, WV- 19973, wv-

19974, WV- 19975, WV- 19976, WV- 19977, WV-19978, WV- 19979, WV-19980, WV-19981, wv-

19982, WV-19983, WV- 19984, WV-19985, WV-19986, WV- 19987, WV-19988, WV-19989, wv-

19990, WV- 19991, WV- 19992, WV- 19993, WV-19994, WV- 19995, WV-19996, WV- 19997, wv-

19998, WV- 19999, WV -20000, WV -20001, WV -20002, WV-20003, W -20004, WV -20005, wv-

20006, WV -20007, WV -20008, WV -20009, WV-20010, WV-20011, WV -20012, WV -20013, wv-

20014, WV-20015, WV-20016, WV-20017, WV-20018, WV-20019, WV -20020, WV-20021 , wv-

20022, WV-20023, WV -20024, WV -20025, WV' -20026, WV -20027, WV -20028, WV -20029, wv-

20030, WV-20031, WV -20032, WV -20033, WV -20034, WV -20035, WV-20036, WV -20037, wv-

20038, WV-20039, WV -20040, WV-20041, WV -20042, WV-20043, WV -20044, WV -20045, wv-

20046, WV -20047, WV-20048, WV-20049, WV -20050, WV -20051, WV -20052, WV -20053, wv-

20054, WV-20055, WV-20056, WV-20057, WV-20058, WV-20059, WV -20060, WV-20061, wv-

20062, WV-20063 WV-20064, WV-20065. WV -20066, WV -20067. WV -20068, WV -20069, wv- 20070, WV-20071, WV -20072, WV -20073, WV -20074, WV -20075, WV -20076, WV -20077, WV-

20078, WV -20079, WV -20080, WV-20081, WV -20082, WV -20083, WV-20084, WV -20085, WV-

20086, WV-20087, WV-20088, WV -20089, WV -20090, WV-20091, WV-20092, WV -20093, WV-

20094, WV-20095, WV-20096, WV -20097, WV -20098, WV -20099, WV-20100, WV-20101 , WV-

20102, WV-20103, WV-20104, WV-20105, WV-20106, WV-20107, WV-20108, WV-20109, WV-

20110, WV-20111, WV-20112, WV-20113, WV-20114, WV-20115, WV-20116, WV-20117, WV-

20118, WV -201 19, WV-20120, WV-20121, WV-20122, WV-20123, WV-20124, WV-20125, WV-

20126, WV-20127, WV-20128, WV-20129, WV-20130, WV-20131, WV -20132, WV -20133, WV-

20134, WV-20135, WV-20136, WV-20137, WV-20138, WV-20139, WV-20140, WV -20141, WV-

20142, WV-20143, WV-20144, WV-20145, WV-20146, WV-20147, WV-20148, WV-20149, WV-

20150, WV-20151, WV-20152, WV-20153, WV-20154, WV-20155, WV-20156, W -20157, WV-

20158, WV-20159, WV-20160, WV-21210, WV-2121 1, WV -21212, WV-21217, WV-21218, WV-

21219, WV-21226, WV-21245, WV-21252, WV-21253, WV -21257, WV-21258, WV -21374, WV-

21375, WV-21376, WV-21377, WV-21378, WV -21379, WV-21380, WV-21381, WV-21382, WV-

21383, WV-21384, WV-21385, WV-21386, WV-21387, WV-21388, WV-21389, WV-21390, WV-

21578, WV-21579, WV-21580, WV-21581, WV-21582, WV-21583, WV-21584, WV-21585, WV-

21586, WV-21587, WV-21588, WV-21589, WV-21590, WV-21591, WV-21592, WV-21593, WV-

21594, WV-21595, WV-21596, WV-21597, WV-21598, WV-21599, WV-21600, WV-21601, WV-

21602, WV-21603, WV-21604, WV -21605, WV-21606, WV-21607, WV-21608, WV-21609, WV-

21610, WV-21611, WV-21612, WV-21613, WV-21614, WV-21615, WV-21616, WV-21617, WV-

21618, WV-21619, WV-21620, WV-21621 , WV-21622, WV -21623, WV-21624, WV -21625, WV-

21626, WV-21627, WV-21628, WV-21629, WV-21630, WV-21631, WV-21632, WV-21633, WV-

21634, WV-21635, WV -21636, WV -21637, WV-21638, WV-21639, WV-21640, WV-21641, WV-

21642, WV-21643, WV-21644, WV-21645, WV-21646, WV -21647, WV-21648, WV-21649, WV-

21650, WV-21651, WV-21652, WV-21653, WV-21654, WV-21655, WV- -21656, WV-21657, WV-

21658, WV-21659, WV-21660, WV-21661, WV-21662, WV-21663, WV-21664, WV-21665, WV-

21666, WV-21667, WV-21668, WV-21669, WV-21670, WV-21671, WV-21672, WV -21673, WV-

21723, WV-21724, WV-21725, WV-21726, WV-21727, WV-21728, WV-21729, WV-21730, WV-

21731, WV-21732, WV-21733, WV-21734, WV-21735, WV -21736, WV-21737, WV -21738, WV-

21739, WV-21740, WV -21741, WV-21742, WV-21743, WV-21744, WV-21745, WV-21746, WV-

21747, WV-21748, WV-21749, WV-21750, WV-21751, WV-21752, WV-21753, WV-21754, WV-

21755, WV-21756, -21757, WV-21758, WV-21759, WV-21760, WV-21761, WV-21762, WV-

21763, WV-21764, -21765, WV-21766, WV-21767, WV-21768, WV-21769, WV -21770, WV-

21771, WV-21773, WV-21774. WV-21775, WV-21776. WV -21777, WV-21778, WV- 21779, WV-21780, WV-21781, WV-21782, WV-21783, WV-21784, WV-21785, WV-21786, WV-

21787, WV-21788, WV-21789, WV-21790, WV-21791, WV-21792, WY-21793, WV-21794, WV-

21795, WV-21796, WV-21797, WV-21798, WV-21799, WV-21800, WV-21801, WV-21802, WV-

21803, WV-21804, WV-21805, WV-21806, WV-21807, WV-21808, WV-21809, WV-21810, WV-

21811, WV-21812, WV -21813, WV-21814, WV -21815, WV-21816, WV-21817, WV-21818, WV-

22753, WV-23576, WV-23577, WV-23578, WV-23579, WV-23936, WV-23937, WY-23938, and WV- 23939.

Example Dystrophin Oligonucleotides and Compositions for Exon Skipping of Exon 23

[00757] In some embodiments, the present disclosure provides oligonucleotides, oligonucleotide compositions, and methods of use thereof for mediating skipping of exon 23 in mouse DMD Non- limiting examples include oligonucleotides and compositions of WV-10256, WV- 10257, WV-10258, WV- 10259, WV- 10260, WV-1G93, WV-1 Q94, WV-1095, WV-1096, WV-1097, WV-1098, WV-1099, WV-1100, WV-1101, WV-1102, WV-1103, WV-1104, WV-1105, WV-1106, WV-1121, WV-1122, WV- 1123, WV-1 1231, WV-11232, WV-11233, WV-11234, WV-11235, WV-11236, WV-1124, WV-1125, WV-1126, WV-1127, WV-1128, WV-1129, WV-1130, WV-11343, WV-11344, WV-11345, WV-11346, WV-1 1347, WV-1141, WV-1142, WV-1143, WV-1 144, WV-1 145, WV-1 146, WV-1 147, WV-1 148, WV-1149, WV-1150, WV-1678, WV-1679, WV-1680, WV-1681, WV-1682, WV-1683, WV-1684, WV- 1685, WV-2733, WV-2734, WV-4610, WV-4611, WV-4614, WV-4615, WV-4616, WV-4617, WV-

4618, WV-4619, WV-4620, WV-4621, WV-4622, WV-4623, WV-4624, WV-4625, WV-4626, WV-

4627, WV-4628, WV-4629, WV-4630, WV-4631, WV-4632, WV-4633, WV-4634, WV-4635, WV-

4636, WV-4637, WV-4638, WV-4639, WV-4640, WV-4641, WV-4642, WV-4643, WV-4644, WV-

4645, WV-4646, WV-4647, WV-4648, WV-4649, WV-4650, WV-4651, WV-4652, WV-4653, WV-

4654, WV-4655, WV-4656, WV-4657, WV-4658, WV-4659, WV-4660, WV-4661, WV-4662, WV-

4663, WV-4664, WV-4665, WV-4666, WV-4667, WV-4668, WV-4669, WV-4670, WV-4671, WV-

4672, WV-4673, WV- 4674, WV-4675, WV-4676, WV-4677, WV-4678, WV-4679, WV-4680, WV-

4681, WV-4682, WV-4683, WV-4684, WV-4685, WV-4686, WV-4687, WV-4688, WV-4689, WV-

4690, WV-4691, WV-4692, WV-4693, WV-4694, WV-4695, WV-4696, WV-4697, WV-6010, WV-

7677, WV-7678, WV-7679, WV-7680, WV-7681, WV-7682, WV-7683, WV-7684, WV-7685, WV-

7686, WV-7687, WV-7688, WV-7689, WV-7690, WV-7691, WV-7692, WV-7693, WV-7694, WV-

7695, WV-7696, WV-7697, WV-7698, WV-7699, WV-7700, WV-7701, WV-7702, WV-7703, WV-

7704, WV-7705, WV-7706, WV-7707, WV-7708, WV-7709, WV-7710, WV-7711, WV-7712, WV-

7713, WV-7714, WV-7715, WV-7716, WV-7717, WV-7718, WV-7719, WV-7720, WV-7721, WV-

7722, WV- 7723, WV-7724, WV- 7725, WV-7726, WV-7727, WV-7728, WV-7729, WV-7730, WV- 7731, WV-7732, WV-7733, WV-7734, WV-7735, WV-7736, WV-7737, WV-7738, WV-7739, WV- 7740, WV-7741, WV-7742, WV-7743, WV-7744, WV-7745, WV-7746, WV-7747, WV-7748, WV- 7749, WV-7750, WV-7751, WV-7752, WV-7753, WV -7754, WV-7755, WV-7756, WV-7757, WV- 7758, WV-7759, WV-7760, WV-7761 , WV-7762, WV-7763, WV-7764, WV-7765, WV-7766, WV- 7767, WV-7768, WV-7769, WV-7770, WV-7771, WV-9163, WV-9164, WV-9165, WV-9166, WV- 9167, WV-9168, WV-9169, WV-9170, WY-9171, WV-9172, WV-9173, WV-9174, WV-9175, WV- 9176, WV-9177, WV-9178, WV-9179, WV-9180, WV-9181, WV-9182, WV-9183, WV-9184, WV- 9185, WV-9186, WV-9187, WV-9188, WV-9189, WV-9190, WV-9191 , WV-9192, WV-9193, WV- 9194, WV-9195, WV-9196, WV-9197, WV-9198, WV-9199, WV-9200, WV-9201, WV-9202, WV- 9203, WV-9204, WV-9205, WV-9206, WV-9207, WV-9208, WV-9209, WV-9210, WV-9408, WV- 9409, WV-9410, WV-9411, WV-9412, WV-9413, WV-9414, WV-9415, WV-9416, WV-9417, WV-

9418, WV-9419, WV-9420, WV-943, WV-9875, WV-9876, WV-9877, WV-9878, and WV-9879, and other oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

[00758] In some embodiments, a DMD oligonucleotide is capable of mediating skipping of exon

23. Non-limiting examples of such DMD oligonucleotides include: WV-12566, WV-12567, WV-12568, WV-12884, WV-12885, WV-12886, WV-12887, WV-12888, WV-12571, and WV-12572, and other DMD oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

[00759] Exon skipping of DMD exon 23 and other exons may be assayed in patient-derived cell lines and in cells from the mdx mouse model (which carries a nonsense point mutation in the in-frame exon 23 (Sicinski et al. 1989 Science 244: 1578-1580). By skipping exon 23 the nonsense mutation is bypassed while the reading frame is maintained). Additional strains of mdx mice, including the mdx ' . mdx 4cv and mdx 5l,v alleles were reported by Wha Bin Im et al. 1996 Hum. Mol. Gen. 5: 1149-1153.

[00760] Data showing the capability of various DMD oligonucleotides to mediate skipping of exon 23 is shown herein, inter alia, in Table 1A.1, Table 1A.2, Table 1A.3, and Table 25C.1 to Table 25C.5.

[00761] Example Dystrophin Oligonucleotides and Compositions Targeting Exon 44 and

Adjoining Intronic Region 3’ to Exon 44

[00762] in some embodiments, a DMD oligonucleotide targets DMD exon 44 or the adjoining intronic region 3’ to DMD exon 44.

100763] In some embodiments, a DMD oligonucleotide targets DMD exon 44 or the adjoining intronic region 3’ to DMD exon 44, and the oligonucleotide is capable of mediating multiple exon skipping (e.g., of exons 45 to 55, or 45 to 57).

[00764] Reportedly, a phenomenon known as back-splicing can occur, in which, for example, a portion of the 3’ end of exon 55 interacts with a portion of the 5’ end of exon 45, forming a circular RNA (circRNA), which can thus skip multiple exons, e.g., all exons from exon 45 to 55, inclusive. The phenomenon can also reportedly occur between exon 57 and exon 45, skipping multiple exons, e.g., all exons from exon 45 to 57, inclusive. Back -splicing is described in the literature, e.g., in Suzuki et a!. 2016 hit. I. Mol. Sci. 17.

[00765] Without wishing to be bound by any particular theory, the present disclosure suggests that it may be possible for a DMD oligonucleotide targeting DMD exon 44 or the adjoining intronic region 3’ to exon 44 may be able to mediate splicing of exons 45 to 55, or of exons 45 to 57, which exons are excised as a single piece of circular RNA (circRNA) designated 45-55 (or 55-45) or 45-57 (or 57-45), respectively.

100766] Several oligonucleotides were designed to target exon 44 or intron 44, or which straddle exon 44 and intron 44. In some embodiments, oligonucleotides designed to target exon 44 or intron 44, or which straddle exon 44 and intron 44 are tested to determine if they can increase the amount of backslicing and/or multiple-exon skipping.

100767] In some embodiments, the present disclosure provides oligonucleotides, oligonucleotide compositions, and methods of use thereof for mediating exon skipping in human DMD, wherein the base sequence of the oligonucleotide is a sequence of exon 44 or intron 44, or a portion of both exon 44 and intron 44. Non-limiting examples include oligonucleotides and compositions of WV-13963, WV- 13964, WV-13965, WV-13966, WV-13967, WV-13968, WV-13969, WV-13970, WV-13971, WV-13972, WV- 13973, WV-13974, WV-13975, WV-13976, WV-13977, WV-13978, WV-13979, WV-13980, WV-

13981, WV-13982, WV-13983, WV-13984, WV-13985, WV-13986, WV-13987, WV-13988, WV-

13989, WV-13990, WV-13991, WV-13992, WV-13993, WV-13994, WV-13995, WV-13996, WV-

13997, WV-13998, WV-13999, WV-14000, WV-14001 , WV-14002, WV-14003, WV-14004, WV-

14005, WV- 14006, WV-14007, WV-14008, WV-14009, WV-14010, WV-14011, WV-14012, WV-

14013, WV-14014, WV-14015, WV-14016, WV-14017, WV-14018, WV-14019, WV-14020, WV-

1402.1, WV-14022, WV-14023, WV-14024, WV-14025, WV-14026, WV-14027, WV-14028, WV-

14029, WW- 14030, WV-14031, WV-14032, WV-14033, WV-14034, WV-14035, WV-14036, WV-

14037, WV-14038, WV-14039, WV-14040, WV-14041, WV-14042, WV-14043, WV-14044, WV-

14045, WV- 14046, WV-14047, WV-14048, WV-14049, WV-14050, WV-14051, WV-14052, WV-

14053, WV- 14054, WV-14055, WV-14056, WV-14057, and WV-14058, and other oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides. [00768] Data showing the capability of various DMD oligonucleotides targeting exon 44 or the adjacent intron 3’ to exon 44 are shown in Table 22A.2 and Table 22A.3.

[00769] Table 1 A.1. Example data of certain oligonucleotides

[00770] Oligonucleotides to DMD exon 23 were tested in vitro for their ability to induce skipping of exon 23.

[00771] H2K cells were dosed with oligonucleotide in differentiation media for 4days RNA was extracted with Trizol, pre-amp then treated with TaqMan with multiplexed reading of skipped and total DMD transcript; absolute quantification was via standard curve g-Blocks. In these and various other studies, numbers indicate amount of skipping (i.e., skipping efficiency; or the percentage of skipping as a percentage of total mRNA transcript).

[00772] Oligonucleotides were tested at 10, 3 33, 1.11, 0.37, or 0 12 uM.

[00773] Table 1A.2. Activity of certain oligonucleotides

[00774] In this study, in vivo skipping activity was measured in MDX mouse model after single IV dose.

[00775] MDX mice received single IV dose of 150mg/kg. Necropsied flash frozen tissues (Quadriceps, Diaphragm, etc.) were pulverized and RNA extracted with Trizol. Skipping efficiency was determined by multiplex TaqMan assay for‘total’ and‘exon-23 skipped’ DMD transcripts, normalized to gBiock standard curves.

[00776] Numbers indicate amount of skipping DMD exon 23 (as a percentage of total niRNA, wfhere 100 would represent 100% skipped).

[00777] Table 1A.3. Activity of certain oligonucleotides

[00778] Oligonucleotides were tested in vitro for ability to skip DMD exon 23.

[00779] Oligonucleotides were tested at 10, 3 3., 1.1, 0.3, and 0.1 uM.

[00780] Numbers indicate amount of skipping DMD exon 23 (as a percentage of total mRNA, where 100 would represent 100% skipped).

Example Dystrophin Oligonucleotides and Compositions for Exon Skipping of Exon 45

[00781] In some embodiments, the present disclosure provides oligonucleotides, oligonucleotide compositions, and methods of use thereof for mediating skipping of exon 45 in DMD (e.g., of mouse, human, etc.).

[00782] In some embodiments, a provided DMD oligonucleotide and/or composition is capable of mediating skipping of exon 45. Non-limiting examples of such DMD oligonucleotides and compositions include those of: WV-1 1047, WV-1 1048, WV-11049, WV-11050, WV-11051, WV-1 1052, WV-11053, WV-11054, WV-11055, WV-11056, WV-11057, WV-11058, WV-11059, WV-1 1060, WV-1 1061, WV- 11062, WV-11063, WV-11064, WV-11065, WV-11066, WV-11067, WV-11068, WV-11069, WV-

11070, WV-11071, WV-11072, WV-11073, WV-11074, WV-11075, WV-11076, WV-1 1077, WV-

11078, WV-11079, WV-11080, WV-1 1081, WV-11082, WV-1 1083, WV-11084, WV-1 1085, WV-

11086, WV-11087, WV-11088, WV-11089, WV-11090, WV-11091, WV-11092, WV-1 1093, WV-

11094, WV-11095, WV-11096, WV-11097, WV-11098, WV-11099, WV-11100, WV-11101, WV-

11102, WV-11103, WV-11104, WV-11105, WV-9594, WV-9595, WV-9596, WV-9597, WV-9598, WV-

9599, WV-9600, WV-9601 , WV-9602, WV-9603, WV -9604, WV-9605, WV-9606, WV-9607, WV- 9608, WV-9609, WV-9610, WV-9611, WV-9612, WV-9613, WV-9614, WV-9615, WV-9616, WV- 9617, WV-9618, WV-9619, WV-9620, WV-9621, WV-9622, WV-9623, WV-9624, WV-9625, WV- 9626, WV-9627, WV-9628, WV-9629, WV-9630, WV-9631, WV-9632, WV-9633, WV-9634, WV- 9635, WV-9636, WV-9637, WV-9638, WV-9639, WV-9640, WV-9641 , WV-9642, WV-9643, WV- 9644, WV-9645, WV-9646, WV-9647, WV-9648, WV-9649, WV-9650, WV-9651, WV-9652, WV- 9653, WV-9654, WV-9655, WV-9656, WV-9657, WV-9658, WV-9659, WV-9762, WV-9763, WV- 9764, WV-9765, WV-9766, WV-9767, WV-9768, WV-9769, WV-9770, WV-9771, WV-9772, WV- 9773, WV-9774, WV-9775, WV-9776, WV-9777, WV-9778, WV-9779, WV-9780, WV-9781, WV- 9782, WV-9783, WV-9784, WV-9785, WV-9786, WV-9787, WV-9788, WV-9789, WV-9790, WV- 9791, WV-9792, WV-9793, WV-9794, WV-9795, WV-9796, WV-9797, WV-9798, WV-9799, WV- 9800, WV-9801, WV-9802, WV-9803, WV-9804, WV -9805, WV -9806, WV-9807, WV-9808, WV- 9809, WV-9810, WV-9811, WV-9812, WV-9813, WV-9814, WV-9815, WV-9816, WV-9817, WV- 9818, WV-9819, WV-9820, WV-9821, WV-9822, 5 W-9823, WV-9824, WV-9825, and WV-9826, and other DMD oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides. [00783] As shown in various tables from Table 1 to Table 22 (and parts thereof), various DMD oligonucleotides comprising various patterns of modifications were testing for skipping of various exons. The Tables show test results of certain DMD oligonucleotides. To assay exon skipping of DMD, certain DMD oligonucleotides were tested in vitro in D52 human patient-derived myoblast cells (also designated DELS 2) and/or D45-52 human patient-derived myoblast cells (human cells wherein the exon 52 or exons 45-52 were already deleted, also designated DEL45-52) Unless noted otherwise, in various experiments, oligonucleotides were delivered gymnotically. In the tables, generally, 100.00 would represent 100% skipping and 0.0 would represent 0% skipping. Various DMD oligonucleotides are described in detail in Table Al .

[00784] Table 1 A.4, below, shows example data of some DMD oligonucleotides in skipping exon

45. Procedure: D48-50 (Del48-50 or D48-50) myoblasts were treated with 10 uM oligonucleotides for 4 days in differentiation media.

Table 1A.4. Example data of certain oligonucleotides.

Numbers represent level of skipping, wherein 100 would represent 100% slapping and 0 would represent 0% skipping. For various data described herein,“Mock” is a negative control, in which water was used instead of an oligonucleotide.

Table 1B.1. and IB.2 Example data of certain oligonucleotides.

The Tables below show example data of some DMD oligonucleotides in skipping exon 45. Procedure: D48-50 (Del48-50 or DEL48-50 or D48-50) myoblasts were treated with 10 or 3 uM oligonucleotides for

4 days in differentiation media.

Oligonucleotides were dosed at 10 m.M and 3 mM for 4 days in DEL48-50 Myoblasts. Certain oligonucleotides comprise a non -negatively charged internucieotidic linkage, as detailed in Table Al . Table 1B.1. Example data of certain oligonucleotides.

Table 1B.2. Example data of certain oligonucleotides.

Additional data related to multiple exon skipping mediated by DMD oligonucleotides which target DMD exon 45 are shown m Table 22A.1.

Example Dystrophin Oligonucleotides and Compositions Which Target Exon 46

[00785] In some embodiments, the present disclosure provides oligonucleotides, oligonucleotide compositions, and methods of use thereof for targeting exon 46 and/or mediating skipping of exon 46 in human DMD Non-limiting examples include oligonucleotides and compositions of WV-13701 , WV- 13702, WV-13703, WV-13704, WV-13705, WV-13706, WV-13707, WV-13708, WV-13709, WV- 13710, WV-13711, WV-13712, WV-137I3, WV-I3714, WV-13715, WV-13716, WV-13780, and WV- 13781, and other oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

[00786] In some embodiments, DMD oligonucleotides are first tested for single exon skipping to select suitable oligonucleotides, then tested combinatonally ( combination with another DMD oligonucleotide) for multi-exon skipping.

[00787] In some embodiments, DMD oligonucleotides targeting DMD exon 46, 47, 52, 54 or 55 are first tested for single exon skipping to select suitable oligonucleotides, then tested combinatorially (in combination with another DMD oligonucleotide) for multi-exon skipping.

Table 2A. Example data of certain oligonucleotides. Numbers indicate percentage of exon 46 skipping.

Example Dystrophin Oligonucleotides and Compositions Which Target Exon 47

[00788] In some embodiments, tire present disclosure provides oligonucleotides, oligonucleotide compositions, and methods of use thereof for targeting exon 47 and/or mediating skipping of exon 47 in human DMD. Non-limiting examples include oligonucleotides and compositions of exon 47 oiigos include: WV-13717, WV-13718, WV-13719, WV-13720, WV-13721, WV-13722, WV-13723, WV- 13724, WV-13725, WV-13726, WV-13727, WV-13728, WV-13729, WV-13730, WV-13731, WW- 13732, WV-13788, and WV-13789, and other oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

Table 3A. Example data of certain oligonucleotides. Numbers represent percentage of exon 47 skipping.

Example Dystrophin Oligonucleotides and Compositions for Exon Skipping of Exon 51

[00789] In some embodiments, the present disclosure provides oligonucleotides, oligonucleotide compositions, and methods of use thereof for mediating skipping of exon 51 in DMD (e.g., of mouse, human, etc.).

[00790] In some embodiments, a provided DMD oligonucleotide and/or composition is capable of mediating skipping of exon 51. Non-limiting examples of such DMD oligonucleotides and compositions include those of: ONT-395, WV-10255, WV-10261, WV-1G262, WV-10634, WV-10635, WV-10636, WV-10637, WV-10868, WV-10869, WV-10870, WV-10871, WV-10872, WV-10873, WV-10874, WW- 10875, WV-10876, WV-10877, WV-10878, WV-10879, WV-10880, WV-10881 , WV-10882, WV- 10883, WV-10884, WV-10885, WV-10886, WV-10887, WV-10888, WV-1107, WV-1 108, WV-1109, WV-1110, WV-1111, WV-1112, WV-1113, WV-1114, WV-1115, WV-1116, WV-1117, WV-1118, WV- 1119, WV-1120, WV-11237, WV-11238, WV-11239, WV-1131, WV-1132, WV-1133, WV-1 134, WV-

1135, WV-1136, WV-1137, WV-1138, WV-1139, WV-1140, WV-1 151, WV-1 152, WV-1 153, WV-

1154, WV-1155, WV-1156, WV-1157, WV-1158, WV-1159, WV-1160, WV-1709, WV-1710, WV-

1711, WV-1712, WV-1713, WV-1714, WV-1715, WV-1716, WV-2095, WV-2096, WV-2097, WV- 2098, WV-2099, WV-2100, WV-2101, WV-2102, WV-2103, WV-2104, WV-2105, WV-2106, WV- 2107, WV-2108, WV-2109, WV-2165, WV-2179, WV-2180, WV-2181, WV-2182, WV-2183, WV- 2184, WV-2185, WV-2186, WV-2187, WV-2188, WV -2189, WV-2190, WV-2191, WV-2192, WV- 2193, WV-2194, WV-2195, WV-2196, WV-2197, WV-2198, WV-2199, WV-2200, WV-2201, WV· 2202, WV- 2203, WV-2204, WV- 2205, WV- 2206, WV -2207, WV-2208, WV-2209, WV-2210, WV 2211, WV-2212, WV-2213, WV-2214, WV-2215, WV-2216, WV-2217, WV-2218, WV-2219, WV 2220, WV-2221, WV-2222, WV-2223, WV-2224, WV-2225, WV -2226, WV-2227, WV-2228, WV· 2229, WV-2230, WV-2231, WV-2232, WV-2233, WV-2234, WV-2235, WV-2236, WV-2237, WV· 2238, WV-2239, WV-2240, WV-2241, WV-2242, WV-2243, WV-2244, WV-2245, WV-2246, WV- 2247, WV-2248, WV-2249, WV-2250, WV-2251, WV-2252, WV-2253, WV-2254, WV-2255, WV- 2256, WV-2257, WV-2258, WV-2259, WV-2260, WV-2261, WV-2262, WV-2263, WV-2264, WV- 2265, WV-2266, WV-2267, WV-2268, WV-2273, WV -2274, WV-2275, WV-2276, WV-2277, WV- 2278, WV- 2279, WV-2280, WV-2281, WV-2282, WV -2283, WV-2284, WV-2285, WV-2286, WV 2287, WV-2288, WV-2289, WV-2290, WV-2291, WV-2292, WV-2293, WV-2294, WV-2295, WV 2296, WV-2297, WV-2298, WV-2299, WV-2300, WV-2301, WV-2302, WV-2303, WV-2304, WV 2305, WV-2306, WV-2307, WV-2308, WV-2309, WV-2310, WV -231 1 , WV-2312, WV-2313, WV- 2314, WV-2315, WV-2316, WV-2317, WV-2318, WV-2319, WV-2320, WV-2321 , WV-2322, WV· 2323, WV-2324, WV-2325, WV-2326, WV-2327, WV-2328, WV-2329, WV-2330, WV-2331, WV- 2332, WV-2333, WV-2334, WV-2335, WV-2336, WV-2337, WV-2338, WV-2339, WV-2340, WV· 2341, WV-2342, WV-2343, WV-2344, WV-2345, WV -2346, WV-2347, WV-2348, WV-2349, WV· 2350, WV-2351 , WV-2352, WV-2353, WV-2354, WV-2361, WV-2362, WV-2363, WV-2364, WV- 2365, WV- 2366, WV-2367, WV-2368, WV-2369, WV -2370, WV-2381, WV-2382, WV-2383, WV 2384, WV-2385, WV-2432, WV-2433, WV-2434, WV-2435, WV-2436, WV-2437, WV-2438, WV 2439, WV-2440, WV-2441, WV-2442, WV-2443, WV-2444, WV-2445, WV-2446, WV-2447, WV- 2448, WV-2449, WV-2526, WV-2527, WV-2528, WV-2529, WV-2530, WV-2531 , WV-2532, WV- 2533, WV-2534, WV-2535, WV-2536, WV-2537, WV-2538, WV-2578, WV-2579, WV-2580, WV- 2581, WV-2582, WV-2583, WV-2584, WV-2585, WV-2586, WV-2587, WV-2588, WV-2625, WV- 2627, WV-2628, WV-2660, WV-2661, WV-2662, WV-2663, WV-2664, WV-2665, WV-2666, WV- 2667, WV-2668, WV-2669, WV-2670, WV-2737, WV-2738, WV-2739, WV-2740, WV-2741, WV- 2742, \VW-2743, WV-2744, WV-2745, WV-2746, WV -2747, WV-2748, WV-2749, WV-2750, WV 2752, WV-2783, WV-2784, WV-2785, WV-2786, WV-2787, WV-2788, WV-2789, WV-2790, WV 2791, WV-2792, WV-2793, WV-2794, WV-2795, WV-2796, WV-2797, WV-2798, WV-2799, WV- 2800, WV-2801, WV-2802, WV-2803, WV-2804, WV-2805, WV -2806, WV-2807, WV-2808, WV- 2812, WV-2813, WV-2814, WV-3017, WV-3018, WV-3019, WV-3020, WV-3022, WV-3023, WV- 3024, WV-3025, WV-3026, WV-3027, WV-3028, WV-3029, WV-3030, WV-3031, WV-3032, WV- 3033, WV-3034, WV-3035, WV-3036, WV-3037, WV-3038, WV-3039, WV-3040, WV-3041, WV- 3042, WV-3043, WV-3044, WV-3045, WV-3046, WV-3047, WV-3048, WV-3049, WV-3050, WV- 3051 , WV-3052, WV-3053, WV-3054, WV-3055, WV-3056, WV-3057, WV-3058, WV-3059, WV- 3060, WV-3061, WV-3070, WV-3071, WV-3072, WV -3073, WV-3074, WV-3075, WV-3076, WV- 3077, WV-3078, WV-3G79, WV-3080, WV-3081, WV-3082, WV-3083, WV-3084, WV-3085, WV- 3086, WV-3087, WV-3088, WV-3089, WV-31 13, WV-31 14, WV-3115, WV-3116, WV-3117, WV- 3118, WV-3120, WV-3121, WV-3152, WV-3153, WV-3357, WV-3358, WV-3359, WV-3360, WV- 3361, WV-3362, WV-3363, WV-3364, WV-3365, WV-3366, WV-3463, WV-3464, WV-3465, WV- 3466, WV-3467, WV-3468, WV-3469, WV-3470, WV-3471, WV-3472, WV-3473, WV-3506, WV- 3507, WV-3508, WV-3509, WV-3510, WV-3511, WV-3512, WV-3513, WV-3514, WV-3515, WV- 3516, WV-3517, WV-3518, WV-3519, WV-3520, WV-3543, WV-3544, WV-3545, WV-3546, WV- 3547, WV-3548, WV-3549, WV-3550, WV-3551, WV -3552, WV-3553, WV-3554, WV-3555, WV- 3556, WV-3557, WV-3558, WV-3559, WV-3560, WV-3753, WV-3754, WV-3820, WV-3821, WV- 3855, WV-3856, WV-3971, WV-4106, WV-4107, WV-4191, WV-4231, WV-4232, WV-4233, WV- 4890, WV-6137, WV-6409, WV-6410, WV-6560, WV-6826, WV-6827, WV-6828, WV-7109, WV- 7110, WV-7333, WV-7334, WV-7335, WV-7336, WV-7337, WV-7338, WV-7339, WV-7340, WV- 7341, WV-7342, WV-7343, WV-7344, WV-7345, WV-7346, WV-7347, WV-7348, WV-7349, WV- 7350, WV-7351, WV-7352, WV-7353, WV-7354, WV-7355, WV-7356, WV-7357, WV-7358, WV- 7359, WV-7360, WV-7361, WV-7362, WV-7363, WV-7364, WV-7365, WV-7366, WV-7367, WV- 7368, WV-7369, WV-7370, WV-7371 , WV-7372, WV-7373, WV-7374, WV-7375, WV-7376, WV- 7377, WV-7378, WV-7379, WV-7380, WV-7381, WV-7382, WV-7383, WV-7384, WV-7385, WV- 7386, WV-7387, WV-7388, WV-7389, WV-7390, WV-7391, WV-7392, WV-7393, WV-7394, WV- 7395, WV-7396, WV-7397, WV-7398, WV-7399, WV-7400, WV-7401, WV-7402, WV-7410, WV- 7411, WV-7412, WV-7413, WV-7414, WV-7415, WV-7457, WV-7458, WV-7459, WV-7460, WV- 7461, WV-7506, WV-7596, WV-8130, WV-8131, WV-8230, WV-8231, WV-8232, WV-8449, WV- 8478, WV-8479, WV-8480, WV-8481, WV-8482, WV-8483, WV-8484, WV-8485, WV-8486, WV- 8487, WV-8488, WV-8489, WV-8490, WV-8491, WV -8492, WV-8493, WV-8494, WV-8495, WV-

8496, WV-8497, WV-8498, WV-8499, WV-8500, WV-8501, WV-8502, WV-8503, WV-8504, WV-

8505, WV -8506, WV-8806, WV- 84, WV-885, WV-886, WV-887, WV-888, WV-889, WV-890, WV- 891, WV -892, WV-893, WV-894, WV-895, WV-896, WV-897, WV-9222, WV-9223, WV-9224, WV- 9225, WV-9226, WV-9227, WV-942, WV-9540, WV-9541, WV-9737, WV-9738, WV-9739, WV-9740, WV-9741, WV-9742, WV-9827, WV-9828, WV-9829, WV-9830, WV-9831, WV-9832, WV-9833, WV- 9834, WV-9835, WV-9836, WV-9837, WV-9838, WV-9839, WV-9840, WV-9841 , WV-9842, WV- 9843, WV-9844, WV-9845, WV-9846, WV-9847, WV-9848, WV-9849, WV-9850, WV-9851, WV-

9852, WV-9858, and WV-8937, and other DMD oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

Additional non-limiting examples of such DMD oligonucleotides and compositions include those of: WV-2444, WV-2528, WV-2531, WV-2578, WV-2579, WV-2580, WV-2581, WV-

2669, WV-2745, WV-3032, WV-3152, WV-3153, WV-3360, WV-3363, WV-3364, WV-3465, WV-

3466, WV-3470, WV-3472, WV-3473, WV-3507, WV-3545, WV-3546, WV-3552, WV-4106, WV-

4231 , WV-4232 WV-4233, WV-887, WV-896, WV-942, and other DMD oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

[00792] Additional non-limiting examples of such DMD oligonucleotides and compositions include those of: WV-12494. WV-12130. WV-12131 WV-12132, WV-12133, WV-12134. WV-1 2135.

WV-12136, WV- 12496, WV- 12495, WV- 12123, WV-12124, WV- 12125, WV-12126, WV-12127, WV-

12128, WV-12129, WV-12553, WV-12554, WV-12555, WV-12556, WV-12557, WV-12558, WV- 12559, WV-12872, WV-12873, WV-12876, WV-12877, WY-12878, WV-12879, WV-12880, WV- 12881, WV-12882, and WV-12883, and other DMD oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides

[00793] In some embodiments, the sequence of the region of interest for exon 51 skipping differs between the mouse and human.

[00794] Various assays can he utilized to assess oligonucleotides for exon skipping in accordance with the present disclosure. In some embodiments, in order to test the efficacy of a particular combination of chemistry and stereochemistry of an oligonucleotide intended for exon 51 skipping in human, a corresponding oligonucleotide can be prepared which has the mouse sequence, and then tested in mouse. The present disclosure recognizes that in the human and mouse homologs of exon 51, a few differences exist (underlined below):

M GTGGTTACTAAGGAAACTGTCATCTCCAAACTAGAAATGCCATCTTCTTTGCTGTTGGAG H GTGGTTACTAAGGAAACTGCCATCTCCAAACTAGAAATGCCATCTTCCTTGATGTTGGAG

where M is Mouse nt 7571-7630; and H is Human nt 7665-7724.

[00795] Because of these differences, slightly different DMD oligonucleotides for skipping exon

51 can he prepared for testing in mouse and human. As a non-limiting example, the following DMD oligonucleotide sequences can be used for testing in human and mouse:

HUMAN DMD oligonucleo de sequence : UCAAGGAAGAUGGGAUUUCU

MOUSE DMD oligonucleo de sequence : GCAAAGAAGAUGGCAUUUCU

Mismatches between human and mouse are underlined.

QQ796] A DMD oligonucleotide intended for treating a human subject can be constructed with a particular combination of base sequence (e.g., UCAACXiAAGAUG CAUUUCU), and a particular pattern of chemistry, miemucieotklic linkages, stereochemistry, and additional chemical moieties (if any). Such a DMD oligonucleotide can be tested in vitro in human cells or in vivo in human subjects, but may have limited suitability for testing in mouse, for example, because base sequences of the two have mismatches.

[00797] A corresponding DMD oligonucleotide can be constructed with the corresponding mouse base sequence (GCAAAGAAGAUGGCAUUUCU) and the same pattern of chemistry, intemucleotidic linkages, stereochemistry, and additional chemical moieties (if any). Such an oligonucleotide can be tested in vivo in mouse. Several DMD oligonucleotides comprising the mouse base sequence were constructed and tested.

[00798] In some embodiments, a human DMD exon skipping oligonucleotide can be tested in a mouse which has been modified to comprise a DMD gene comprising the human sequence.

|00799] Various DMD oligonucleotides comprising various patterns of modifications are described herein. The Tables below show test results of certain DMD oligonucleotides. To assay exon skipping of DMD, DMD oligonucleotides were tested in vitro in D52 human patient-derived myoblast cells and/or D45-52 human patient-derived myoblast cells (human cells wherein the exon 52 or exons 45- 52 were already deleted). Unless noted otherwise, in various experiments, oligonucleotides were delivered gymnotically.

Table 4A. Example data of certain oligonucleotides.

DMD oligonucleotides were tested in vitro at lOuM and 3uM, in triplicates. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown. Full descriptions of the oligonucleotides tested in this Table (and other Tables) are provided in Table A1.

In Table 4B, below, additional data of DMD oligonucleotides for skipping exon 51 were presented. Table 4B. Example data of certain oligonucleotides.

DMD oligonucleotides were tested at lOuM and 3uM, in triplicates. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

[00801] In Table 4C, below, additional data of DMD oligonucleotides for skipping exon 51 were presented.

Table 4C. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

[00802] In Table 4D, below, additional data of DMD oligonucleotides for skipping exon 51 were presented.

Table 4D. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

00803] In Table 5, below, additional data of DMD oligonucleotides for skipping exon 51 were presented.

Table 5. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency: results from replicate experiments are shown.

Table 6. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency: results from replicate experiments are shown. Numbers are approximate.

Oligonucleotides were delivered gymnotica!ly to D48-50 patient-derived myoblasts (4 days post- differentiation). The oligonucleotide designated as“PMO” in this table and other tables related to skipping of DMD exon 51 is WV-8806 CTCCAACATCAAGGAAGATGGCATTTCTAG, which is fully PMO (Morpholino).

In Table 7, below, additional data of DMD oligonucleotides for skipping exon 51 were presented.

Table 7. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown. Numbers are approximate.

[00805] In some embodiments, the present disclosure pertains to metabolites of any oligonucleotide, e.g., DMD oligonucleotide, disclosed herein, or any combination thereof. In some embodiments, a metabolite of an oligonucleotide, e.g., a DMD oligonucleotide is the result of an oligonucleotide, e.g., a DMD oligonucleotide being acted upon by a nuclease (e.g., an exonuclease or endonuclease or other enzymes, including those may chemically process one or more modifications of an oligonucleotide). In some embodiments, a “metabolite” of an oligonucleotide, e.g., a DMD oligonucleotide is not the physical product of such an oligonucleotide being metabolized or physically treated with a nuclease, but rather a compound which corresponds chemically to a product of tin oligonucleotide being metabolized or treated with an enzyme, e.g., a nuclease. In some embodiments, metabolite of an oligonucleotide, e.g., a DMD oligonucleotide, is chemically synthesized, without any metabolic process, and optionally administered to a subject.

[00806] In some embodiments, a metabolite is a truncation of an oligonucleotide on the 5’ end and/or 3’ end by one or two nucleotides or nucleosides. In some embodiments, the present disclosure provides an oligonucleotide, e.g., DMD oligonucleotide which corresponds to an oligonucleotide, e.g., DMD oligonucleotide listed herein, but is truncated at the 5’ end by one or two nucleotides. In some embodiments, the present disclosure provides an oligonucleotide, e.g., a DMD oligonucleotide which corresponds to an oligonucleotide, e.g., a DMD oligonucleotide listed herein, but is truncated at the 3’ end by one or two nucleotides. In some embodiments, the present disclosure provides an oligonucleotide, e.g., a DMD oligonucleotide which corresponds to an oligonucleotide, e.g., a DMD oligonucleotide listed herein, but is truncated at the 3’ end and 5’ end by one or two nucleotides. Among other things, such oligonucleotides may perform various of biological functions, e.g., such DMD oligonucleotides can mediate skipping of exon 23, 45, 51 , 53, or any other DMD exon.

[00807] In some embodiments, the present disclosure pertains to a DMD oligonucleotide which has the base sequence of a DMD oligonucleotide listed herein, except that the base sequence is shorter on the 5’ end by one or two bases. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which has the base sequence of a DMD oligonucleotide listed herein, except that the base sequence is shorter on the 3’ end by one or two bases in some embodiments, the present disclosure pertains to a DMD oligonucleotide which has the base sequence of a DMD oligonucleotide disclosed herein, except that the base sequence is shorter on the 3’ end and the 5’ end by one or two bases. Such DMD oligonucleotides, among other things, can mediate skipping of exon 23, 45, 51, 53, or any other DMD exon.

[00808] In some embodiments, a metabolite of a DMD oligonucleotide has removed from the oligonucleotide an additional moiety (e.g., a lipid or other conjugated moiety).

[00809] In some embodiments, an oligonucleotide of the present disclosure may be a metabolite of another oligonucleotide. For example, several oligonucleotides may be metabolite of WV-3473, for example, WV-4231 (3' n-1 , truncated at the 3’ end by one nucleotide), WV-4232 (3' n-2), WV-4233 (5' n- 1), etc. Example data of such‘ metabolite” oligonucleotides were presented in Table 9 below (at 1, 3 and 10 uM, in replicates). Generally, an oligonucleotide can be used independently whether or not it can be a metabolite of another oligonucleotide.

Table 9. Example data of certain oligonucleotides.

Results of replicate experiments are shown. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown. In tins and other tables, PMO is a Morpholino oligonucleotide control.

[00810] In some embodiments, the present disclosure pertains to DMD oligonucleotides corresponding to any DMD oligonucleotide to exon 51 or any other exon listed herein (e.g., in Table Al), but which are truncated by one, two or more nucleotides on the 5’ end and/or 3’ end.

1008111 In some embodiments, the length of a provided oligonucleotide, e.g., a DMD oligonucleotide, is 15 to 45 bases. In some embodiments, the length of a provided oligonucleotide, e.g., a DMD oligonucleotide, is 20 to 45 bases. In some embodiments, the length of a provided oligonucleotide, e.g., a DMD oligonucleotide, is 20 to 40 bases. In some embodiments, the length of a provided oligonucleotide, e.g., a DMD oligonucleotide, is 35 bases. In some embodiments, the length of a provided oligonucleotide, e.g., a DMD oligonucleotide, is 20 to 25 bases. [00812] In some experiments, lengths of DMD oligonucleotides for slapping exon 51 are 20 or 25 bases.

Tables 10A and 10B. Example data of certain oligonucleotides.

Table 10.4 shows data of 20-mers for skipping DMD exon 51; Table 10B shows data of 25-mers for skipping DMD exon 51. Sequences are provided in Table Al. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

Table 10A. 20-mers

Table 10B. 25-mers

|00813] Additional data are provided.

Table 10C. Example data of certain oligonucleotides.

Oligonucleotides were tested in vitro at 10, 3 and 1 mM. Results of replicate experiments are shown. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents

0% efficiency; results from replicate experiments are shown.

Table 10D. Example data of certain oligonucleotides.

Oligonucleotides were tested in vitro at 10, 3 and 1 mM. Results of replicate experiments are shown. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

Table 10E. Example data of certain oligonucleotides.

Oligonucleotides were tested in vitro at 10, 3 and 1 m.M. Results of replicate experiments are shown. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

Table 10F. Example data of certain oligonucleotides.

Oligonucleotides were tested in vitro at 10, 3 and 1 mM. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

Table 10G. Example data of certain oligonucleotides.

Oligonucleotides were tested in vitro at 10, 3 and 1 m.M. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

Table 10H. Example data of certain oligonucleotides.

Oligonucleotides were tested in vitro at 10 and 3 DM. In this table, in some cases, serum and/or BSA were added to test the effect on exon skipping. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

Table 101. Example data of certain oligonucleotides.

Oligonucleotides were tested in vitro at 10, 3 and 1 m.M. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

Table 10J. Example data of certain oligonucleotides.

Oligonucleotides were tested in vitro at 10, 3 and 1 mM. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

Table 10K. Example data of certain oligonucleotides.

Oligonucleotides were tested in vitro at 10 iiM. In this table, numbers represent skipping efficiency relative to WV-942 (ave); results from replicate experiments are shown .

Table 10L. Example data of certain oligonucleotides.

Oligonucleotides were tested in vitro at 10 and 3 mM In this table, numbers represent skipping efficiency relative to WV-942 (ave); results from replicate experiments are shown .

[00814] In some embodiments, an oligonucleotide, e.g., a DMD oligonucleotide, can be tested in vivo for capability to skip an exon in a tissue in a live animal; in some embodiments, a tissue is gastrocnemius, triceps, quadriceps, diaphragm, and/or heart. In some embodiments, a live animal is a mouse, rat, monkey, dog, or non-human primate in some embodiments, an oligonucleotide, e.g., a DMD oligonucleotide, is capable of mediating skipping, e.g., of exon 23, 45, 51, 53, or any other DMD exon. Various DMD oligonucleotides were shown to mediate skipping of DMD exon 51 in a tissue in a non human primate (NHP), wherein the tissue was gastrocnemius, triceps, quadriceps, diaphragm, or heart j00815] In some embodiments, the present disclosure pertains to methods of administering oligonucleotides, e.g., DMD oligonucleotides, wherein the timeline of pre-differentiation (of myoblast cells to myotubules) and treatment with the oligonucleotide are suitably altered. In some embodiments, in a test in vitro, an oligonucleotide, e.g., a DMD oligonucleotide to exon 51, was tested with treatment of 1 day or 4 day.

Table 11A. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100 0 would represent 100% skipping and 0.0 represents 0% efficiency. PMC) is a Morpholino having the sequence of

CTCCAACATCAAGGAAGATGGCATTTCTAG.

Conditions for Groups A to€ in Table 1 LA.

Example 19 describes various timelines for experiments suitable for testing oligonucleotides, e.g., DMD oligonucleotides, e.g., in patient-derived myoblasts in vitro.

Table 1 IB. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency. PMO is a control oligonucleotide which is a Morpholino corresponding to Eteplirsen . WV-942 is an oligonucleotide corresponding to Drisapersen. Oligonucleotides were delivered gyrnnotically.

Table 11 C. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0 0 represents 0% efficiency. PMO is a control oligonucleotide winch is a Morpholmo corresponding to Etepiirsen. WV-942 is an oligonucleotide corresponding to Drisapersen. Oligonucleotides were delivered gymnotically.

[00816] In some embodiments, an oligonucleotide comprises a derivative of U. In some embodiments, an oligonucleotide capable of mediating skipping of an exon of DMD comprises a derivative of U. In some embodiments, an oligonucleotide capable of mediating skipping of an exon of DMD and comprises a derivative of U and at least one chi rally controlled intemucleotidic linkage. In some embodiments, an oligonucleotide capable of mediating skipping of an exon of DMD and comprises a derivative of U and at least one chirally controlled phosphorothioate intemucleotidic linkage . In some embodiments, a derivative of U is BrlJ or AcetSU

[00817] In some embodiments, an oligonucleotide comprises BrU. In some embodiments, an oligonucleotide capable of mediating skipping of an exon of DMD comprises BrU. In some embodiments, an oligonucleotide capable of m diating skipping of an exon of DMD and comprises BrU and at least one chiraJly controlled intemucleotidic linkage. In some embodiments, an oligonucleotide capable of mediating skipping of an exon of DMD and comprises BrU and at least one chi rally controlled phosphorothioate intemucleotidic linkage.

[00818] In some embodiments, an oligonucleotide comprises AcetSU. In some embodim nts,

AcetSU is also designated AcetU or acetU. In some embodiments, an oligonucleotide capable of mediating skipping of an exon of DMD comprises AcetSU. In some embodiments, in an oligonucleotide, e.g., DMD oligonucleotide, any U or T can be optionally replaced by AcetSU (e.g., in a first wing, a core, a second wing, or anywhere in the oligonucleotide). In some embodiments, an oligonucleotide capable of mediating skipping of an exon of DMD comprises an AcetSmU nucleoside unit, wherein the base is AcetSU and the sugar is the common natural RNA sugar wherein the 2’ -OH is replaced with 2’-OMe. In some embodiments, an oligonucleotide comprises an AcetSfU nucleoside unit, wherein the base is AcetSU and the sugar is the common natural RNA sugar wherein the 2’ -OH is replaced with 2’-F. In some embodiments, an oligonucleotide capable of mediating skipping of an exon of DMD and comprises AcetSU and at least one chirally controlled intemucleotidic linkage. In some embodiments, an oligonucleotide capable of mediating skipping of an exon of DMD and comprises AcetSU and at least one chiraily controlled phosphorothioate intemucleotidic linkage.

[00819] As shown in Table ! ID, Table HE, and Table Al, certain oligonucleotides, e.g., DMD oligonucleotides, were designed and constructed comprising BrU or acetSU. In some oligonucleotides, the nucleoside at the 5’ end comprises BrU or acetSU. In some embodiments, oligonucleotides comprise a BrfU nucleoside unit, wherein the base is BrU and the sugar is the common natural RNA sugar wherein the 2’-OH is replaced with 2’-F. In some oligonucleotides, the oligonucleotide comprises a BrdU nucleoside unit, wherein the base is BrU and the sugar is 2-deoxyribose (common natural DNA sugar). In some embodiments, any U or T can be replaced by BrU (e.g., in a first wing, a core, a second wing, or anywhere within an oligonucleotide). In some embodiments, in an oligonucleotide, e.g., a DMD oligonucleotide, any number of U or T can be replaced by BrU and/or AcetSU.

[00820] In some embodiments, an oligonucleotide comprises an acetSfU nucleoside unit, wherein the base is acetSU and the sugar is the common natural RNA sugar wherein the 2 -011 is replaced with 2’-F.

[00821] Table 1 ID shows data of various DMD oligonucleotides which mediate skipping of exon

51, including oligonucleotide WV-7410, which comprises BrfU, and WV-7413, which comprises acet5fU. Percentage was measured using RT-qPCR. Gymnotic deliver}' of 10 mM and 3 mM oligonucleotides in D48-50 patient derived myoblasts (4 days post-differentiation). The experiment was done in technical replicates.

Table 1 ID. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency. Approximate numbers are provided. in some embodiments, the present disclosure provides oligonucleotides, e.g , various DMD oligonucleotides, that comprise BrdlJ at or near the center of the oligonucleotides (e.g., in a core region, middle region, etc.). In some embodiments, example such oligonucleotides include WV-2812, WV-2813, and WV-2814. Certain exon skipping data of these oligonucleotides were presented below.

Table 1 IE. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 1.000 would represent 100% skipping and 0.0 represents 0% efficiency. Approximate numbers are provided.

Table 1 IF. Example data of certain oligonucleotides.

Additional DMD oligonucleotides for skipping Exon 51 were constructed. Various DMD oligonucleotides comprise Bril in some eases, a BrU is attached to a sugar which is 27 -F modified (BrfU). D48-50 myoblasts were dosed at 10 uM and 3 uM in differentiation media for 4 days. Percentage of skipping is shown, wherein 100 would represent 100% skipping and 0 would represent 0% skipping.

Table 1 1G. Activity of certain oligonucleotides

Activity of various DMD exon 51 oligonucleotides was tested in vitro.

Numbers indicate amount of skipping DMD exon 23 (as a percentage of total mRNA, where 100 would represent 100% skipped).

Amounts tested were: 10, 3.3 and 1.1 uM.

Table 1 1 1 1 Acti vity of certain oligonucleoti des

Oligonucleotides for skipping DMD exon 51 were tested in vitro.

Numbers indicate amount of skipping DMD exon 23 (as a percentage of total mRNA, where 100 would represent 100% skipped).

Concentrations of oligonucleotides used: 10, 3.3 and 1.1 uM.

Table 111. Activity of certain oligonucleotides

Oligonucleotides for skipping DMD exon 51 were tested in vitro.

Numbers indicate amount of skipping DMD exon 23 (as a percentage of total mRNA, where 100 would represent 100% skipped).

Concentrations of oligonucleotides used: 10 and 3.3 uM.

Table I D. Activity of certain oligonucleotides

Oligonucleotides for skipping DMD exon 51 were tested in vitro.

Oligonucleotides were dosed 4d at lOuM.

Numbers indicate amount of skipping DMD exon 51 (as a percentage of total mRNA, where 100 would represent 100% skipped).

Example Dystrophin Oligonucleotides and Compositions Which Target Exon 52

00822] In some embodiments, the present disclosure provides oligonucleotides, oligonucleotide compositions, and methods of use thereof for targeting exon 52 and/or mediating skipping of exon 52 in human DMD. Non-limiting examples include oligonucleotides and compositions of Exon 52 oligos include: WV-13733, WV-13734, WV-13735, WV-13736, WV-13737, WV-13738, WV-13739, WV- 13740, WV-13741, WV-13742, WV-13743, and WV-13744, WV-13782, and WV-13783, and other oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

Table 12A. Example data of certain oligonucleotides.

Skipping efficiency o various DMD oligonucleotides, tested for skipping of DMD exon 52.

Example Dystrophin Oligonucleotides and Compositions for Exon Skipping of Exon 53

[00823] In some embodiments, the present disclosure provides oligonucleotides, oligonucleotide compositions, and methods of use thereof for mediating skipping of exon 53 in DMD (e.g., of mouse, human, etc.). [00824] In some embodiments, an oligonucleotide, e.g., a human DMD exon 53 slapping oligonucleotide can be tested in a mouse which has been modified to comprise a DMD gene comprising the human exon 53 sequence.

[00825] In some embodiments, an oligonucleotide, e.g., a DMD oligonucleotide, is capable of mediating skipping of exon 53. Non-limiting examples of such oligonucleotides include: WV-10439,

WV- 10440, WV- 10441, WV- 10442, WV- 10443, WV- 10444, WV- 10445, WV 10446, WV-10447, WW- 10448, WV- 10449, WV-10450, WV-10451, WV-10452, WV-10453, WV 10454, WV-10455, WW-

10456, WV-10457, WV-10458, WV-10459, WV-10460, WV-10461, WV 10462, WV-10463, WV-

10464, WV- 10465, WV-10466, WV-10467, WV-10468, WV-10469, WV 10470, WV-10487, WW-

10488, WV- 10489, WV-10490, WV-10491, WV-10492, WV-10493, WV 10494, WV-10495, WV-

10496, WV- 10497, WV-10498, WV-10499, WV-10500, WV-10501, WV 10502, WV-10503, WV-

10504, WV-10505, WV-10506, WV-10507, WV-10508, WV-10509, WV 10510, WV-1051 1 , WV-

10512, WV-10513, WV-10514, WV-10515, WV-10516, WV-10517, WV 10518, WV-10519, WV-

10520, WV- 10521, WV-10522, WV-10523, WV-10524, WV-10525, WV 10526, WV-10527, WV-

10528, WV-10529, WV-10530, WV-10531, WV-10532, WV-10533, WV 10534, WV-10535, WW-

10536, WV-10537, WV-10538, WV-10539, WV-10540, WV-10541, WV 10542, WV-10543, WW-

10544, WV-10545, WV-10546, WV-10547, WV-10548, WV-10549, WV 10550, WV-10551, WW-

10552, WV-10553, 'V-10554, WV-10555 V- 10556, WV-10557, WV 10558, WV-10559, WV- 10560, WV-10561, 'V- 10562, WV-10563 V- 10564, WV-10565, WV 10506, WV-10567, WW- 10568, WV-10569, WV-10570, WV-10571 V- 10572. WV-10573, WV 10574, WV-10575, WV-

10576, WV-10577, WV-10578, WV-10579, WV-10580, WV-10581 , WV 10582, WV -10583, WV-

10584, WV-10585, WV-10586, WV-10587, WV-10588, WV-10589, WV 10590, WV-10591 , WV-

10592, WV-10593, WV-10594, V-10595, WV-10596, WV-10597, WV 10598, WV-10599, WV-

10600, WV- 10601, WV-10602, WV-10603, WV-10604, WV-10605, WV 10606, WV-10607, WW-

10608, WV-10609, WV-10610, WV-1061 1, WV-10612, WV-10613, WV 10614, WV-10615, WW-

10616, WV-10617, WV-10618, WV-10619, WV-10620, WV-10621, W 10622, WV-10623, WW-

10624, WV-10625, V- 10626, WV-10627, WV-10628, WV-10629, WV 10630, WV-10670, WW-

10671, WV- 10672, WV- 11340, 1341, WV-11342. WV-11544, WV ' -11545, WV-11546, WV- i 1547, WV-13835, WV-13864, WV-14344, WV-4698, WV-4699, WV-4700, WV-4701 , WV-4702, WV-

4703, WV-4704, WV-4705, WV-4706, WV-4707, WV-4708, WV-4709, WV-4710, WV-4711, WV-

4712, WV-4713, WV-4714, WV-4715, WV-4716, WV-4717, WV-4718, WV-4719, WV-4720, WV-

4721, WV-4722, WV-4723, WV-4724, WV-4725, WV-472.6, WV-4727, WV-4728, WV-4729, WV-

4730, WV-4731, WV-4732, WV-4733, WV-4734, WV-4735, WV-4736, WV-4737, WV-4738, WV-

4739, WV-4740, WV-4741, WV-4742, WV-4743, WV-4744, WV-4745, WV-4746, WV-4747, WV- 4748, WV-4749, WV-4750, WV-4751, WV-4752, WV-4753, WV-4754, WV-4755, WV-4756, WV-

4757, WV-4758, WV-4759, WV-4760, WV-4761, WV-4762, WV-4763, WV-4764, WV-4765, WV-

4766, WV-4767, WV-4768, WV-4769, WV-4770, WV-4771, WV-4772, WV-4773, WV-4774, WV-

4775, WV-4776, WV-4777, WV-4778, WV-4779, WV-4780, WV-4781, WV-4782, WV-4783, WV-

4784, WV-4785, WV-4786, WV-4787, WY-4788, WV-4789, WV-4790, WV-4791, WV-4792, WV-

4793, WV-9067, WV-9068, WV-9069, WV-9070, WV-9071, WV-9072, WV-9073, WV-9074, WV-

9075, WV-9076, WV-9077, WV-9078, WV-9079, WV-9080, WV-9081, WV-9082, WV-9083, WV-

9084, WV-9085, WV-9086, WV-9087, WV-9088, WV-9089, WV-9090, WV-9091 , WV-9092, WV-

9093, WV-9094, WV-9095, WV-9096, WV-9097, WV-9098, WV-9099, WV-9100, WV-9101, WV-

9102, WV-9103, WV-9104, WV-9105, WV-9106, WV-9107, WV-9108, WV-9109, WV-9110, WV-

911 1 , WV-9112, WV-9113, WV-9114, WV-9115, WV-9116, WV-9117, WV-9118, WV-9119, WV-

9120, WV-9121 , WV-9122, WV-9123, WV-9124, WV-9125, WV-9126, WV-9127, WV-9128, WV-

9129, WV-9130, WV-9131, WV-9132, WV-9133, WV-9134, WV-9135, WV-9136, WV-9137, WV-

9138, WV-9139, WV-9140, WV-9141, WV-9142, WV-9143, WV-9144, WV-9145, WV-9146, WV-

9147, WV-9148, WV-9149, WV-9150, WV-9151, WV-9152, WV-9153, WV-9154, WV-9155, WV-

9156, WV-9157, WV-9158, WV-9159, WV-9160, WV-9161, WV-9162, WV-9422, WV-9423, WV-

9424, WV-9425, WV-9426, WV-9427, WV-9428, WV-9429, WV-951 1 , WV-9512, WV-9513, WV-

9514, WV-9515, WV-9516, WV-9517, WV-9518, WV-9519, WV-9520, WV-9521, WV-9522, WV-

9523, WV-9524, WV-9525, WV-9534, WV-9535, WV-9536, WV-9537, WV-9538, WV-9539, WV-

9680, WV-9681, WV-9682, WV-9683, WV-9684, WV-9685, WV-9686, WV-9687, WV-9688, WV-

9689, WV-9690, WV-9691 , WV-9699, WV-9700, WV-9701, WV-9702, WV-9703, WV-9704, WV-

9709, WV-9710, WV-9711, WV-9712, WV-9713, WV-9714, WV-9715, WV-9743, WV-9744, WV-

9745, WV-9746, WV-9747, WV-9748, WV-9749, WV-9750, WV-9751, WV-9752, WV-9753, WV-

9754, WV-9755, WV-9756, WV-9757, WV-9758, WV-9759, WV-9760, WV-9761 , WV-9897, WV-

9898, WV-9899, WV-9900, WV-9901, WV-9902, WV-9903, WV-9904, WV-9905, WV-9906, WV-

9907, WV-9908, WV-9909, WV-9910, WV-991 1, WV-9912, WV-9913, WV-9914, WV-7436, WV-

7437, WV-7438, WV-7439, WV-7440, WV-7441, WV-7442, WV-7443, WV-7444, WV-7445, WV-

7446, WV-7447, WV-7448, WV-7449, WV-7450, WV-7451, WV-7452, WV-7453, WV-7454, WV-

7455, and WV-7456, and other DMD oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

[00826] Additional examples of such DMD oligonucleotides include: WV-9422, WV-9425, WV- 9426, WV-9517, WV-9519, WV-9521, WV-9522, WV-9524, WV-9710, WV-9714, WV-9715, WV-

9743, WV-9744, WV-9745, WV-9746, WV-9747, WV-9748, WV-9749, WV-9750, WV-9751, WV-

9756, WV- 9757, WV-9758, WV- 9759, WY-976G, WV-9761, WV-9897, WV-9898, WV-9899, WV- 9900, WV-9906, and WV-9912, and other DMD oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

[00827] Non-limiting examples of such DMD oligonucleotides also include: WV-12123, WV- 12124, WV-12125, WV-12126, WV-12127, WV-12128, WV-12129, WV-12553, WV-12554, WV- 12555, WV- 12556, WV-12557, WV-12558, WV-12559, WV-12872, WV-12873, WV-12876, WV- 12877, WV-12878, WV-12879, WV-12880, WV-12881, WV-12882, and WV-12883, and other DMD oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

100828] Results of various experiments for skipping Dystrophin exon 53 are described in the present disclosure. For example, data from a sequence identification screen are shown below, in Table

13 A.

Table 13A. Example data of certain oligonucleotides.

Skipping efficiency of various DMD oligonucleotides, tested for skipping of DMD exon 53 in vitro in Delta 52 human myoblast cells. Oligonucleotides tested were 6-8-6 gapmers (2’-F-2 -QMe-2’-F), wherein each intemucleotidic linkage is a stereorandom phosphorothioate. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

[00829] A number of oligonucleotides were generated and tested for efficacy in skipping DMD

Exon 53 in vitro in human patient-derived myoblast ceils; certain results are shown below in Tables 13B to 21 (A and B). Oligonucleotides were used at concentrations of 3 and 10 uM, in two replicates (R1 and R2). Numbers indicate the percentage of skipping of DMD exon 53, wherein 0 0 would indicate no skipping, and 100.0 would indicate 100% skipping. Several base sequences were tested in combination with a variety of chemical formats. For example, in some embodiments, a base sequence is GUACUUCAUCCCACUGAUUC, GUGUUCTTGTACTTCAUCCC,

UUCUGAAGGTGTTCUUGUAC, or CUCCGGTTCTGAAGGUGUUC, wherein U is optionally substituted with T and vice versa. Various chemical formats were utilized, including, e.g., gapmers (for example, 6-8-6 wing-core-wing gapmers). In some embodiments, both wings are 2’-F, while the core was all 2’-MOE, alternating 2’-MOE/2-OMe, alternating 2’-OMe/2’-MOE, alternating 2’-MOE/2’-F, alternating 2’-F/2’-MOE, alternating 2’-OMe/2’-F, and alternating 2 , -F/2’-OMe, etc. In some embodiments, the first wing was 2’-MQE or 27-OMe and the second wing was 2’-F (a type of asymmetrical gapmers). In some embodiments, each intemucleotidic linkage is a stereorandom phosphorothioate. In some embodiments, some alternating phosphorothioate linkages are replaced by phosphodiester linkages. In some embodiments, 5’ -methyl 2’-MQE C is used. Descriptions of certain oligonucleotides tested are provided in Table Al .

Table 13B. Example data of certain oligonucleotides.

Efficacy of DMD Exon 53 skipping of various DMD oligonucleotides in vitro. Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency. Results from replicate experiments are shown.

Table 14. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments (R1 and R2) are shown.

Table 15. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency.

[00830] Additional oligonucleotides were generated and tested for skipping DMD exon 53 in vitro in cells. Certain data are shown below in Table 16. Oligonucleotides were used at concentrations of 3 and 10 uM, in two replicates. Numbers indicate the percentage of skipping of DMD exon 53. As shown, oligonucleotides can have different base sequences in combination with a variety of chemical formats. In some embodiments, oligonucleotides tested were 20-mers, each having a gapmer format of wing-core-wing, wherein each wing was 2’-F, and the core was 2’-OMe or a mixture of 2’-OMe and 2’-F. In some embodiments, each intemucleotidic linkage was a chirally controlled phosphorothioate intemucleotidic linkage in Sp configuration. In some embodiments, oligonucleotides comprise one or more natural phosphate linkages. In some embodiments, oligonucleotides of the present disclosure

comprise one or more 5" -methyl nucleoside

wherein BA is nucleobase C, R & is -F). Table 16. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments are shown.

[00831] A number of DMD oligonucleotides were also designed, constructed and tested for efficacy in skipping DMD Exon 53 in vitro in differentiated myoblast cells. Certain data are shown below in Table 17. Oligonucleotides were delivered gymnoticaily at concentrations of 3 and 10 mM, in two biological replicates (R1 and R2). Numbers indicate the percentage of skipping of DMD exon 53, as determined by RT-qPCR.

Table 17. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments (R1 and R2) are shown.

[00832] A number of oligonucleotides were designed, constructed and tested for efficacy in skipping DMD Exon 53 in vitro in D52 differentiated myoblast cells. Certain data were shown below in Table 18. In an example procedure, cells were pre-differentiated for 4 days and oligonucleotides were delivered gymnotically for 4 days. Differentiation medium was DMEM, 2% horse serum and lOpg/ml insulin. In some embodiments, with certain oligonucleotides, without pre -differentiating these cells, skipping efficiency was relatively low'. Oligonucleotides were delivered gymnotically at concentrations of 1, 3 and 10 mM, in biological replicates (Rl and R2). Numbers indicate the percentage of skipping of

DMD exon 53, as determined by RT-qPCR. PM053 is an oligonucleotide also designated as WV-13405, HumDMDEx53, or PMO (in DMD exon 53 experiments), or PMO SR, which has a base sequence of GTTGCCTCCGGTTCTGAAGGTGTTC and is fully PMO (Morpholmo).

indicates that no data were available for that particular sample.

Table 18. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping relative to control and 0.0 would represent 0% efficiency; results from replicate experiments (R1 and R2) are shown.

[00833] A number of DMD oligonucleotides were designed, constructed and tested for efficacy in skipping DMD Exon 53 in vitro in D45-52 differentiated myoblast cell. Certain results, normalized to SFSR9, are shown below in Table 19. Oligonucleotides were delivered gymnotically at concentrations of 1, 3 and 10 mM, in biological replicates (R1 and R2). Numbers indicate the percentage of skipping of DMD exon 53, as determined by RT-qPCR.

Table 19. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents 0% efficiency; results from replicate experiments (R1 and R2) are shown.

Additional testing of oligonucleotides was performed, and the results were shown below in Tables 20 and 21.

Table 20. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100.0 would represent 100% skipping and 0.0 represents

0% efficiency; results from replicate experiments are shown.

Table 21. Example data of certain oligonucleotides.

Oligonucleotides were tested in vitro in delta 52 cells. A, Exon skipping at 10 uM is shown. B, protein restoration. Different replicates or experiments are designated as a), b), and c).

A.

100835] Additional DMD oligonucleotides were tested for their ability to mediate skipping of a

DMD exon, as shown below'. Full PMO (Morpholino) oligonucleotides have the following sequences:

WV- 13407 is also designated PMO NS.

Table 21C. Example data of certain oligonucleotides.

Numbers represent skipping efficiency, wherein 100 would represent 100% skipping and 0 would represent 0% skipping. Replicate data is shown.

In some embodiments, oligonucleotides, e.g , DMD oligonucleotides, are designed to target Intronic Splice Enhancer elements, e.g., for DMD oligonucleotides for exon 53 skipping, elements within 4kb of Exon53. In some embodiments, provided oligonucleotides are 30-mers. Example data for certain such oligonucleotides are presented in Table 21D.

Table 2 ID. Example data of certain oligonucleotides.

Results: Gymnotic delivery of 10mM Intron ASO’s in D45-52 patient derived myoblasts (4 days post differentiation). Done in biological replicates. Numbers represent percentage of exon skipping, as determined by RT-qPCR.

Table 2 IE. Example data of certain oligonucleotides.

D45-52 DMD patient derived myoblasts, with 7d of pre-differentiation, were treated with oligonucleotides tn muscle differentiation medium at indicated concentrations under free uptake condition before being collected and analyzed for RNA skipping efficiency (4d dosing) by qPCR Relative (SRSF9 normalization) quantification. Oligonucleotides were tested at a concentration of 0 to 10 mM. Results of replicate experiments are shown. Some of the oligonucleotides tested comprise a non -negatively charged intemucleotidic linkage (WV-12887 and WV-12880).

Table 2 IF. Example data of certain oligonucleotides.

D45-52 DMD patient derived myoblasts were treated with oligos in muscle differentiation medium at indicated concentrations for 4d under free uptake conditions and analyzed for RNA skipping efficiency by

Table 21G. Example data of certain oligonucleotides.

D45-52 DMD patient derived myoblasts, with 7d of pre-differentiation, were treated with oligos in muscle differentiation medium at indicated concentrations for 4d under free uptake conditions and analyzed for RNA skipping efficiency by qPCR

Table 21H. Example data of certain oligonucleotides.

Full length oligonucleotide stability at 5 day timepoint in Human Liver homogenate was tested. Numbers are replicates and represent percentage of full-length oligonucleotide remaining, wherein 100 would represent 100% oligonucleotide remaining (complete stability) and 0 would represent 0% oligonucleotide remaining (complete instability). Some nucleotides tested comprise a non-negatively charged intemucieotidic linkage.

Table 211. Example data of certain oligonucleotides. Numbers indicate amount of skipping relative to control.

Table 211.1. Example data of certain oligonucleotides.

Skipping efficiency of various DMD oligonucleotides, tested for skipping of DMD exon 53. Numbers represent skipping of exon 53.

D45-52 patient myoblasts were differentiated for 7days, then treated with oligonucleotide for 4d under gymnotic conditions in differentiation media. RNA w'as harvested by Trizol extraction and skipping analyzed by TaqMan.

Table 211.2. Example data of certain oligonucleotides.

Slapping efficiency of various DMD oligonucleotides, tested for skipping of DMD exon 53. Numbers represent skipping of exon 53.

D45-52 patient myoblasts were treated with oligonucleotide for 4d (4 days) under gymnotic conditions in differentiation media. RNA was harvested by Trizol extraction and skipping analyzed by TaqMan.

Several oligonucleotides (including WV-9517, WV-13864, WV-13835, and WV-14791) were tested at various concentrations up to 30 uM for TLR9 activation in vitro in HEK-blue-TLR9 cells (16 hour gymnotic uptake). WV-13864 and WV-14791 comprise a chi rally controlled non-negatively charged intemucleotidic linkage the Rp configuration. WV-9517, WV-13864, WV-13835, and WV-14791 did not exhibit significant TLR9 activation (less than 2-fold TLR9 induction; data not shown) WV-13864 and WV-14791 also exhibited negligible signal up to 30uM in PBMC cytokine release assay compared to water (data not shown).

Example Dystrophin Oligonucleotides and Compositions Which Target Exon 54

[00836] In some embodiments, the present disclosure provides oligonucleotides, oligonucleotide compositions, and methods of use thereof for targeting exon 54 and/or mediating skipping of exon 54 in human DMD. Non-limiting examples include oligonucleotides and compositions of Exon 54 oligos include: WV-I3745, WV-13746, WV-13747, WV-13748, WV-13749, WV-13750, WV-13751, WV- 13752, WV-13753, WV-13754, WV-13755, WV-13756, WV-13757, WV-13758, WV-13759, WV- 13760, WV-13784, and WV-13785, and other oligonucleotides having a base sequence which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

Table 21J. Example data of certain oligonucleotides.

Skipping efficiency of various DMD oligonucleotides, tested for skipping of DMD exon 54.

Example Dystrophin Oligonucleotides and Compositions Which Target Exon 55

[00837] In some embodiments, the present disclosure provides oligonucleotides, oligonucleotide compositions, and methods of use thereof for targeting exon 55 and/or mediating skipping of exon 55 in human DMD. Non-limiting examples include oligonucleotides and compositions of Exon 55 oligos include: WV-13761, WV-13762, WV-13763, WV-13764, WV-13765, WV-13766, WV-13767, WV- 13768, WV-13769, WV-13770, WV-13771, WV-13772, WV-13773, WV-13774, WV-13775, WV- 13776, WV-13777, WV-13778, WV-13779, WV-13786, and WV-13787, and other oligonucleotides having a base sequence (naked sequence) which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

[00838] In some embodiments, two or more oligonucleotides capable of skipping or targeting exon 44, 46, 47, 51, 52, 53, 54 and/or 55 can be used in any combination to mediate multiple exon skipping.

Table 2 IK. Example data of certain oligonucleotides.

Skipping efficiency of various DMD oligonucleotides, tested for skipping of DMD exon 55.

Example Dystrophin Oligonucleotides and Compositions Which Target Exon 57

[00839] in some embodiments, the present disclosure provides oligonucleotides, oligonucleotide compositions, and methods of use thereof for targeting exon 57 and/or mediating skipping of exon 57 in human DMD. Non-limiting examples include oligonucleotides and compositions of Exon 57 oligos include: WV-18853, WV-18854, WV-18855, WV-18856, WV-18857, WV-18858, WV-18859, WV- 18860, WV-18861, WV-18862, WV-18863, WV-18864, WY-18865, WV-18866, WY-18867, WV-

18868, WV-18869, WV-18870, WV-18871, WV-18872, WV-18873, WV-18874, WV-18875, WV-

18876, WV- 18877, WV-18878, WV-18879, WV-18880, WV-18881, WV-18882, WV-18883, WV-

18884, WV-18885, WV-18886, WV-18887, WV-18888, WV-18889, WV-18890, WV-18891, WV-

18892, WV-18893, WV-18894, WV-18895, WV-18896, WV-18897, WY-18898, WV-18899, WV- 18900, WV-18901, WV-18902, WV-18903, WV-18904, and other oligonucleotides having a base sequence (naked sequence) which comprises at least 15 contiguous bases of any of these DMD oligonucleotides.

Example Dystrophin Oligonucleotides and Compositions for Exon Skipping of Mutipie Exons (Multi-

Exon Skipping)

[00840] In some embodiments, the present disclosure provides oligonucleotides, compositions, and methods for splicing modulation, including skipping of multiple exons. In some embodiments, a DMD oligonucleotide or composition thereof is capable of mediating skipping of multiple exons in the human or mouse Dystrophin gene

[00841] In some embodiments, in a patient with muscular dystrophy, the symptoms of muscular dystrophy can at least be partially relieved and/or the disorder at least partially treated by administration of a DMD oligonucleotide capable of skipping one exon or multiple exons. Without wishing to be bound by any particular theory, the present disclosure notes that BMD patients with a deletion of exons 45 to 55 of DMD showed a milder or asymptomatic phenotype.

[00842] A non-limiting example of a scheme for multiple exon skipping is shown in Figure 1. In this Figure, various numbers (43 to 57) indicate exons; and the shapes of the exons (e.g., <, > or j ) indicate which reading frame is represented at the 5’ and 3’ end of each exon. Normally exon 44 is joined to exon 45. In a non-limiting example of multiple exon skipping, exons 45 to 55 are skipped, allowing exon 44 to join to exon 56. Tire 3 end of exon 44 is represented by the same reading frame ( < ) as the 5’ end of exon 56; thus skipping exons 45 to 55 maintains or restores the correct reading frame. In some embodiments, skipping multiple exons restores the reading frame if one of the skipped exons comprises a mutation which alters the reading frame (in many cases, for example, producing a missense or prematurely truncated protein).

100843] Among other things, the present disclosure notes that various exons represent at their 5’ and/or 3 ends different reading frames; thus, some combinations of skipping adjacent reading frames but not other combinations are capable of maintaining or restoring the reading frame. In some embodiments, provided compositions and methods for multiple exon skipping skip, as non-limiting examples, exons 45- 46, 45-47, 45-48, 45-49, 45-51 , 45-53, 45-55, 47-48, 47-49, 47-51, 47-53, 47-55, 48-49, 48-51, 48-53, 46- 55, 50-51, 50-53, 50-55, 49-51, 49-53, 49-55, 52-53, 52-55, 44-45, 44-54, or 44-56, wherein in each case multiple exon skipping maintains or restores the correct reading frame. In some embodiments, skipping of non-overlapping sets of exons is capable of maintaining or restoring reading frame, e.g., skipping of exons 45-46 and exons 49-55; skipping of exons 45-47 and 49-55; skipping of exons 45-49 and 52-55; etc. [00844] Without wishing to be bound by any particular theory, the present disclosure notes that some DMD exons may be spliced transcriptionally, while others are spliced post-transcriptionally. For example, each of exons 45 to 55 are reportedly not simultaneously spliced, but rather first as three groups: exons 45 to 49, 50 to 52, and 53 to 55, the individual exons within each group being spliced transcriptionally. Reportedly, the remaining introns (between exons 44/45, 49/50, 52/53, and 55/56) are later spliced post-transcriptionally. Without wishing to be bound by any particular theory, the present disclosure notes that this lag in the timing of splicing may be exploited by oligonucleotides capable of increasing the splicing between exons whose adjacent introns are spliced post-transcriptionally, such as exon 44 and 56. It is reported that in nature, such multi-exon skipping joining exon 44 to exon 56 occurs at a low but detectable frequency (approximately 1/600). Without wishing to be bound by any particular theory, the present disclosure pertains in part to DMD oligonucleotides capable of skipping multiple exons at a therapeutically and clinically significant level.

[00845] In some embodiments, a composition capable of mediating multiple exon skipping comprises a DMD oligonucleotide. In some embodiments, a composition capable of mediating multiple exon skipping comprises a combination of (e.g., two or more different) DMD oligonucleotides in some embodiments, a composition capable of mediating multiple exon skipping comprises a combination of (e.g., two or more different) DMD oligonucleotides, wherein at least one oligonucleotide recognizes a target associated with skipping the 5’ exon to be skipped, and at least one oligonucleotide recognizes a target associated with skipping the 3’ exon to be skipped. In some embodiments, a composition capable of mediating multiple exon skipping comprises a oligonucleotide capable of recognizes both (1) a target associated with skipping the 5’ exon to be skipped and (2) a target associated with skipping the 3’ exon to be skipped.

[00846] In some embodiments, an advantage of a composition capable of multiple exon skipping is that it is useful for treatment of dystrophy associated with a mutation in any individual exon included in the group of exons which is skipped. As a non-limiting example, a DMD oligonucleotide capable of mediating skipping of exon 48 is only capable of treating mutations within that exon (or, in some cases, an adjacent or nearby exon) but not mutations within other exons. However, a composition capable of mediating skipping of exons 45 to 55 is capable of treating mutations in any of exons 45, 46, 47, 48, 49, 50, 51, 52, 53, 54 or 55. Thus, both a patient with a mutation in exon 48 and a patient with a mutation in exon 54 can be treated with a composition capable of skipping exons 45 to 55. In some embodiments, a composition capable of mediating skipping of exons 45 to 55 is capable of treating up to about 63% of DMD patients.

[00847] In some embodiments, a composition comprises one or more DMD oligonucleotides, wherein the composition is capable of mediating skipping of multiple (two or more) DMD exons. [00848] In some embodiments,, a MESO (a composition comprising one or more oligonucleotides, which composition is capable of mediating multiple exon skipping) has an advantage over a DMD oligonucleotide capable of skipping only one exon. In some embodiments, a composition which is capable of mediating skipping of a single exon, is only useful for treating patients treatable by skipping that exon (e.g., patients having a genetic lesion in that exon). In some embodiments, a MESO is useful for treating patients treatable by skipping any of the exons winch the MESO is able to skip, which is likely a larger percentage of the patient population. In some embodiments, double or multiple exon skipping can potentially be applicable to 90% of patients

100849] In addition, in some embodiments, because the 5’ and 3’ ends of an exon are sometimes not in the same frame, deletion of such an exon would cause a frameshifi. Skipping of multiple exons, in various such cases, can restore the reading frame.

[00850] In some embodiments, multiple exon skipping is useful to treat DMD patients with deletion, duplication, and nonsense mutations.

[00851] In addition, in some embodiments, skipping of multiple exons can mimic the genetics of the milder Becker muscular dystrophy. In some embodiments, the more severe Duchenne muscular dystrophy, mediated by a genetic lesion in one exon, can be converted into a milder Becker muscular dystrophy, mediated by an in -frame deletion of multiple exons. It is reported that some BMD patients and an asymptomatic person have in-frame deletions of exons 48 to 51 or 45 to 51. Singh et al. 1997 Hum. Genet. 99: 206-208; Melacini et al. 1993 J. Am. Col.. Cardiol. 22: 1927-1934; Melis et al. 1998 Eur. I. Paediatr. Neurol. 2: 255-261 ; and Aartsma-Rus et al. 2003 Hum. Mol. Genet. 8: 907-914.

100852] In some embodiments, certain exons may be more challenging than others to skip. In some embodiments, the present disclosure provides technologies to skip such exons, e.g., through chemical modifications, linkage phosphorus stereochemistry, and combinations thereof. In some embodiments, the present disclosure encompasses the recognition that multiple exon skipping can be useful for skipping such challenging exons. In some embodiments, the present disclosure provides multiple exon skipping technologies for skipping such challenging exons.

[00853] In some embodiments, exon skipping, e.g., DMD exon skipping, can be used to treat patients, e.g., DMD patients, with circular or circularized RNA transcripts (e.g., those of DMD). Circular DMD transcripts are reported in, as a non-limiting example: Gualandi et al. 2003 J. Med. Gen. 40:eI00.

[00854] In some embodiments, a composition capable of mediating multiple exon skipping

(MESO) comprises one DMD oligonucleotide capable of mediating skipping of multiple exons. In some embodiments, a composition capable of mediating multiple exon skipping (MESO) comprises two DMD oligonucleotides which are together (e.g., when used in combination) capable of mediating skipping of multiple exons. In some embodiments, a composition capable of mediating multiple exon skipping (MESO) comprises a cocktail of (e.g., a mixture of three or more) DMD oligonucleotides which are together (e.g., when used in combination as a cocktail) capable of mediating skipping of multiple exons. Combinations or cocktails of oligonucleotides capable of mediating skipple of multiple exons have been reported by, for example, Yokota et al. 2009 Arch. Neurol 66: 32; Yokota et al. 2012 Nuc! Acid Ther. 22: 306; Adkin et al. 2012 Neur. Dis. 22: 297-305; Echigoya et al. 2013 Nucl. Acid. Ther.; and Echigoya et al. 2015 Molecular Therapy— Nucleic Acids 4: e225. Among oilier things, the present disclosure provides more effective combinations, through, e.g., selected sequences, chemical modifications, and/or linkage phosphorus chemistry', etc.

[00855] In some embodiments, the present disclosure provides oligonucleotides that, when combined with other oligonucleotides, can provide dramatically increased activities compared to either oligonucleotides individually prior to combination. For example, in some embodiments, the present disclosure provides DMD oligonucleotides winch are individually incapable of mediating efficient skipping of a particular exon; when combined with other oligonucleotides, such oligonucleotides are capable of mediating slapping of multiple exons. Among other things, the present disclosure provides combination therapy, wherein two or more oligonucleotides are used together to provide desired and/or enhanced properties and/or activities. When used in combination therapy, the two or more agents, e.g., oligonucleotides, may be administered concurrently, or separately in suitable ways for them to achieve their combination effects. In some embodiments, two or more oligonucleotides in a combination are all (primarily) for skipping of the same exon, and their combination provides enhanced skipping of such exon, in some embodiments, significantly more than the addition of their separate effects. In some embodiments, two or more oligonucleotide in a combination are for skipping of difference exons, and their combination provides effective skipping, sometimes more than the oligonucleotides individually can achieve, of two or more exons. In some embodiments, the present disclosure provide combinations of oligonucleotides with synergies between two or more different oligonucleotides. In some embodiments, the present disclosure provides combinations of different oligonucleotides wherein one or more, or each oligonucleotide by itself is not effective for exon skipping. Certain combinations are described in Adams et al. 2007 BMC Mol. Biol. 8:57. Among other tilings, the present disclosure provides more effective combinations, through, e.g., designed control of one or more or all structural elements of oligonucleotides. In some embodiments, a provided combination provides exon skipping of DMD exon 45. In some embodiments, a provided combination provides exon skipping of another DMD exon, including those described herein or otherwise desirable for skipping (e.g., for prevention or treatment of one or more conditions, diseases or disorders etc.) as known in the art.

[00856] In some embodiments, cocktails, combinations and mixtures of oligonucleotides, e.g , for multiple exon skipping may have disadvantages compared to single oligonucleotides which can perform the same or comparable functions, such as higher costs of goods, complications in manufacturing and delivery, increased regulatory burden, etc. In accordance with FDA regulations, each component in a combination may need to be separately tested for toxicity, as well as the entire combination. In some embodiments, the present disclosure provides single oligonucleotides that can achieve the same or comparable functions of oligonucleotide combinations, and may be utilized to replace oligonucleotide combinations, through precise and designed control of one or more structural elements of oligonucleotides, e.g., chemical modifications, stereochemistry-, and combinations thereof.

[00857] Various technologies are suitable for assessing multiple exon skipping in accordance with the present disclosure. Non-limiting examples are described in Example 20 and Figure 2.

[00858] In some embodiments, a composition for skipping multiple DMD exons comprises a

DMD oligonucleotide capable of skipping DMD exon 45. Various DMD oligonucleotides were tested for their capability to skip exon 45, as shown in Table 1 A. Various DMD oligonucleotides for skipping exon 45 were also tested for their ability to skip multiple exons, as shown in Table 22A. Among other things, the present disclosure demonstrates that several oligonucleotides, including WV-11088 and WV-11089, can provide low levels of skipping of exons 45-55 (creating a junction between exon 44 and exon 56 or 44-56).

[00859] In another experiment, oligonucleotides WV- 11047, WV-11051 to WV-11059 did not demonstrate significant skipping under the specific tested condition, and oligonucleotides WV-11062 to WV-l 1069 each exhibited detectable levels of skipping which were <1% under the specific tested condition. Oligonucleotides WV-1 1091 to WV-I I096, WV-l 1098, and WV-11 100 to WV-1 1 105 exhibited <.5% skipping of exon 45 under the specific tested condition.

Table 22A. Example data of certain oligonucleotides.

Oligonucleotides were tested for their ability to skip DMD exon 45 in D48-50 cells.

Numbers indicate skipping level, wiierein 100 would represent 100% skipping and 0 would represent 0% skipping.

Several oligonucleotides, including WV-11088 and WY-11089, showed detectable levels of multiple exon skipping (specifically exons 45-55) (approximately 0.1 % skipping).

100860] In another experiment, various DMD oligonucleotides targeting exon 45 were tested in

D48-50 for an ability to skip multiple exons (specifically 45 to 53, creating a junction between exon 44 and exon 54 or 44-54). Oligonucleotides tested were: WV-11047, WV-11051, WV-11052, WV-11053, WV-11054, WV-11055, WV-11056, WV-11057, WV-11058, WV-11059, WV-11062, WV-11063, WV- 11064, WV-11065, WV-11066, WV-1 1067, WV-11068, WV-1 1069, WV-11070, WV-1 1071, WV-

11072, WV-11073, WV-11074, WV-11075, WV-11076, WV-11077, WV-11078, WV-1 1079, WV-

11080, WV-11081, WV-11082, WV-11083, WV-11084, WV-11085, WY-11086, WV-11087, WV-

11088, WV-11089, WV- 11090, WV-11091, WV-11092, WV-11093, WV-11094, WV-11095, WV-

11096, WV-l 1098, WV-l 1100, WV-l 1101. All these oligonucleotides, in one experiment, demonstrated on average about 0.05% or less skipping of exons 44-54 (data not shown).

[00861] Oligonucleotides targeting exon 45 were also tested for skipping of exons 45 to 57, as shown m Table 22A.1.

Table 22A.1. Example data of certain oligonucleotides.

Oligonucleotides were tested in D48-50 for their ability to skip DMD exons 45 to 57, creating a junction between exon 44 and exon 58 or 44-58. Numbers indicate skipping level, wherein 100 would represent 100% skipping and 0 would represent 0% skipping. Replicate data in this and other tables are shown.

[00862] In some embodiments, a DMD oligonucleotide targets DMD exon 44 or the adjoining intronic region 3’ to DMD exon 44 and is capable of mediating multiple exon skipping.

[00863] In some embodiments, a DMD oligonucleotide targets DMD exon 44 or the adjoining intronic region 3' to DMD exon 44, and the oligonucleotide is capable of mediating multiple exon skipping (e.g., of exons 45 to 55, or 45 to 57).

[00864] Reportedly, a phenomenon known as back-splicing can occur, in which, for example, a portion of the 3’ end of exon 55 interacts with a portion of the 5’ end of exon 45, forming a circular RNA (circRNA), which can thus skip multiple exons, e.g., all exons from exon 45 to 55, inclusive. The phenomenon can also reportedly occur between exon 57 and exon 45, skipping multiple exons, e.g., all exons from exon 45 to 57, inclusive. Back -splicing is described in the literature, e.g., in Suzuki et al. 2016 ini. J. Mol. Sci. 17.

[00865] Without wishing to be bound by any particular theory, the present disclosure suggests that it may be possible for a DMD oligonucleotide targeting DMD exon 44 or the adjoining intronic region 3 to exon 44 may be able to mediate splicing of exons 45 to 55, or of exons 45 to 57, which exons are excised as a single piece of circular RNA (circRNA) designated 45-55 (or 55-45) or 45-57 (or 57-45), respectively

[00866] Several oligonucleotides were designed to target exon 44 or intron 44, or which straddle exon 44 and intron 44. In some embodiments, oligonucleotides designed to target exon 44 or intron 44, or which straddle exon 44 and intron 44 are tested to determine if they can increase the amount of backs!icing and/or multiple-exon skipping.

[00867] As shown in Table 22A.2 and Table 22A.3, below, DMD oligonucleotides targeting Exon44 were tested for the ability to increase circRNA 55-45 (e.g., mediate multiple exon skipping of exons 45 to 55); or for the ability to increase circRNA 57-45 (e.g., mediate multiple exon skipping of exons 45 to 57). Various DMD oligonucleotides comprise various difference including, inter aha, base sequence and length (18 or 20 bases). Numbers indicate relative amount of circRNA 55-45 (Table 22A.2) or circRNA 57-45 (Table 22A.3). In tins and various other tables, Rep indicates Replicate.

Table 22 A.2. Example data of certain oligonucleotides.

Table 22A.3. Example data of certain oligonucleotides.

[00868] In some embodiments, a composition capable of mediating exon skipping of a particular

DMD exon comprises two or more oligonucleotides targeting a particular exon. In some embodiments, a combination of two or more oligonucleotides provides skipping levels significantly higher than the addition of the skipping level of each oligonucleotide individually. In some embodiments, a combination of two or more oligonucleotides provides significant (1%, 5%, 10%, or more) and/or detectable levels of skipping while each oligonucleotide individually does not provide detectable levels of slapping. Combinations of traditional oligonucleotides (e.g., stereorandom oligonucleotide and/or oligonucleotides without non-negative!y charged intemucleotidic linkages described in the present disclosure) has been reported to provide certain improved effects, e.g., in Wilton et al. 2007 Mol. Ther. 7: 1288-1296 (exons 10, 20, 34, 65, etc.). Among other tilings, provided combinations comprise at least one oligonucleotide comprising one or more ehiraily controlled intemucleotidic linkages and/or one or more non-negatively charged intemucleotidic linkages, and can provide significantly increased levels of exon skipping.

[00869] Among oilier things, the present disclosure recognizes that certain exons are particularly challenging for skipping. For example, in one report, for exons 47 and 57. individual DMD oligonucleotides were not capable of mediating exon skipping, but pairs of oligonucleotides were capable of mediating exon skipping. In one report, effective skipping of exon 45 was mediated by combining two DMD oligonucleotides which were individually not effective in skipping of this exon. Aartsma-Rus et al. 2006 Mol. Ther. 14: 401. Aartsma-Rus et al. 2006 Mol. Ther. 14: 401. In some embodiments, the present disclosure provides oligonucleotides (e.g., ehiraily controlled oligonucleotides), and compositions and methods of use thereof, for exon skipping of such challenging exons. With chemistry modifications and/or stereochemistry technologies described herein, the present disclosure provides technologies with greatly improved exon skipping efficiency. In some embodiments, the present disclosure provides single oligonucleotide (e.g., a chi rally controlled oligonucleotide) and compositions thereof (e.g., a chirally controlled oligonucleotide composition) for exon skipping of one or more exons that are challenging to skip. In some embodiments, the present disclosure provides combinations of oligonucleotides (e.g.,, chirally controlled oligonucleotides) and compositions thereof (e.g., chirally controlled oligonucleotide compositions) for exon skipping of one or more exons that are challenging to skip. In some embodiments, combinations of DMD oligonucleotides targeting the same exon mediate increased exon skipping levels relative to individual DMD oligonucleotides.

[00870] In some embodiments, a composition comprises two or more DMD oligonucleotides, wherein each individual DMD oligonucleotide mediates low' levels of exon skipping, while the combination mediates a higher level of skipping (higher than the addition of levels achieved by each oligonucleotide individually) .

[00871] In some embodiments, a composition comprises two or more DMD oligonucleotides, wherein the oligonucleotides target different exons.

[00872] In some embodiments, a combination of multiple DMD oligonucleotides targeting different exons is capable of mediating skipping of two or more (e.g., multiple) exons.

[00873] In some embodiments, a composition comprises two or more DMD oligonucleotides. In some embodiments, a composition comprises two or more DMD oligonucleotides, at least one of which is described herein or has a base sequence, stereochemistry or other chemical characteristic described herein.

Oligonucleotides Comprising Non-Negatively Charged Intemucleotidic Linkages Can Provide Significantly Improved Activities.

[00874] In some embodiments, the present disclosure provides oligonucleotides comprising one or more non-negatively charged intemucleotidic linkages. In some embodiments, a non-negatively charged intemucleotidic linkage is a neutral intemucleotidic linkage. In some embodiments, the present disclosure provides oligonucleotides comprising one or more neutral intemucleotidic linkages. In some embodiments, a non-negatively charged intemucleotidic linkage has the structure of formula I-n-1, 1-n-2,

I-n-3, I-n-4, II, IT-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof.

[00875] In some embodiments, a non-negatively charged intemucleotidic linkage comprises a triazole moiety. In some embodiments, a non-negatively charged intemucleotidic linkage comprises an optionally substituted triazolyl group. In some embodiments, a non-negatively charged intemucleotidic

linkage has the structure In some embodiments, a non-negatively charged intemucleotidie linkage has the structure In some embodiments, a non-neeatively charged intemucleotidie linkage comprises a substitxrted triazoiyl group. In some embodiments, a non-

negatively charged intemucleotidie linkage has the structure , wherein W is O or

S. in some embodiments, a non-negative ly charged intemucleotidie linkage comprises an optionally substituted alkynyl group. In some embodiments, a non-negatively charged intemucleotidie linkage has

the structure , wherein W is O or S.

100876] In some embodiments, the present disclosure provides oligonucleotides comprising an intemucleotidie linkage, e.g., a non-negatively charged intemucleotidie linkage, which comprises a cyclic guanidine moiety. In some embodiments, an intemucleotidie linkage comprises a cyclic guanidine and

has the structure of: . In some embodiments, an intemucleotidie linkage negatively charged intemucleotidie linkage, comprising a cyclic guanidine is stereochemically controlled

In some embodiments, a non -negatively charged intemucleotidie linkage, or a neutral

intemucleotidie linkage, is or comprising a structure selected from

wherein W is O or S. In some embodiments, a non-negatively charged intemucleotidie linkage is a chirally controlled intemucleotidie linkage. In some embodiments, a neutral intemucleotidie linkage is a chirally controlled intemucleotidie linkage. In some embodiments, a nucleic acid or an oligonucleotide comprising a modified intemucleotidie linkage comprising a cyclic guanidine moiety is a siRNA, double-straned siRNA, single- stranded siRNA, gapmer, skipmer, blockmer, antisense oligonucleotide, antagomir, microRNA, pre- microRNs, antimir, supermir, ribozyme, U1 adaptor, RNA activator, RNAi agent, decoy oligonucleotide, triplex forming oligonucleotide, aptamer or adjuvant.

[00878] In some embodiments, an oligonucleotide comprises a neutral intemucleotidic linkage and a chirally controlled intemucleotidic linkage. In some embodiments, an oligonucleotide comprises a neutral intemucleotidic linkage and a chirally controlled intemucleotidic linkage which is a phosphorothioate in the Rp or Sp configuration. In some embodiments, the present disclosure provides an oligonucleotide comprising one or more non-negatively charged intemucleotidic linkages and one or more phosphorothioate intemucleotidic linkage, wherein each phosphorothioate intemucleotidic linkage in tire oligonucleotide is independently a chirally controlled intemucleotidic linkage. In some embodiments, the present disclosure provides an oligonucleotide comprising one or more neutral intemucleotidic linkages and one or more phosphorothioate intemucleotidic linkage, wherein each phosphorothioate intemucleotidic linkage in the oligonucleotide is independently a chirally controlled intemucleotidic linkage. In some embodiments, a provided oligonucleotide comprises at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more chirally controlled phosphorothioate intemucleotidic linkages.

[00879] Without wishing to be bound by any particular theory, the present disclosure notes that a neutral intemucleotidic linkage is more hydrophobic than a phosphorothioate intemucleotidic linkage (PS), which is more hydrophobic than a phosphodiester linkage (natural phosphate linkage, PO). Typically, unlike a PS or PO, a neutral intemucleotidic linkage bears less charge. Without wishing to be bound by any particular theory, the present disclosure notes that incorporation of one or more neutral intemucleotidic linkages into an oligonucleotide may increase oligonucleotides’ ability to be taken up by a cell and/or to escape from endosomes. Without wishing to be bound by any particular theory, the present disclosure notes that incorporation of one or more neutral intemucleotidic linkages can be utilized to modulate melting temperature between an oligonucleotide and its target nucleic acid.

[00880] Without wishing to be bound by any particular theory 7 , the present disclosure notes that incorporation of one or more non-negatively charged intemucleotidic linkages, e.g., neutral intemucleotidic linkages, into an oligonucleotide may be able to increase the oligonucleotide’s ability to mediate a function such as exon skipping or gene knockdown. In some embodiments, an oligonucleotide capable of altering skipping of one or more exons in a target gene comprises one or more neutral intemucleotidic linkages. In some embodiments, an oligonucleotide capable of mediating skipping of an exon(s) in a target gene comprises one or more neutral intemucleotidic linkages. In some embodiments, an oligonucleotide capable of mediating skipping of one or more DMD exon(s) comprises one or more neutral intemucleotidic linkages.

100881] In some embodiments, an oligonucleotide capable of mediating knockdown of level of a nucleic acid or a product encoded thereby comprises one or more non-negatively charged internucleotidic linkages. In some embodiments, an oligonucleotide capable of mediating knockdown of expression of a target gene comprises one or more non-negatively charged internucleotidic linkages. In some embodiments, an oligonucleotide capable of mediating knockdown of expression of a target gene comprises one or more neutral internucleotidic linkages.

[00882] In some embodiments, a non-negatively charged internucleotidic linkage is not chirally controlled. In some embodiments, a non-negatively charged internucleotidic linkage is chirally controlled. In some embodiments, a non-negatively charged internucleotidic linkage is chirally controlled and its linkage phosphorus is Rp. In some embodiments, a non-negatively charged internucleotidic linkage is chirally controlled and its linkage phosphorus is 5p.

[00883] In some embodiments, a provided oligonucleotide comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more non-negatively charged internucleotidic linkages. In some embodiments, a provided oligonucleotide comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more neutral internucleotidic linkages. In some embodiments, each of non-negatively charged internucleotidic linkage and/or neutral internucleotidic linkages is optionally and independently chirally controlled. In some embodiments, each non-negatively charged internucleotidic linkage in an oligonucleotide is independently a chirally controlled internucleotidic linkage. In some embodiments, each neutral internucleotidic linkage in an oligonucleotide is independently a chirally controlled internucleotidic linkage. In some embodiments, at least one non-negatively charged internucleotidic linkage/neutral internucleotidic linkage has the structure

wherein W is O or S. In some embodiments, at least one non-negatively charged

internucleotidic linkage/neutral internucleotidic linkage has the structure In some embodiments, at least one non-negatively charged internucleotidic linkage/neutral intemucleotidic linkage

has the structure In some embodiments, at least one non-negatively charged

internucleotidic linkage/neutral internucleotidic linkage has the structure wherein W is 0 or S. In some embodiments, at least one non-negatively charged internucleotidic linkage/neutral temucleotidic linkage has the structure In some embodiments, at least one non- negatively charged internucleotidic linkage/neutral internucleotidic linkage has the structure of In some embodiments, at least one non-negatively charged internucleotidic

iinkage/neutral internucleotidic linkage has the structure wherein W is O or S. In some embodiments, at least one non-negatively charged internucleotidic linkage/neutral internucleotidic

linkage has the structure . In some embodiments, at least one non-negatively charged

internucleotidic linkage/neutral internucleotidic linkage has the structure In some embodiments, a provided oligonucleotide comprises at least one non-negatively charged internucleotidic linkage wherein its linkage phosphorus is in Rp configuration, and at least one non-negatively charged internucleotidic linkage wherein its linkage phosphorus is in Sp configuration.

[00884] In some embodiments, an oligonucleotide capable of increasing the frequency of skipping of an exon of a target gene comprises a non-negatively charged internucleotidic linkage. In some embodiments, an oligonucleotide capable of increasing the frequency of skipping of an exon of a target gene comprises a non-negatively charged internucleotidic linkage and is useful for treatment of a disease wherein the exon comprises a deleterious or disease-associated mutation. A non-limiting example is the DMD gene, wherein the skipping of an exon comprising a mutation contributes to muscular dystrophy [00885] Various oligonucleotides, including DMD oligonucleotides, that comprise one or more non-negatively charged internucleotidic linkages/neutral internucleotidic linkages were designed and/or constructed and/or tested, for example, WV-1 1343, WV-1 1344, WV-11345, WV-11346, WV-11347, WV- 1 1237, WV-1 1238, WV-11239, WV-12130, WV-1213 I, WV-12132, WV-12133, WV-12134, WV- 12135, WV-12136, WV-11340, WV-11341, WV-11342, WV-12123, WV-12124, WV-12125, WW-

12126, WV-12I27, WV-12128, WV-12129, WV-12553, WV-12554, WV-12555, WV-12556, WV-

12557, WV-12558, WV-12559, WV-12872, WV-12873, etc. Example DMD oligonucleotides for skipping exon 23 and comprising a non-negatively charged intemudeotidic linkage (e.g., a neutral intemudeotidic linkage) include: WV-l 1343, WV-l 1344, WV-l 1345, WV-l 1346, and WV-l 1347. Example DMD oligonucleotides for skipping exon 51 and comprising a non-negatively charged intemudeotidic linkage (e.g., a neutral intemudeotidic linkage) include: WV-11237, WV-l 12.38, WV- 11239, WV-12130, WV-12131 , WV-12132, WV-12133, WV-12134, WV-12135, and WV-12136.

Example DMD oligonucleotides for skipping exon 53 and comprising a non-negatively charged intemudeotidic linkage (e.g., a neutral intemudeotidic linkage) include: WV-l 1340, WV-11341, WV- 11342, WV-12123, WV-12124, WV-12125, WV-12126, WV-12127, WV-12128, WV-12129, WV- 12553, WV-12554, WV-12555, WV-12556, WV-l 2557, WV-12558, WV-12559, WV-12872, and WV-

12873. Certain oligonucleotides are in Table Al.

[00886] Additional DMD oligonucleotides comprising a non-negatively charged intemudeotidic linkage were designed and/or constructed. These include DMD oligonucleotides for skipping DMD exon 45, WV-14528, WV-14529, WV-14532, and WV-14533.

100887] The efficacy of various DMD oligonucleotides comprising a non-negatively charged intemudeotidic linkage slapping DMD exon 45 is shown in Table 1B.1 and Table IB.2 herein.

[00888] The efficacy of various DMD oligonucleotides comprising a non-negatively charged intemudeotidic linkage m skipping DMD exon 53 is shown in Table 21 E, Table 21F, Table 21G, and Table 21H herein.

[00889] In some embodiments, a non-negatively charged intemudeotidic linkage may be designated as nX if stereorandom, or nS chirally controlled and linkage phosphorus in the Sp configuration, or nR if chirally controlled and the linkage phosphorus in the Rp configuration.

[00890] In some embodiments, a non-negatively charged intemudeotidic linkage may be designated as nOOl if stereorandom, or nOOlS chirally controlled and linkage phosphorus in the Sp configuration, or nOOIR if chirally controlled and the linkage phosphorus in the Rp configuration (e.g., in Table A 1).

[00891] Various DMD oligonucleotides comprising a non-negatively charged intemudeotidic linkage in the Rp configuration were constructed, including WV-12872, WV-13408, WV-12554, WV- 13409, WV-12555, and WV-12556.

[00892] Various DMD oligonucleotides comprising a non-negatively charged intemudeotidic linkage in the Sp configuration were constructed, including WV-l 2557, WV-12558, and WV-l 2559

[00893] Data showing activity and stability of various oligonucleotides comprising a non- negatively charged intemucleotidic linkage in the Rp or Sp configuration are shown in Table 21H Table 211, Table 211.1, and Table 211.2

[00894] Several oligonucleotides (including WV-9517, WV-13864, WV~13835, and WV-14791) were tested at various concentrations up to 30 uM for TLR9 activation in HEK-blue~TLR9 cells (16 hour gymnotic uptake). WV-13864 and WV-14791 comprise a chirally controlled non-negatively charged intemucleotidic linkage in the Rp configuration. WV-9517, WV-13864, WV-13835, and WV-14791 did not exhibit significant TLR9 activation (data not shown).

[00895] Several oligonucleotides which target a gene other than DMD were designed and/or constructed which comprise a non-negatively charged intemucleotidic linkage.

[00896] Below are presented oligonucleotides comprising a cyclic guanidine moiety which target

DMD or Malat-1 (MaJatl). The DMD oligonucleotides are designed to mediate skipping of exon 23 (in mouse) or exon 51 or exon 53 (in human). The Malat-1 oligonucleotides are designed to for Malatl mRNA knockdown, e.g., mediated through RNase H.

Table 22B. Example Malat-1 oligonucleotides comprising a neutral backbone.

All of these oligonucleotides have the base sequence of UGCCAGGCTGGTTATGACUC.

[00897] Oligonucleotides comprising non-negatively charged intemucleotidic linkages and targeting other gene targets were also designed, constructed and/or tested for their properties and activities, including activities for reducing levels of target mRNAs and/or proteins, e.g., via RNaseH- mediated knockdown. Such oligonucleotides are active in reducing target levels.

[00898] Various Malatl oligonucleotides were designed, constructed and tested which comprise a non-negatively charged intemucleotidic linkage. Various Malatl oligonucleotides comprise 1, 2 or 3 non-negatively charged intemucleotidic linkages in a wing and/or a core.

Table 22C. Malatl oligonucleotides

All of the oligonucleotides in this table have the base sequence of UGCCAGGCTGGTTATGACUC. Stereochemistry

Table 22D. Data of Malat l oligonucleotides

Numbers represent knockdown of Malatl mR A relative to HPRT1, wherein 1.000 would represent no (0.0%) knockdown and 0.000 represents 100.0% knockdown; results from replicate experiments are shown. WV-9491 is a negative control that is not designed to target Malatl.

00899] Various Malatl oligonucleotides were designed, constructed and tested which comprise one or more non-negatively charged intemueleotidic linkages in a core. In various embodiments of a Malatl oligonucleotide, a phosphorothioate in the Rp configuration is replaced by a non-negatively charged intemueleotidic linkage.

Table 22E. Data of Malatl oligonucleotides

Numbers represent knockdown of Malatl mKNA relative to HPRT1, wherein 1.000 would represent no (0.0%) knockdown and 0.000 represents 100.0% knockdown; results from replicate experiments are shown.

Various Malatl oligonucleotides were designed, constructed and which comprise a non-negatively charged intemueleotidic linkage. Various Malatl oligonucleotides comprise 1 or more non-negatively charged intemueleotidic linkages.

Table 22F. Data of certain oligonucleotides.

Numbers represent knockdown of Malat l mRNA relative to HPRT1, wherein 1.000 would represent no

(0.0%) knockdown and 0.000 represents 100 0% knockdown; results from replicate experiments are shown.

[00901] Various Malatl oligonucleotides were designed, constructed and tested which comprise a non -negatively charged intemucleotidic linkage. Various Malatl oligonucleotides comprise 1 or more non -negatively charged intemucleotidic linkages. In various tables and throughout the text herein, the presence or absence of a hyphen in the designation of an oligonucleotide is irrelevant. For example, WV8582 is equivalent to WV-8582.

Table 22G. Data of certain oligonucleotides.

Numbers represent knockdown of Malatl mRNA relative to HPRT1, wherein 1.000 would represent no (0.0%) knockdown and 0.000 represents 100.0% knockdown; results from replicate experiments are shown.

00902] Various Malatl oligonucleotides were designed, constructed and tested which comprise a non-negatively charged intemucleotidic linkage. Various Malatl oligonucleotides comprise 1 or more non-negatively charged intemucleotidic linkages.

Table 22H. Data of certain oligonucleotides.

Numbers represent knockdown of Malatl mRNA relative to HPRT1, wherein 1.000 would represent no (0.0%) knockdown and 0.000 represents 100.0% knockdown; results from replicate experiments are shown.

[00903] In some embodiments, oligonucleotides were designed, constructed and tested in vitro agamst suitable reference oligonucleotides which do not comprise any non -negatively charged internucleotidic linkages, e.g., in iCeli Astrocytes, at several suitable doses (e.g., 0,0.014,0.041,0.123,0.37,1.11,3.33,10 uM) gymnotic for a suitable period of time, e.g., 2 days.

[00904] Tables 23, 24 and 25 present experimental results.

Table 23. Data of certain oligonucleotides.

Numbers represent knockdown of Malatl mENA, wherein 1.000 would represent no (0.0%) knockdown and 0.000 represents 100.0% knockdown; results from replicate experiments are shown.

Table 24. IC5G of certain Maiatl oligonucleotides.

[00905] Among other things, the present disclosure demonstrates that oligonucleotides comprising one or more non-negatively charged intemucleotidic linkages can provide dramatically improved activities - as illustrated in Table 24, more than 15-fold improvement can be achieved in terms of 1C50.

[00906] in another experiment, several Maiatl oligonucleotides including WV-11533, which comprises three neutral intemucleotidic linkages, were assessed for knockdown of Maiatl, measured by a decrease in the abundance of a Maiatl RNA, WV-7772, which is complementary to the tested oligonucleotides, in the presence of RNaseH.

100907] At a time point of 45 minutes less than 20% of the Malatl RNA remained in the presence of RNase H and WV-11533 or WV-8587, indicating greater than 80% knockdown; and about 60% of the Malatl RNA remained in the presence of RNase H and WV-8556, which is stereorandom and does not comprise a neutral backbone. Among other things, the present disclosure demonstrates that oligonucleotides comprising non-negatively charged intemudeotidic linkages and/or chirally controlled intemudeotidic linkages showed significantly improved activities in reducing levels of target nucleic acids, e.g., through RNase H-mediated knockdown.

[00908] Certain oligonucleotides were also tested for stability in rat liver homogenate at 0, 1 and

2 days. For both WV-11533 and WV-8587, over 80% of the full-length oligonucleotide remained at 2 days; about 40% of the stereorandom WV-8556 remained.

[00909] Oligonucleotides were also tested for Tm with the Malatl RNA, WV-7772. One example set of test conditions: 1 mM Duplex in IX PBS (pH 7.2); Temperature Range: !5°C-90°C; Temperature Rate: 0.5°C/min; Measurement Interval: 0.5°C. The results showed the following duplex Tm (°C) with WV-7772: WV-8556, 73.52; WV-8587, 69.57; and WV-1 1533, 68.67.

[00910] In some embodiments, oligonucleotides comprising non -negatively charged intemudeotidic linkages provide improved splicing modulation activities. Various oligonucleotides for mediating skipping of an exon in DMD were prepared and/or tested, wherein the oligonucleotides comprise non -negatively charged intemudeotidic linkages. Certain oligonucleotides comprising non- negatively charged intemudeotidic linkages are listed in Table Al.

Table 25A. Example data of certain oligonucleotides.

Numbers indicate the level of exon skipping; e.g., 27.13 in column 2, row 2, represents 27.13% skipping of a DMD exon. Oligonucleotides were tested in vitro on cells at 10 or 3 uM.

Table 25B. Example data of certain oligonucleotides.

Numbers indicate the level of exon skipping relative to control; numbers are approximate.

Oligonucleotides were tested in vitro on cells at 10 or 3 uM.

PMO indicates an all-PMO oligonucleotide.

[00911] Various DMD oligonucleotides for skipping exon 23 in mouse were constructed, several of which comprise a non-negative!y charged intemucleotidic linkage, including WV-11343, WV-11344, WV-11345, WV-11346, and WV-11347. These oligonucleotides were tested and demonstrated skipping of exon 23, as shown in the table below.

Table 25 C.1. Example data of certain oligonucleotides.

Numbers represent exon 23 skipping level relative to control.

[00912] In some experiments, de!45-52 cells (patient derived myoblasts) wore treated with various oligonucleotides, including WV-13405 (PMO), WV-9517 and WV-9898, in muscle differentiation medium at 15, 10, 3.3, 1.1 , .3, .1 and 0 uM under free uptake conditions for 6 days before being collected and analyzed for dystrophin protein restoration by Western blot. WV-9517 and WY -9898 demonstrated significant DMD production at concentrations of 3.3 uM and higher; WY- 13405 did not show significant DMD product at a concentration of 3.3 uM, but did show DMD production at concentrations of 10 and 15 uM. Control was Vinculin.

[00913] As shown in Table 25D, additional oligonucleotides were constructed which were capable of mediating skipping of exon 53 and which comprise at least one neutral intemucleotidic linkage.

[00914] Various additional DMD oligonucleotides for skipping exon 23 m mouse were constructed. These oligonucleotides were tested and demonstrated skipping of exon 23, as shown in the table below .

Table 25C.2. Example data of certain oligonucleotides.

DMD oligonucleotides were tested in vitro for their ability to skip DMD exon 23 in H2K murine cells. Oligonucleotide delivery was gymnotic, and 4 day treatment was used.

Numbers represent exon 23 skipping level relative to control. 100.0 would represent 100% of transcripts skipped; 0 would represent 0% of transcripts skipped. Data from replicates are shown.

Table 25C.3. Example data of certain oligonucleotides.

DMD oligonucleotides were tested in vitro for their ability to skip DMD exon 23 in H2K murine cells. Oligonucleotide delivery was gymnotic, and 4 day treatment was used.

Numbers represent exon 23 skipping level relative to control. 100.0 would represent 100% of transcripts skipped; 0 would represent 0% of transcripts skipped. Data from replicates are shown.

Table 25 C.4. Example data of certain oligonucleotides .

DMD oligonucleotides were tested in vitro for their ability to skip DMD exon 23 in H2K murine cells. Oligonucleotide deliver was gyrnnotic, and 4 day treatment was used. Some of the tested oligonucleotides comprise one or more LNA.

Numbers represent exon 23 skipping level relative to control. 100.0 would represent 100% of transcripts skipped; 0 would represent 0% of transcripts skipped. Data from replicates are shown.

Table 25C.5. Example data of certain oligonucleotides.

DMD oligonucleotides were tested in vitro for their ability to skip DMD exon 23 in H2K murine cells. Oligonucleotide delivery was gyrnnotic, and 4 day treatment was used. Some of the tested oligonucleotides comprise one or more non-negatively charged internucleotidic linkage.

Numbers represent exon 23 skipping level relative to control. 100.0 would represent 100% of transcripts skipped; 0 would represent 0% of transcripts skipped. Data from replicates are shown.

Table 25C.6. Example data of certain oligonucleotides.

Oligonucleotides targeting Malat-1, wherein the oligonucleotides comprise a non-negatively charged internucleotidic linkage, were tested for their ability to knock down Malat-1 GABA neurons in vitro, with 4 day treatment. Numbers represent Malat-1 level relative to HPRT1 control and water, wherein 1.0 would represent 100% Malat-1 level (0% knockdown) and 0 would represent 0% Malat-1 level (100% knockdown). Concentrations (Cone.) tested are provided as [Log (dose uM)j.

Data from replicates are shown.

IC50 of WV-24104 was 132 nM; and IC50 of WV-24109 was 12 nM.

Table 25D. Example data of certain oligonucleotides.

D45-52 myoblasts were treated for 4 days with 10 and 3uM oligonucleotide. Numbers in this and various other tables indicate amount of skipping relative to control.

[00915] Various DMD oligonucleotides comprising a chirally controlled neutral backbone were constructed, including WV-12555, which comprises a neutral intemucleotidic linkage in the Rp configuration, and WV-12558, which comprises a neutral intemucleotidic linkage in the Sp configuration. These were also tested for skipping a DMD exon, as shown in Table 25E.

Table 25E. Example data of certain oligonucleotides.

D45-52 myoblasts were treated for 4 days with 10 and 3uM oligonucleotide. Oligonucleotides were delivered gymnotically. Numbers represent amount of skipping relative to control.

00916] In some embodiments, >2 fold increase in exon skipping efficiency was achieved.

Table 25F. Example data of certain oligonucleotides.

Various DMD oligonucleotides for skipping exon 53 or 51 were incuted in tissue lysate for 5 -days; full length oligonucleotides detected by LC-MS. Numbers represent percentage of full-length oligonucleotide remaining. Greater than 75% oligonucleotide remains in human and MDX muscle lysates at 3d incubation. Data was from a previous experiment performed for WV-3473, with 2d incubation in MDX muscle lysate. ND: Not determined; WV-3473 stability in human muscle lysate was not performed.

[00917] In some embodiments, an oligonucleotide comprising a neutral intemucleotidic linkage

(e.g., a cyclic guanidine type) demonstrated a higher level of exon skipping than a corresponding oligonucleotide which did not comprise such a neutral intemucleotidic linkage.

[00918] In some embodiments, the present disclosure pertains to an oligonucleotide or an oligonucleotide composition which is capable of mediating single-stranded RNA interference, wherein the oligonucleotide or oligonucleotide composition comprises a non-negatively charged intemucleotidic linkage.

[00919] As described herein, various oligonucleotides comprising a non-negatively charged intemucleotidic linkage and targeting any of several different genes, with different base sequences, patterns of sugar modifications, backbone chemistry, and patterns of stereochemistr ' of backbone intemucleotidic linkages were constructed, including but not limited to various oligonucleotides which target C9orf72 (a different gene than DMD, or Malatl).

[00920] Described herein are various non-limiting examples of oligonucleotides which target

C9orf72 (which is a gene different from the other genes mentioned herein) and which comprise a non- negatively charged intemucleotidic linkage.

[00921] A hexanucleotide repeat expansion in the C9orf72 gene (Chromosome 9, open reading frame 72) is reportedly the most frequent genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). C9orf72 gene variants comprising the repeat expansion and/or products thereof are also associated with other C9orf72-related disorders, such as corticobasal degeneration syndrome (CBD), atypical Parkinsonian syndrome, olivopontocerebellar degeneration (OPCD), primary lateral sclerosis (PLS), progressive muscular atrophy (PMA), Huntington’s disease (HD) phenocopy, Alzheimer’s disease (AD), bipolar disorder, schizophrenia, and other non-motor disorders. Various oligonucleotides were designed and constructed which comprise a neutral intemucleotidic linkage and which target a C9orf72 target (e.g., a C9orf72 oligonucleotide) and are capable of knocking down or decreasing expression, level and/or activity of the C9orf72 target gene and/or a gene product thereof (a transcript, particularly a repeat expansion containing transcript, a protein, etc.).

[00922] Various oligonucleotides designed to target C9orf72 and comprising a non-negatively charged intemucleotidic linkage include, but are not limited to: WV-11532, WV -13305, WV-13307, WV- 13309, WV-13311, WV-13312, WV-13313, WV-13803, WV-138G4, WV-13805, WV-13806, WV- 13807, WV-13808, WV-14553, and WV-14555. These are described below in Table 25G.

Table 25G. Oligonucleotides targeting C9orf72 comprising a neutral intemucleotidic linkage.

Several variants of a C9orf72 rnRNA are produced from the C9or†72 gene: V2 (which does not comprise the deleterious hexanucleotide repeat and which comprises about 90% of all transcripts); V3 (which comprises the hexanucleotide repeat and comprises about 9% of all transcripts); and VI (which comprises the hexanucleotide repeat and compri ses about 1% of all transcripts)

Hexanucleotide repeats reportedly elicit gain of function toxicities, at least partially mediated by the dipeptide repeat proteins and foci formation by, for example, repeat-expansion containing transcripts and/or spliced-out repeat-expansion containing introns and/or antisense transcription of the repeat- expansion containing region and various nucleic-acid binding proteins.

Both WV-8008 and WV-11532 have the same base sequence (or naked sequence), CCTCACTCACCCACTCGCCA. They differ, inter alia, in that the latter comprises 3 contiguous neutral intemucleotidic linkages (Xn), but tire former does not comprise any neutral intemucleotic linkages. The structures of these oligonucleotides is provided below, in Table 25H

Table 25H. C9or†72 oligonucleotides.

WV-8008 and WV-11532 were tested for their ability to knock down expression of hexanucleotide- compnsmg (i.e., disease-associated) transcript V3 compared to total transcripts (all V), as shown below Table 251.

Table 251 and J. Activity of various c9orf72 oligonucleotides. In Tables 251 to 251, various c9orf72 oligonucleotides were tested in motor neurons, with oligonucleotides delivered gymnotically at concentrations from 0.003 to 10 mM (Concentrations are provided as explO). Tested c9orf72 oligonucleotide WV-11532 comprises three neutral internucleotidic linkages. In Tables 14A and 14B, shown are residual levels of c9orf72 transcriptions [e.g , all transcripts (all V) or only V3] relative to HPRT1 , after treatment with c9orf72 oligonucleotides, wherein 1.000 would represent 100% relative transcript level (no knockdown) and 0.000 would represent 0% relative transcript level (e.g., 100% knockdown). Results from replicate experiments are shown.

Table 251 Activity of various c9orf72 oligonucleotides (residual level of all V C9orf72 transcripts)

Table 25 j. Activity of various c9orf72 oligonucleotides (residual level of V3 C9orf72 transcripts)

[00923] As described herein and in data not shown, various oligonucleotides comprising a non- negatively charged intemuc!eotidic linkage and targeting different genes, with different base sequences, patterns of sugar modifications, backbone chemistries, and patterns of stereochemistr of backbone mtemucleotidic linkages were constructed, including but not limited to various oligonucleotides which target DMD, Malatl, or C9orf?2.

[00924] Oligonucleotides comprising a non-negatively charged internucleotidic linkage were also constructed to target six other genes not described herein (wherein the six genes were not DMD, Malatl, or C9orf72); these oligonucleotides include oligonucleotides designed to target these genes and reduce the expression, level and/or activity of the gene or its gene product. These and various oligonucleotides comprising a neutral internucleotidic linkage described herein are capable of performing various functions, including reducing the level, expression and/or activity of a gene or its gene product (e.g., via a RNaseH- or stenc-hindrance-mediated mechanism, or via a single-stranded RNA interference-mediated mechanism) and inducing skipping of an exon (e.g , skipping modulation).

100925] Without wishing to be bound by any particular theor ', Applicant notes that a non- negatively charged and/or neutral internucleotidic linkage can improve an oligonucleotide’s entry into a cell and/or escape from an endosome.

Oligonucleotides Which Comprise a Non-Negativelv Charged Internucleotidic Linkage Can Provide Desired Levels of TLR9 Activation

[00926] Among other things, oligonucleotides comprising non-negativeiy charged internucleotidic linkages can provide desired levels of properties and/or activities, e.g., TLR9 antagonist or agonist activities. In some embodiments, oligonucleotides comprising non-negative!y charged internucleotidic linkages demonstrate lower levels of TLR9 activation in human and/or an animal model (e.g., a mouse) compared to certain comparable oligonucleotides of the same base sequences but having no non-negatively charged internucleotidic linkages. In some embodiments, oligonucleotides comprising non -negatively charged internucleotidic linkages have lower toxicity compared to certain oligonucleotides of the same base sequences but having no non-negatively charged internucleotidic linkages. In some embodiments, a non-negatively charged internucleotidic linkage is within a CpG motif and is the internucleotidic linkage between tire C and G.

[00927] In an experiment, several oligonucleotides to target gene C were constructed. Gene C is a different gene than DMD, or SMalat-l. The sequence of these oligonucleotides comprises a CpG, a motif known to activate TLR9.

[00928] Table 25K.

[00929] This experiment represents a test of induction of human TLR9 or mouse TLR9 in

HEK293 cells. Numbers represent relative inductive relative to negative control, water. Concentrations tested: 0.93uM, 2.77uM, 8.33uM, 25uM, 75uM. Positive control: WV-BZ21. The experiment w¾s performed in biological duplicates.

00930] Table 25K. Oligonucleotides used in this study

Table 25L. Activity of certain oligonucleotides.

All the tested oligonucleotides (WV-HZ12, WV-BZ761, WV-BZ762, WV-BZ763, WV-BZ764, WV- BZ765, WV-BZ766, WV-BA207, WV-BA208, and WV-BA209) target gene C and all have the same base sequence, wherein each base is indicated generically by N, except that the single CpG motif is indicated. WV-BZ2 I , positive control, has a base sequence of TCGTCGTTTTGTCGTTTTGTCGTT, which comprises several CpG motifs, and is not designed to target gene C. Numbers indicate relative induction of hTLR9 activity relative to water.

Table 25M. Activity of certain oligonucleotides.

These oligonucleotides were also tested for induction of mouse TLR9.

Numbers indicate relative induction of mTLR9 activity relative to water.

[00931 ] In some embodiments, it was observed that in some instances certain oligonucleotides that did not induce appreciable TLR9 activation, or induced very low level of TLR9 activation above mock against human or mouse TLR9.

Example Oligonucleotides Comprising Additional Moieties [00932] In some embodiments, the present disclosure provides oligonucleotides comprising one or more additional moieties, e.g., targeting moieties, carbohydrate moieties, etc. In some embodiments, the present disclosure provides oligonucleotides comprising one or more sulfonamide moieties. In some embodiments, a provided oligonucleotide comprise one or two or more sulfonamide moieties. In some embodiments, the present disclosure provides oligonucleotides that can modulate splicing, e.g., DMD oligonucleotides that can modulate exon skipping, wherein the oligonucleotides comprise one or more sulfonamide moieties in some embodiments, the present disclosure provides oligonucleotides that mediate skipping of DMD exon 23, 45, 51 or 53, or multiple DMD exons, wherein the oligonucleotides comprise one or more sulfonamide moieties.

[00933] In some embodiments, a sulfonamide moiety has or comprises the structure of

— L— S 0 2 N (R ! ) 2 . In some embodiments, a sulfonamide moiety has or comprises the structure of -S0 2 N(R 1 ) 2 . In some embodiments, a sulfonamide moiety has or comprises the structure of -Cy-S0 2 N(R 1 ) 2 . In some embodiments, -Cy- is aromatic. In some embodiments, -Cy- is an optionally substituted phenyl ring. In some embodiments, -Cy- is '= H- . In some embodiments, -Cy- is an optionally substituted heteroaryl ring. In some embodiments, -Cy- is an optionally substituted 5-6

N--N membered heteroaryl ring having 1-4 heteroatoms. In some embodiments, -Cy- is

some embodiments, each R 5 is -H.

[00934] A sulfonamide moiety can be connected to an oligonucleotide chain via various suitable linkers in accordance with the present disclosure, such as those described herein and/or in WO/2017/062862, linkers of which is incorporated herein by reference. Example sulfonamides moieties, including mono-, bi-, and tri -sulfonamide moieties, are described below:

[00935] In some embodiments, an oligonucleotide comprise a modified intemucleotidic linkage and a sulfonamide moiety optionally through a linker. In some embodiments, an oligonucleotide comprising a modified intemucleotidic linkage and a sulfonamide moiety is a siRNA, doub!e-straned siRNA, single -stranded siRNA, gapmer, skipmer, blockmer, antisense oligonucleotide, antagomir, microRNA, pre-microRNs, antimir, supermir, ribozyme, U1 adaptor, RNA activator, RNAi agent, decoy oligonucleotide, triplex forming oligonucleotide, aptamer or adjuvant. In some embodiments, the present disclosure provides an oligonucleotide which comprises a modified intemucleotidic linkage which comprises a sulfonamide. In some embodiments, an oligonucleotide comprises a sulfonamide and a chiraily controlled intemucleotidic linkage. In some embodiments, an oligonucleotide comprises a sulfonamide and a chiraily controlled intemucleotidic linkage which is a phosphorothioate intemucleotidic linkage.

[00936] In some embodiments, the present disclosure pertains to an oligonucleotide which comprises a sulfonamide moiety or a derivative or variant thereof. In some embodiments, the present disclosure pertains to an oligonucleotide composition, wherein the oligonucleotide comprises a sulfonamide moiety or a derivative or variant thereof and the oligonucleotide comprises at least one chiraily controlled intemucleotidic linkage.

[00937] In some embodiments, the present disclosure pertains to an oligonucleotide which comprises a sulfonamide moiety or a derivative or variant thereof, wherein tire oligonucleotide is capable of mediating a decrease the expression, level and/or acti vity of a target gene or gene product thereof.

[00938] In some embodiments, the present disclosure pertains to an oligonucleotide which comprises a sulfonamide moiety or a derivative or variant thereof, wherein the oligonucleotide is capable of mediating modulation of exon skipping of a target gene. In some embodiments, the present disclosure pertains to an oligonucleotide which comprises a sulfonamide moiety or a derivative or variant thereof, wherein the oligonucleotide is capable of increasing skipping of an exon of a target gene.

[00939] Example oligonucleotides that can be utilized for splicing modulation, e.g., exon skipping, that comprise a sulfonamide moiety include WV-3548, WV-3366, etc. Other oligonucleotides comprising a sulfonamide moiety were designed, constructed and/or tested for various activities. For example, oligonucleotides comprising a“mono-sulfonamide” moiety, such as WV-2836, WV-7419, WV- 7421 , WV-7422, WV-74G8, WV-74G9, WV-7427, WV-7863, and WV-7864; oligonucleotide comprising a“bi-sulfonamide”, WV-7423; and oligonucleotide comprising a“tri -sulfonamide”, WV-7417.

Table 26A. Certain Malatl oligonucleotides.

For this Table, descriptions match those of Table Al, and Mod045 :

Mod046:

Mod048:

Mod054:

In these Mods, -C(O)- connects to -NH- of a linker (e.g., L001).

[00940] Oligonucleotides comprising a sulfonamide moiety were tested for their ability to knockdown Malatl. Tested oligonucleotides were gymnotically delivered to D48-50 patient derived myotubes, which were dosed at 3,1, 0.3 and 0.1 11M concentrations. Cells were allowed to differentiate for 4 days (e.g., this experiment was 4 days post-differentiation) qPCR was used to evaluate knockdown of Malat-1. The results are shown in Table 26B.

Table 26B. Example data of Malatl oligonucleotides.

Numbers represent relative Malat-1 mRNA level.

Various Malatl oligonucleotides, many comprising a sulfonamide moiety, were tested for their ability to knockdown Malatl in pre-differentiated myotubes. Certain data are shown in Table 26C. D48-50 patient derived myoblasts were differentiated for 4 days prior to dosing with at 1 and 0.1 mM concentrations. R A was harvested 48 hours post-treatment for measurement.

Table 26C. Example data of Malatl oligonucleotides.

Numbers represent relative Malat-1 mRNA level. Numbers are approximate.

[00941] In some experiments, animals were dosed with oligonucleotides, including some which comprise a sulfonamide moiety, and the animals were later sacrificed and their tissues tested for the level of the ligonucleotides.

[00942] In some experiments, the following protocol was used: Animals: 32 male Mdx mice and

32 male C57BL/6 mice (all 8-10 week-old). Test animals were acclimated to the facility for at least 3 days upon arrival. Dosing: S.C. (subcutaneous) dosing on days 1, 3 and 5 (5 niL/kg). Necropsy: animals were euthanized 72 hours after the last SC injection. All animals were perfused with PBS. The following tissues were collected: brain, sciatic nerves, spinal cord, eyes, liver, kidney, spleen, heart, diaphragm, gastrocnemius, quadriceps and triceps, white fat, brown fat. Fresh tissues will be rinsed briefly with PBS, gently blotted dry, weighed and snap frozen in Liquid Nitrogen in 2-mL tubes and stored at -80C (on dry ice). Histology: Quadricep and Kidney postfixed in 10% Formalin and processed to slides (paraffin embedded sections). In some experiments, suitable variants of this protocol were used

[00943] Certain results are shown in Tables 27, 28 and 29.

Table 27. Knock-down and oligonucleotide presence in various tissues.

Numbers indicate Malatl mRNA levels relative to mHprt (mHPRT or mHPRTl), and presence of oligonucleotide (ug/g). Experimental procedure: Study Species: 5-6 wks MDX mice; Route: Subcutaneous; # Doses: QD for 3 days; Time Point Post Last Dose: 2 days; Daily Dose Level (ug): 12.5 mg/kg.

Table 28. Knock-down and oligonucleotide presence in various tissues.

Numbers indicate Malatl mRNA levels relative to mHprt, and presence of oligonucleotide (ug/g). Experimental procedure: Study Species: 10-12 wks MDX mice; Route: Subcutaneous; # Doses: QD for 3 days; Time Point Post Last Dose: 3 days; and Daily Dose Level (ug): 12 mg/kg.

Table 29. Knock-down and oligonucleotide presence in various tissues.

Numbers indicate Malatl mRNA levels relative to mHprt, and presence of oligonucleotide (ug/g).

Experimental procedure: Study Species: 10-12 wks wt niice; Route: Subcutaneous; # Doses: QD for 3 days; Time Point Post Last Dose: 3 days; and Daily Dose Level (ug): 12 mg/kg.

Table 30 Knock-down and oligonucleotide presence in various tissues.

Numbers indicate Malatl mRNA levels relative to mHprt, and presence of oligonucleotide (ug/g).

Experimental procedure: Study Species: 5-6 wks wt mice; Route: Subcutaneous; # Doses: QD for 1 days;

Time Point Post Last Dose: 3 days; and Daily Dose Level (ug): 200 mg/kg.

Example Methods for Preparing Oligonucleotides and Compositions

[00944] Among other things, the present disclosure provides technologies (methods, reagents, conditions, purification processes, etc.) for prepamg oligonucleotides and oligonucleotide compositions, including chirally controlled oligonucleotides and chirally controlled oligonucleotide nucleotides. Various technologies (methods, reagents, conditions, purification processes, etc.), as described herein, can be utilized to prepare provided oligonucleotides and compositions thereof in accordance with the present disclosure, including but not limited to those described in US 9695211, US 9605019, US 9598458, US 2013/0178612, US 2015021 1006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741 , WO 2017/192664, WO 2017/192679, WO 2017/210647, WO 2018/223056, WO 2018/237194, and/or WO 2019/055951, the preparation technologies of each of which are incorporated herein by reference.

[00945] In some embodiments, the present disclosure provides chiral!y controlled oligonucleotides. In some embodiments, a provided chirally controlled oligonucleotide is over 50% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 55% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 60% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 65% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 70% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 75% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 80% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 85% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 90% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 91 % pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 92% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 93% pure hi some embodiments, a provided chirally controlled oligonucleotide is over about 94% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 95% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 96% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 97% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 98% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 99% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 99 5% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 99.6% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 99.7% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 99.8% pure. In some embodiments, a provided chirally controlled oligonucleotide is over about 99.9% pure. In some embodiments, a provided chirally controlled oligonucleotide is over at least about 99% pure.

[00946] In some embodiments, a chirally controlled oligonucleotide composition is a composition designed to comprise a single oligonucleotide type. In certain embodiments, such compositions are about 50% diastereomerically pure. In some embodiments, such compositions are about 50% diastereornerically pure. In some embodiments, such compositions are about 50% diastereomerically pure hi some embodiments, such compositions are about 55% diastereomerically pure. In some embodiments, such compositions are about 60% diastereomerically pure. In some embodiments, such compositions are about 65% diastereomerically pure. In some embodiments, such compositions are about 70% diastereomerically pure. In some embodiments, such compositions are about 75% diastereomerically pure. In some embodiments, such compositions are about 80% diastereomerically pure. In some embodiments, such compositions are about 85% diastereomerically pure. In some embodiments, such compositions are about 90% diastereomerically pure. In some embodiments, such compositions are about 91% diastereomerically pure. In some embodiments, such compositions are about 92% diastereomerically pure. In some embodiments, such compositions are about 93% diastereomerically pure. In some embodiments, such compositions are about 94% diastereomerically pure. In some embodiments, such compositions are about 95% diastereomerically pure. In some embodiments, such compositions are about 96% diastereomerically pure. In some embodiments, such compositions are about 97% diastereomerically pure. In some embodiments, such compositions are about 98% diastereomerically pure. In some embodiments, such compositions are about 99% diastereomerically pure. In some embodiments, such compositions are about 99.5% diastereomerically pure. In some embodiments, such compositions are about 99.6% diastereomerically pure. In some embodiments, such compositions are about 99.7% diastereomerically pure. In some embodiments, such compositions are about 99.8% diastereomerically pure. In some embodiments, such compositions are about 99.9% diastereomerically pure. In some embodiments, such compositions are at least about 99% diastereomerically pure.

[00947] Among other things, the present disclosure recognizes the challenge of stereoselective

(rather than stereorandom or racemic) preparation of oligonucleotides. Among other things, the present disclosure provides methods and reagents for stereoselective preparation of oligonucleotides comprising multiple (e.g., more than 5, 6, 7, 8, 9, or 10) intemucleotidic linkages, and particularly for oligonucleotides comprising multiple (e.g., more than 5, 6, 7, 8, 9, or 10) chiral intemucleotidic linkages. In some embodiments, in a stereorandom or racemic preparation of oligonucleotides, at least one chiral intemucleotidic linkage is formed with less than 90: 10, 95:5, 96:4, 97:3, or 98:2 diastereoselectivity. in some embodiments, for a stereoselective or chirally controlled preparation of oligonucleotides, each chiral intemucleotidic linkage is formed with greater than 90: 10, 95:5, 96:4, 97:3, or 98:2 diastereoselectivity. In some embodiments, for a stereoselective or chirally controlled preparation of oligonucleotides, each chiral intemucleotidic linkage is fomied with greater than 95:5 diastereoselectivity. In some embodiments, for a stereoselective or chirally controlled preparation of oligonucleotides, each chiral intemucleotidic linkage is fomied with greater than 96:4 diastereoselectivity. In some embodiments, for a stereoselective or chirally controlled preparation of oligonucleotides, each chiral intemucleotidic linkage is fomied with greater than 97:3 diastereoselectivity. In some embodiments, for a stereoselective or chirally controlled preparation of oligonucleotides, each chiral intemucleotidic linkage is fomied with greater than 98:2 diastereoselectivity. In some embodiments, for a stereoselective or chirally controlled preparation of oligonucleotides, each chiral intemucleotidic linkage is fomied with greater than 99: 1 diastereoselectivity. In some embodiments, diastereoselectivity of a chiral intemucleotidic linkage in an oligonucleotide may be measured through a model reaction, e.g. formation of a dimer under essentially the same or comparable conditions wherein the dimer has the same intemucleotidic linkage as the chiral intemucleotidic linkage, the 5’-nucleoside of the dimer is the same as the nucleoside to the 5’ -end of the chiral intemucleotidic linkage, and the 3 -nucleoside of the dimer is the same as the nucleoside to the 3’- end of the chiral intemucleotidic linkage.

[00948] In some embodiments, a c!u rally controlled oligonucleotide composition is a composition designed to comprise multiple oligonucleotide types. In some embodiments, methods of the present disclosure allow for the generation of a library of chiraliy controlled oligonucleotides such that a pre selected amount of any one or more chiraliy controlled oligonucleotide types can be mixed with any one or more other chiraliy controlled oligonucleotide types to create a chiraliy controlled oligonucleotide composition. In some embodiments, the pre-selected amount of an oligonucleotide type is a composition having any one of the above-described diastereomeric purities.

[00949] In some embodiments, the present disclosure provides methods for making a chiraliy controlled oligonucleotide comprising steps of:

(1 ) coupling;

(2) capping;

(3) optionally modifying;

(4) deblocking; and

(5) repeating steps (1) - (4) until a desired length is achieved.

10001 In some embodiments, the present disclosure provides a method, e.g. , for preparing an oligonucleotide, comprising one or more cycles, each of which independently comprises:

(1) a coupling step;

(2) optionally a pre-modification capping step;

(3) a modification step;

(4) optionally a post-modification capping step; and

(5) optionally a de -blocking step.

[00950] In some embodiments, a cycle comprises one or more pre-modification capping steps. In some embodiments, a cycle comprises one or more post-modification capping steps. In some embodiments, a cycle comprises one or more pre- and post-modification capping steps. In some embodiments, a cycle comprises one or more de -blocking steps. In some embodiments, a cycle comprises a coupling step, a pre-modification capping step, a modification step, a post-modification capping step, and a de-blocking step. In some embodiments, a cycle comprises a coupling step, a pre-modification capping step, a modification step, and a de-blocking step. In some embodiments, a cycle comprises a coupling step, a modification step, a post-modification capping step and a de-blocking step. In some embodiments, comprise a coupling step, a pre -modification capping step, a modification step, a post- modification capping step, and a de-blocking step. In some embodiments, one or more cycles comprise a coupling step, a pre-modification capping step, a modification step, and a de-blocking step. In some embodiments, one or more cycles comprise a coupling step, a modification step, a post-modification capping step and a de-blocking step.

[00951] When describing the provided methods, the word“cycle” has its ordinary meaning as understood by a person of ordinary skill in the art. In some embodiments, one round of steps (I)-(4) is referred to as a cycle. In some embodiments, some cycles comprise modifying. In some embodiments, some cycles do not comprise modifying. In some embodiments, some cycles comprise and some cycles do not comprise modifying in some embodiments, each cycle independently comprises a modifying step. In some embodiments, each cycle does not comprise a cycling step.

[00952] In some embodiments, to fomi a chirally controlled intemucleotidic linkage, a chi rally pure phosphoramidite comprising a chiral auxiliary is utilized to stereoselectively form the chirally controlled intemucleotidic linkage. Various phosphoramidite and chiral auxiliaries, e.g., those described m US 969521 1 , US 9605019, US 9598458, US 2013/0178612, US 2015021 1006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, WO 2017/210647, WO 2018/223056, WO 2018/237194, and/or WO 2019/055951, the phosphoramidite and dural auxiliaries of each of which are incorporated herein by reference, may be utilized in accordance with the present disclosure.

100953] In some embodiments, a coupling step provides an oligonucleotide comprises an intemucleotidic linkage of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, 1-n-4, II, II-a-1, II-a-2, II-b-1, II- b-2, ll-c-l, II-c-2, II-d-1, II-d-2, etc., or a salt form thereof, wherein P L is P. In some embodiments, such an intemucleotidic linkage is a chirally controlled intemucleotidic linkage. In some embodiments, such an intemucleotidic linkage comprises a chiral auxiliary moiety

[00954] In some embodiments, a modifying step provides an oligonucleotide comprises an intemucleotidic linkage of formula 1, 1-a, I-b, I-c, I-n-1, I-n-2, I-n-3, 1-n-4, II, II-a-1, II-a-2, II-b-1, II- b-2, II-c-I, II-c-2, II-d-1, II-d-2, III, etc., or a salt form thereof, wherein P 1 is P=W. In some embodiments, a modifying step provides an oligonucleotide comprises an intemucleotidic linkage of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-i, II-c-2, II-d-1, II-d-2, etc., or a salt form thereof, wherein P L is P=W. hi some embodiments, W is S. In some embodiments, W is O. In some embodiments, such an intemucleotidic linkage is a chirally controlled intemucleotidic linkage. In some embodiments, such an intemucleotidic linkage comprises a chiral auxiliary moiety. In some embodiments, a modifying step provides a non -negatively charged intemucleotidic linkage. In some embodiments, a non -negatively charged intemucleotidic linkage has the structure of formula I, I-a, I-b, I-c, 1-n-l, l-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II- c-2, II-d-1, II-d-2, etc., or a salt form thereof. In some embodiments, such an intemucleotidic linkage is a neutral intemucleotidic linkage. In some embodiments, such an intemucleotidic linkage is a chi rally controlled intemucleotidic linkage. In some embodiments, such an internucleotidic linkage comprises a chiral auxiliary moiety. In some embodiments, such an intemucleotidic linkage comprises no chiral auxiliary moiety. In some embodiments, a chiral auxiliary moiety falls off during modification.

[00955] Provided technologies provide various advantages. Among other things, as demonstrated herein, provided technologies can greatly improve oligonucleotide synthesis crude purity and yield, particularly for modified and/or chirally pure oligonucleotides that provide a number of properties and activities that are critical for therapeutic purposes. With the capability to provide unexpectedly high crude purity and yield for therapeutically important oligonucleotides, provided technologies can significantly reduce manufacturing costs (through, e.g., simplified purification, greatly improved overall yields, etc.). In some embodiments, provided technologies can be readily scaled up to produce oligonucleotides in sufficient quantities and qualities for clinical purposes. In some embodiments, provided technologies comprising chiral auxiliaries that comprise electron-withdrawing groups in G 2 (e.g, PSM chiral auxiliaries) are particularly useful for preparing chirally controlled internucleotidic linkages comprising P-N bonds (e.g., non-negatively charged intemucleotidic linkages such as nOOl, n002, n003, nOQ4, n005, n006, n007, n008, n009, nOlO, etc.) and can significantly simplify manufacture operations, reduce cost, and/or facilitate downstream formation.

[00956] In some embodiments, provided technologies provides improved reagents compatibility. For example, as demonstrated in the present disclosure, provided technologies provide flexibility to use different reagent systems for oxidation, sulfurization and/or azide reactions, particularly for chirally controlled oligonucleotide synthesis.

[00957] Among other things, the present disclosure provides oligonucleotide compositions of high crude purity. In some embodiments, the present disclosure provides chirally controlled oligonucleotide composition of high crude purity. In some embodiments, the present disclosure provides chirally controlled oligonucleotide of high crude purity. In some embodiments, the present disclosure provides oligonucleotide of high crude purity and/or high stereopurity.

Support and Linkers [00958] In some embodiments, oligonucleotides can be prepared m solution. In some embodiments, oligonucleotides can be prepared using a support. In some embodiments, oligonucleotides are prepared using a solid support. Suitable support that can be utilized in accordance with the present disclosure include, e.g., solid support described in US 9695211, US 9605019, US 9598458, US 2013/0178612, US 2015021 1006, US 20170037399, WO 2017/015555, WO 2017/062862, WO

2017/160741, WO 2017/192664, WO 2017/192679, WO 2017/210647, WO 2018/223056, WO

2018/237194, and/or WO 2019/055951, the solid support of each of which is incorporated herein by reference.

100959] In some embodiments, a linker rnoiety is utilized to connect an oligonucleotide chain to a support during synthesis. Suitable linkers are widely utilized in the art, and include those described in US 9695211, US 9605019, US 9598458, US 2013/0178612, US 20150211006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, WO

2017/210647, WO 2018/223056, WO 2018/237194, and/or WO 2019/055951, the linker of each of which is incorporated herein by reference

[00960] In some embodiments, the linking moiety is a succinamic acid linker, or a succinate linker (-CO-CH 2 -CH 2 -CO-), or an oxaiyl linker (-CO-CO-). In some embodiments, the linking moiety and the nucleoside are bonded together through an ester bond. In some embodiments, a linking rnoiety and a nucleoside are bonded together through an amide bond. In some embodiments, a linking moiety connects a nucleoside to another nucleotide or nucleic acid. Suitable linkers are disclosed in, for example, Oligonucleotides And Analogues A Practical Approach, Ekstein, F. Ed., IRL Press, N.Y., 1991 , Chapter 1 and Solid-Phase Supports for Oligonucleotide Synthesis, Pon, R. T , Curr. Prot. Nucleic Acid Chern., 2000, 3.1.1-3.1.28. In some embodiments, a universal linker (UnyLinker) is used to attached the oligonucleotide to the solid support (Ravikumar et al., Org. Process Res. Dev., 2008, 12 (3), 399-410). In some embodiments, other universal linkers are used (Pon, R. T., Curr. Prot. Nucleic Acid Cfaetn., 2000, 3.1 1-3 1.28). In some embodiments, various orthogonal linkers (such as disulfide linkers) are used (Pon, R. T., Curr. Prot. Nucleic Acid Chem., 2000, 3.1.1-3.1.28).

[00961] Among other things, the present disclosure recognizes that a linker can be chosen or designed to be compatible with a set of reaction conditions employed in oligonucleotide synthesis. In some embodiments, to avoid degradation of oligonucleotides and to avoid desulfurization, auxiliary ' groups are selectively removed before de -protection. In some embodiments, DPSE group can selectively be removed by F ions. In some embodiments, the present disclosure provides linkers that are stable under a DPSE de-protection condition, e.g., 0.1M TBAF in MeCN, 0.5M HF-Et j N in THF or MeCN, etc. In some embodiments, a provided linker is a linker as exemplified below:

succinyl-piperidine (SP) linker suednyi Sinker oxa!yl linker

G-lirtker CNA linker (with sucdnyl linker)

Solvents

[00962] Syntheses of provided oligonucleotides are generally performed in aprotie organic solvents. In some embodiments, a solvent is a nitrile solvent such as, e.g., acetonitrile. In some embodiments, a solvent is a basic amine solvent such as, e.g., pyridine. In some embodiments, a solvent is an ethereal solvent such as, e.g., tetrahydrofuran. In some embodiments, a solvent is a halogenated hydrocarbon such as, e.g., dichloromethane. In some embodiments, a mixture of solvents is used in certain embodiments a solvent is a mixture of any one or more of the above-described classes of solvents.

[00963] In some embodiments, when an aprotie organic solvent is not basic, a base is present in the reacting step. In some embodiments where a base is present, the base is an amine base such as, e.g., pyridine, quinoline, or AyV-dimethylaniline. Example other amine bases include pyrrolidine, piperidine, yV-methyi pyrrolidine, pyridine, quinoline, YiV-dimethylaminopyridine (DMAP), or AvY-dimethylaniline.

[00964] In some embodiments, a base is other than an amine base.

[00965] In some embodiments, an aprotie organic solvent is anhydrous. In some embodiments, an anhydrous aprotie organic solvent is freshly distilled. In some embodiments, a freshly distilled anhydrous aprotie organic solvent is a basic amine solvent such as, e.g., pyridine. In some embodiments, a freshly distilled anhydrous aprotie organic solvent is an ethereal solvent such as, e.g., tetrahydrofuran. In some embodiments, a freshly distilled anhydrous aprotie organic solvent is a nitrile solvent such as, e.g., acetonitrile. Chiral reagents/ Chiral auxiliaries

[00966] In some embodiments, chiral reagents (may also he referred to as chiral auxiliaries) are used to confer stereoselectivity in the production of chirally controlled oligonucleotides. Many chiral reagents, also referred to by those of skill in the art and herein as chiral auxiliaries, may be used in accordance with methods of the present disclosure. Examples of such chiral reagents are described herein and in US 9695211, US 9605019, US 9598458, US 2013/0178612, US 20150211006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, WO 2017/210647, WO 2018/098264, WO 2018/223056, WO 2018/237194, and/or WO 2019/055951 , the chiral auxiliaries of each of which is incorporated by reference.

[00967] In some embodiments, a chiral reagent for use in accordance with the methods of the present disclosure is of Formula 3-1, below:

Formula 3-1

where :

W 1 and W 2 are any of-O-, -S-, -NG 3 -, or -NG 5 -0-;

U and U 3 are carbon atoms which are bonded to U 2 if present, or to each other if r is 0, via a single, double or triple bond;

U 2 is— C , -CG 8 -, -CG 8 G 8 -, -NG 8 -, -N-, -0-, or -S- where r is an integer of 0 to 5; and each of G 1 , G 2 , G’, G 4 , G", and G 8 is independently R 1 as described in the present disclosure.

[00968] In some embodiments, W 1 and W 2 are any of -O-, -S-, or -NG 5 -, Ip and U 3 are carbon atoms which are bonded to U 2 if present, or to each other if r is 0, via a single, double or triple bond. U 2 is— C— , -CG 8 -, -CG 8 G 8 -, -NG 8 -, -N-, -0-, or -S- where r is an integer of 0 to 5 and no more than two heteroatoms are adjacent. When any one of U 2 i s C, a triple bond must be formed between a second instance of U 2 , which is C, or to one of Uj or U 3 . Similarly, when any one of U 2 is CG 8 , a double bond is formed between a second instance of U 2 which is -CG 8 - or -N-, or to one of Ui or U 3

[00969] In some embodiments, -UiG J G 4 -(U 2 ) r- U3G 1 G 2 - is -CG J G 4 -CG i G 2 -. In some embodiments, -U.-(U 2 ) r- U 3- i s -CG 3 = CG 2 -. In some embodiments, -Lp-(U 2 ) f- U 3- is -CºC- In some embodiments, L , {1 . 4, I, is -CG 3 =CG 8 -CG G 2 -. In some embodiments, -Lp-(U 2 ) r- U 3 is -CG 3 G 4 -0-CG 1 G 2 -. In some embodiments, -lp-(U 2 ) r- U 3- is -CG 3 G 4 -NG 8 -CG ! G 2 -. In some embodiments, -Ui-(U 2 ) r -U 3 - is -CG J G 4 -N-CG -. In some embodiments, -Tp-(U 2 ) r- U 3- is -CG 3 G 4 -N=CG 8 -CG 1 G 2 -.

[00970] In some embodiments, G 1 , G 2 , G 3 , G 4 , G 5 , and G 8 are independently R 1 as described in the present disclosure. In some embodiments, G 1 , G z , G 3 , G 4 , G 5 , and G 8 are independently R as described in the present disclosure. In some embodiments, G 1 , G z , G 5 , G 4 , G s , and G s are independently hydrogen, or an optionally substituted group selected from aliphatic, alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heteroahphatic, heterocyclyl, heteroaryl, and aryl; or two of G 1 , G 2 , G’, G 4 , and G are G b (taken together to form an optionally substituted, saturated, partially unsaturated or unsaturated carbocyclic or heteroatom -containing ring of up to about 20 ring atoms which is monocyclic or polycyclic, and is fused or umfused). in some embodiments, a ring so formed is substituted by oxo, thioxo, alkyl, alkenyl, alkynyl, heteroaryl, or aryl moieties. In some embodiments, when a ring formed by taking two G 6 together is substituted, it is substituted by a moiety which is bulky enough to confer stereoselectivity during the reaction.

[00971] In some embodiments, a ring formed by taking two of G b together is optionally substituted cyclopentyl, pyrroly!, cyclopropyl, cyclohexenyl, cyclopenteny!, tetrahydropyranyl, or piperazinyl. In some embodiments, a ring formed by taking two of G 6 together is optionally substituted cyclopentyl, pyrrolyl, cyclopropyl, cyclohexenyl, cyclopentenyl, tetrahydropyranyl, pyrrohdinyl, or piperazinyl.

[00972] In some embodiments, G 1 is optionally substituted phenyl. In some embodiments, G is phenyl. In some embodiments, G 2 is methyl or hydrogen. In some embodiments, G z is hydrogen. In some embodiments, G 1 is optionally substituted phenyl and G 2 is methyl. In some embodiments, G 1 is phenyl and G 2 is methyl. In some embodiments, G 1 is -CH 2 Si(R)3, wherein one R is optionally substituted C 6 aliphatic, and the other two R are each independently an optionally substituted 3-20 memhered, monocyclic or polycyclic, saturated, partially unsaturated or aromatic ring having 0-5 heteroatoms. In some embodiments, the other two R are each independently optionally substituted phenyl. In some embodiments, G 1 is -CH 2 SiMePh 2.

[00973] In some embodiments, r is 0.

[00974] In some embodiments, W 1 is -NG 5 -0- In some embodiments, W 1 is -NG 5 -0-, wherein the () is bonded to H. In some embodiments, W is -NG 5 -. In some embodiments, one of G 3 and G 4 is taken together with G s to form an optionally substituted 3-10 membered ring. In some embodiments, one of G 3 and G 4 is taken together with G J to form an optionally substituted pyrrohdinyl ring. In some embodiments, one of G and G 4 is taken together with G 5 to form a pyrrohdinyl ring. In some embodiments, G 5 is optionally substituted C _ 6 aliphatic. In some embodiments, G 5 is methyl. In some embodiments, one of G ! and G z and one of G J and G 4 are taken together with their intervening atoms to form an optionally substituted 3-10 membered ring having 0-3 heteroatoms. In some embodiments, a fonned ring 3 -membered. In some embodiments, a formed ring 4-membered. In some embodiments, a fonned ring 5 -membered. In some embodiments, a formed ring 6-membered. In some embodiments, a formed ring 7-membered. In some embodiments, a fomied ring is substituted. In some embodiments, a formed ring is unsubstituted. In some embodiments, a formed ring has no heteroatom. In some embodiments, a formed ring is saturated. For example compounds, see WV-CA-293 and WV-CA- 294.

[00975] In some embodiments, W z is -0-.

[00976] In some embodiments, a chiral reagent is a compound of Formula 3-AA:

H- i/¥ 1 W 2 -H

G‘ -- AG

G 3 G 2 1

Formula 3-AA

wherein each variable is independently as defined above and described herein.

[00977] In some embodiments of Formula 3AA, W 1 and W 2 are independently -NG 5 -, -0-, or -S-;

G 1 , G , G , G ' . and G 5 are independently hydrogen, or an optionally substituted group selected from alkyl, aralkyl, cycloalkyl, cycloaikylalkyl, heteroaliphatic, heterocyclyl, heteroaryl, or aryl; or two of G 1 , G 2 , G 3 , G 4 , and G J are G b (taken together to form an optionally substituted saturated, partially unsaturated or unsaturated carbocyclic or heteroatom-containing ring of up to about 20 ring atoms which is monocyclic or polycyclic, fused or unfused), and no more than four of G 1 , G 2 , G 3 , G 4 , and G s are G 6 . Similarly to the compounds of Formula 3-1, any of G 1 , G 2 , G 3 , G 4 , or G 5 are optionally substituted by oxo, thioxo, alkyl, alkenyl, alkynyl, heteroaryl, or aryl moieties. In some embodiments, such substitution induces stereoselectivity in chi rally controlled oligonucleotide production. In some embodiments, a heteroatom- containing moiety, e.g., heteroaliphatic, heterocyclyl, heteroaryl, etc., has 1-5 heteroatoms. In some embodiments, the heteroatoms are selected from nitrogen, oxygen, sulfure and silicon. In some embodiments, at least one heteroatom is nitrogen.

[00978] In some embodiments, W is -NG 5 -0-. In some embodiments, W 5 is -NG 5 -0-, wherein the -Q- is bonded to -H. In some embodiments. W 1 is -NG ' -. In some embodiments. G s and one of G 3 and G 4 are taken together to form an optionally substituted 3-10 membered ring having 0-3 heteroatoms in addition to the nitrogen atom of W 1 . In some embodiments, G 5 and G 3 are taken together to form an optionally substituted 3-10 membered ring having 0-3 heteroatoms in addition to the nitrogen atom of W 1 . In some embodiments, G 5 and G 4 are taken together to fonn an optionally substituted 3-10 membered ring having 0-3 heteroatoms in addition to the nitrogen atom of W . In some embodiments, a formed ring is an optionally substituted 4, 5, 6, 7, or 8 membered ring. In some embodiments, a formed ring is an optionally substituted 4-membered ring. In some embodiments, a fomied ring is an optionally substituted 5-membered ring. In some embodiments, a formed ring is an optionally substituted 6- membered ring. In some embodiments, a formed ring is an optionally substituted 7-membered ring. HO HN-G ®

G 2"l '"" G

[00979] In some embodiments, a provided chiral reagent has the structure of s ® . In

HO HN-G® some embodiments, a provided chiral reagent has the structure of . In some embodiments a

provided chiral reagent has the structure of In some embodiments, a provided chiral

reagent has the structure of . In some embodiments, a provided chiral reagent has the

In some embodiments, a provided chiral reagent has the structure of embodiments, a provided chiral reagent has the structure . In

some embodiments, a provided chiral reagent has the structure of ®

[00980] In some embodiments, W l is -NG\ W 2 is O, each of G 1 and G is independently hydrogen or an optionally substituted group selected from Ci -S o aliphatic, heterocydyl, heteroaryl and aryl, G 2 is -C(R) 2 Si(R) 3 , and G 4 and G ' are taken together to form an optionally substituted saturated, partially unsaturated or unsaturated heteroatom-containing ring of up to about 2.0 ring atoms which is monocyclic or polycyclic, fused or unfused. In some embodiments, each R is independently hydrogen, or an optionally substituted group selected from Cr-C 6 aliphatic, carbocyclyl, aryl, heteroaryl, and heterocydyl. In some embodiments, G 2 is -C(R) 2 Si(R) 3 , wherein -C(R) 2- is optionally substituted -CH 2 ~ , and each R of -Si(R) 3 is independently an optionally substituted group selected from Ci -iS aliphatic, heterocydyl, heteroaryl and aryl. In some embodiments, at least one R of -Si(R)3 is independently optionally substituted C MO alkyl. In some embodiments, at least one R of -Si(R) 3 is independently optionally substituted phenyl. In some embodiments, one R of -Si(R) 3 is independently optionally substituted phenyl, and each of the other two R is independently optionally substituted C J .J O alkyl. In some embodiments, one R of -Si(R) 3 is independently optionally substituted C O alkyl, and each of the other two R is independently optionally substituted phenyl. In some embodiments, G 2 is optionally substituted -CH 2 Si(Ph)(Me) 2 . In some embodiments, G is optionally substituted CH 2 Si(Me)(Ph) 2 . In some embodiments, G 2 is -CH 2 Si(Me)(Ph) 2 . hr some embodiments, G 4 and G 2 are taken together to form an optionally substituted saturated 5-6 membered ring containing one nitrogen atom (to which G is attached). In some embodiments, G and G are taken together to form an optionally substituted saturated 5-membered ring containing one nitrogen atom. In some embodiments, G 1 is hydrogen. In some embodiments, G 3 is hydrogen. In some embodiments, both G 1 and G 3 are hydrogen.

[00981] In some embodiments, W 1 is -NG\ W 2 is O, each of G 1 and G is independently R ! , G 2 is

-R 1 , and G 4 and G ' are taken together to form an optionally substituted saturated, partially unsaturated or unsaturated heteroatom-containing ring of up to about 20 ring atoms which is monocyclic or polycyclic, fused or unfused. In some embodiments, each of G 1 and Gri is independently R In some embodiments, each of G 1 and G J is independently -H. In some embodiments, G 2 is connected to the rest of the molecule through a carbon atom, and the carbon atom is substituted with one or more electron- withdrawing groups. In some embodiments, G 2 is methyl substituted with one or more electron- withdrawing groups. In some embodiments, G 2 is methyl substituted with one and no more than one electron-withdrawing group. In some embodiments, G 2 is methyl substituted with two or more electron- withdrawing groups. Among other things, a chiral auxiliary having G 2 comprising an electron- withdrawing group can be readily removed by a base (base-labile, e.g., under an anhydrous condition substantially free of water; in many instances, preferably before oligonucleotides comprising intemucleotidic linkages comprising such chiral auxiliaries are exposed to conditions/reagent systems comprising a substantial amount of water, particular in the presence of a base(e. ., cleavage conditions/reagent systems using NH4OH)) and provides various advantages as described herein, e.g., high crude purity, high yield, high stereoselectivity, more simplified operation, fewer steps, further reduced manufacture cost, and/or more simplified downstream formulation (e.g., low amount of salt(s) after cleavage), etc. In some embodiments, as described in the Examples, such auxiliaries may provide alternative or additional chemical compatibility with other functional and/or protection groups. In some embodiments, as demonstrated in the Examples, base-labile chiral auxiliaries are particularly useful for construction of chirally controlled non-negatively charged intemucleotidic linkages (e.g., neutral intemucleotidic linkages such as nOOl); in some instances, as demonstrated in the Examples, they can provide significantly improved yield and/or crude purity with high stereoselectivity, e.g, when utilized with removal using a base under an anhydrous condition. In some embodiments, such a chiral auxiliary' is bonded to a linkage phosphorus via an oxygen atom (e.g, which corresponds to a -OH group in a corresponding chiral auxiliary compound, e.g., a compound of formula I), the carbon atom in the chiral auxiliary' to which the oxygen is bonded (the alpha carbon) also bonds to -H (in addition to other groups; in some embodiments, a secondary carbon), and the next carbon atom (the beta carbon) in the chiral auxiliary is boned to one or two electron-withdrawing groups. In some embodiments, -W z -H is -OH. In some embodiments, G is -H. In some embodiments, G 2 comprises one or two electron-withdrawing groups or can otherwise facilitate remove of the chiral auxiliary by a base. In some embodiments, G 1 is -H, G comprises one or two electron-withdrawing groups, -W ~ H is -OH. In some embodiments, G 1 is -H, G 2 comprises one or two electron-withdrawing groups, -W 2~ H is -OH, -W l -H is NG 5 -H, and one of G 3 and G 4 is taken together with G 5 to form with their intervening atoms a ring as described herein (e.g., an optionally substituted 3-20 membered monocyclic, bicyclic or polycyclic ring having in addition to the nitrogen atom to which G 5 is on, 0-5 heteroatoms (e.g., an optionally substituted 3, 4, 5, or 6-membered monocyclic saturated ring having in addition to the nitrogen atom to which G 5 is on no other heteroatoms)).

[00982] As appreciated by those skilled in the art, various electron-withdrawing groups are known in the art and can he utilized in accordance with the present disclosure. In some embodiments, an electronic-withdrawing group comprises and/or is connected to the carbon atom through, e.g., -S(O)-, -S(0) 2- , -PiOXR 1 )-, -P(S)R -, or -C(O)-. In some embodiments, an electron-withdrawing group is -CN, NIK halogen, -C(0)R l , -C(0)OR\ t (O)X(R ) -S(0)R\ -S(0) 2 R ] , P<\Y)( R ' ) .- PiOXR ' ) ·. — P(0)(OR’) 2 , or -P(S)(R 1 ) 2 . In some embodiments, an electron-withdrawing group is and or heteroaryl, e.g., phenyl, substituted with one or more of -CN, -N0 2 , halogen, -C(0)R ] , -C(0)OR’, -C(0)N(R’) 2 ,

S(0)R'. SiOuRf FiWKR 1 } , ROH R 1 ) ·. -P(0)(0R ) 2 , or i > (S)(R i )

[00983] In some embodiments, G 2 is -L-R’. In some embodiments, G 2 is -L’-L’-R’, wherein

L’ is— C(R) 2— or optionally substituted -CH 2- , and L” is HOUR ) .. -P(0)(R’)0-, -P(0)(OR’)-, -P(0)(0R )0-, -P(0)[N(R’)]- -P(0)[N(R’)]0-, -P(0)[N(R’)][N(R’)]-, -P(S)(R’)-, S(O). .

SiO) . . S{0 ; () . -S(O)-, (·(()) . -C(0)N(R’)-, or S . In some embodiments, L’ is ( (R) . In some embodiments, L’ is optionally substituted -CH 2- .

[00984] In some embodiments, L’ is -C(R) 2- . In some embodiments, each R is independently hydrogen, or an optionally substituted group selected from Ci-C 6 aliphatic, carbocycly!, and, heteroaryl, and heterocyclyl. In some embodiments, 1/ is -CH 2- . In some embodiments, L” is -P(0)(R’)-, -P(S)(R’)-,— S(0) 2— . In some embodiments, G 2 is -L’-C(0)N(R’) 2 . In some embodiments, G z is — L’— P(0)(R’) 2 . In some embodiments, G" is -L’-P(S)(R’) 2 . In some embodiments, each R’ is independently optionally substituted aliphatic, heteroaliphatic, aryd, or heteroaryd as described in the present disclosure (e.g., those embodiments described for R). In some embodiments, each R’ is independently optionally substituted phenyl. In some embodiments, each R is independently optionally substituted phenyl wherein one or more substituents are independently selected from -CN, -OMe, -Cl, -Br, and -F. hi some embodiments, each R’ is independently substituted phenyl wherein one or more substituents are independently selected from -CN, -OMe, -Cl, -Br, and -F. In some embodiments, each R’ is independently substituted phenyl wherein the substituents are independently selected from -CN, -OMe, -Cl, -Br, and -F. In some embodiments, each R’ is independently mono-substituted phenyl, wherein the substituent is independently selected from -CN, -OMe, -Cl, -Br, and -F. In some embodiments, two R’ are the same. In some embodiments, two R’ are different. In some embodiments, G z is -L’-S(0)R’. In some embodiments, G 2 is -L’-C(0)N(R’) 2 . In some embodiments, G z is -L’-S(0) 2 R’. In some embodiments, R’ is optionally substituted aliphatic, heteroaliphatic, aryl, or heteroaryl as described in the present disclosure (e.g., those embodiments described for R). In some embodiments, R’ is optionally substituted phenyl. In some embodiments, R’ is optionally substituted phenyl wherein one or more substituents are independently selected from -CN, -OMe, -Cl, -Br, and -F. In some embodiments, R’ is substituted phenyl wherein one or more substituents are independently selected from -CN, -OMe, -Cl, -Br, and -F. In some embodiments, R’ is substituted phenyl wherein each substituent is independently selected from -CN, -OMe, -Cl, -Br, and -F. In some embodiments, R’ is mono-substituted phenyl. In some embodiments, R’ is mono-substituted phenyl, wherein the substituent is independently selected from -CN, -OMe, -Cl, -Br, and -F In some embodiments, a substituent is an electron -withdrawing group. In some embodiments, an electron -withdrawing group is -CN, -NO2, halogen,

-P(0)(OR’) 2 , or -P(S

100985] In some embodiments, G is optionally substituted Ci b 1. R. wherein each of L” and

R is independently as described in the present disclosure. In some embodiments, G 2 is optionally- substituted -CH(-L ’-R) 2 , wherein each of L” and R is independently as described in the present disclosure. In some embodiments, G 2 is optionally^ substituted -CH(-S-R) 2 . In some embodiments, G 2 is optionally substituted -CH 2- S-R. In some embodiments, the two R groups are taken together with their intervening atoms to form a ring. In some embodiments, a fomied ring is an optionally substituted 5, 6, 7-membered ring having 0-2 heteroatoms m addition to the intervening heteroatoms. In some embodiments, G 2 is optionally substituted In some embodiments, G 2 is . In some embodiments, -S- may be converted to -S(O)- or -S(0) 2 -, e.g., by oxidation, e.g.. to facilitate removal by a base.

[00986] In some embodiments, G 2 is I . R . wherein each variable is as described in the present disclosure. In some embodiments, G 2 is CH 2 R’. hi some embodiments, G z is -CH(R’) 2. In some embodiments, G is -C(R’) 3 . In some embodiments, R’ is optionally substituted aryl or heteroaryl. In some embodiments, R" is substituted aryl or heteroaryl wherein one or more substituents are independently an electron-withdrawing group. In some embodiments, -L’- is optionally substituted CH 2 , and R’ is R, wherein R is optionally substituted aryl or heteroaryl. In some embodiments, R is substituted aryl or heteroaryl wherein one or more substituents are independently an electron -withdrawing group. In some embodiments, R is substituted aryl or heteroaryl wherein each substituent is independently an electron-withdrawing group. In some embodiments, R is aryl or heteroaryl substituted with two or more substituents, wherein each substituent is independently an electron-withdrawing group. In some embodiments, an electron-withdrawing group is -CN, -N0 2 , halogen, -C(0)R‘, -C(0)0R\ -C(0)N(R’) 2 , WXR'R, -P(0)(R 1 ) 2 , -P(0)(OR’) 2 , or -P(S)(R 1 ) 2 . In some

embodiments some embodiments, R’ is o-NO ? Ph-. In some embodiments, R’ some embodiments. R’ is . In some embodiments. R’ is

. In some embodiments. R’ is In some embodiments, R’ some embodiments, CR is . In some embodiments R’ is . In some embodiments, R' is . In some embodiments, R’ is

2 4,6-trichlorophenyl. In some embodiments R’ is 2,4,6-triiluorophenyl. In some embodiments, G 2 is

-CH(4-chlorophenyl) 2 . In some embodiments, wherein each R’ is

In some embodiments, G 2 is --CH(R’) 2 , wherein each R’ is In some embodiments.

R’ is -C(0)R. In some embodiments, R is CH 3 C(0)-.

[00987] In some embodiments, G 2 is -L’-S(0) 2 R’, wherein each variable is as described in the present disclosure. In some embodiments, G 2 is -CH 2- S(0) 2 R’. In some embodiments, G 2 is -L’-S(0)R’, wherein each variable is as described in the present disclosure. In some embodiments, G is -CH 2- S(0)R’. In some embodiments, G 2 is -L’-C(0) 2 Ry wherein each variable is as described in the present disclosure. In some embodiments, G is -CH 2- C(0) 2 R’ . In some embodiments, G 2 is -L’-C(0)R’, wherein each variable is as described in the present disclosure. In some embodiments, G 2 is -CH 2- C(0)R’. In some embodiments, L’ is optionally substituted -CH 2- , and R" is R. In some embodiments, R is optionally substituted aryl or heteroaryl. In some embodiments, R is optionally substituted aliphatic. In some embodiments, R is optionally substituted heteroaliphatic. In some embodiments, R is optionally substituted heteroaryl. In some embodiments, R is optionally substituted aryl. In some embodiments, R is optionally substituted phenyl. In some embodiments, R is not phenyl, or mono-, di- or tri-substituted phenyl, wherein each substituent is selected from -N0 2 , halogen, -CN, C i -3 alkyl, and C :i-3 alkyloxy. In some embodiments, R is substituted aiyl or heteroaryl wherein one or more substituents are independently an electron-withdrawing group. In some embodiments, R is substituted aryl or heteroaryl wherein each substituent is independently an electron-withdrawing group. In some embodiments, R is aryl or heteroaryl substituted with two or more substituents, wherein each substituent is independently an electron-withdrawing group. In some embodiments, an electron- withdrawing group is -CN, -N0 2 , halogen, -C(0)R 1 , -C(0)OR’, -C(Q)N(R’) 2 , -S(Q)R l , 8(0 ! -R 1 . -P(W)(R 1 ) 2 ,— P(0)(R‘) 2 ,— P(0)(OR , ) 2 , or -P(S)(R 1 ) 2 . In some embodiments, R’ is phenyl. In some

NC— V - embodiments, R’ is substituted phenyl. In some embodiments, R’ is Cl In some embodiments, R’ is . In some embodiments, R’ is . In some embodiments, R’ is optionally substituted C j-6 aliphatic. In some embodiments, R is t-butyl. hi some embodiments, R’ is isopropyl. In some embodiments, R’ is methyl. In some embodiments, G 2 is -CH 2 C(0)0Me. In some embodiments, G is -CH 2 C(0)Ph. In some embodiments, G 2 is -CH 2 C(0)- tBu.

[00988] In some embodiments, G 2 is -L’-N0 2. In some embodiments, G 2 is -CH 2- N0 2 . In some embodiments, G 2 is --L , --S(Q) 2 N(R , ) 2 . In some embodiments, G 2 is -CH 2 -S(0) 2 N(R’) 2 . In some embodiments, G is -L’-S(0) 2 NHR\ In some embodiments, G 2 is -CH 2- S(0) 2 NHR\ In some embodiments, R’ is methyl. In some embodiments, G 2 is -CH 2- S(0) 2 NH(CH 3 ). In some embodiments, R’ is CH 2 Ph. In some embodiments, G 2 is ~CH 2~ S(0) 2 NH(CH 2 Ph) . In some embodiments, G 2 is -CH 2 -S(0) 2 N(CH 2 Ph) 2 . In some embodiments, R’ is phenyl. In some embodiments, G 2 is -CH 2- S(0) 2 NHPh. In some embodiments, G 2 is -CH 2- S(0) 2 N(CH 3 )Ph. In some embodiments, G 2 is -CH 2- S(0) 2 N(CH 3 ) 2 . In some embodiments, G 2 is -CH 2- S(0) 2 NH(CH 2 Ph). In some embodiments, G" is -CH 2- S(0) 2 NHPh. In some embodiments, G 2 is -CH 2- S(0) 2 NH(CH 2 Ph). In some embodiments, G 2 is -CH 2 -S(0) 2 N(CH 3 ) 2 . hi some embodiments, G 2 is ~CH 2 -~S(0) 2 N(CH )Ph. hi some embodiments, G 2 is— L’— S(0) 2 N(R’)(OR’). In some embodiments, G 2 is -CH 2- S(0) 2 N(R’)(0R’). In some embodiments, each R’ is methyl. In some embodiments, G 2 is -CH 2- S(0) 2 N(CH 3 )(0CH 3 ). In some embodiments, G 2 is -CH 2- S(0) 2 N(Ph)(0CH 3 ). In some embodiments, G 2 is -CH 2- S(0) 2 N(CH 2 Ph)(0CH 3 ). In some embodiments, G z is -CH 2- S(0) 2 N(CH 2 Ph)(0CH 3 ). In some embodiments, G 2 is ~-L’--S(0) 2 OR\ In some embodiments, G 2 is -CH 2- S(0) 2 0R\ In some embodiments, G 2 is -CH 2- S(0) 2 0Ph. In some embodiments, G 2 is -CH 2- S(0) 2 0CH 3 . in some embodiments, G z is ---CH 2--- S(0) 2 0CH 2 Ph.

[00989] In some embodiments, G z is -L’-P(0)(R’) 2 . In some embodiments, G 2 is

-CH 2 -P(0)(R’) 2 . In some embodiments, G 2 is -L , -P(0)[N(R , ) 2 ] 2 . In some embodiments, G is -CH 2- P(0)[N(R’) 2 ] 2. In some embodiments, G 2 is L’-P(0)j0(R’) 2j2 . In some embodiments, G 2 is -CH 2- P(0)[0(R’) 2 ] 2 . In some embodiments, G 2 is -L’-P(0)(R , )[N(R’) 2 ] 2 . In some embodiments, G 2 is -CH 2- P(0)(R , )[N(R’) 2 ]. In some embodiments, G is 1. P(0)( R )|0(R )i. In some embodiments, G 2 is -€H 2- R(0)^ , )[0(R’)]. In some embodiments, G 2 is -L -P(0)(OR’)[N(R , ) 2 ]. hi some embodiments, G 2 is -CH 2- P(0)(0R’)[N(R , ) 2 ]. In some embodiments, G 2 is -L’--C(0)N(R’) 2 , wherein each variable is as described in the present disclosure. In some embodiments, G 2 is CH 2- C(0)N(R’) 2, In some embodiments, each R’ is independently R. In some embodiments, one R’ is optionally substituted aliphatic, and one R is optionally substituted aryl. In some embodiments, one R’ is optionally substituted C s 6 aliphatic, and one R is optionally substituted phenyl. In some embodiments, each R’ is independently optionally substituted C !-6 aliphatic. In some embodiments, G 2 is -CH 2- P(0)(CH 3 )Ph. In some embodiments, G 2 is -CH 2- P(0)(CH 3 ) 2 . In some embodiments, G 2 is -CH 2- P(0)(Ph) 2 . In some embodiments, G z is -CH 2- P(0)(0CH 3 ) 2 . In some embodiments, G z is -CH 2- P(0)(CH 2 Ph) 2 . In some embodiments, G z is -CH 2- P(0)[N(CH 3 )Ph] 2 . In some embodiments, G 2 is -CH 2- P(0)[N(CH 3 ) 2 ] 2 . In some embodiments, G 2 is -CH 2- P(0)[N(CH 2 Ph) 2 ] 2. In some embodiments, G 2 is -CH 2- P(0)(0CH 3 ) 2 . In some embodiments, G 2 is -CH 2- P(0)(0Ph) 2 .

[00990] In some embodiments, G 2 is -L’-SR’. In some embodiments, G 2 is -CH 2 -SR\ In some embodiments, R’ is optionally substituted phenyl. In some embodiments, R’ is phenyl.

In some embodiments, a provided chiral reagent has the structure

wherein each R 1 is independently as described in the present disclosure. In some embodiments, a

provided chiral reagent has the structure , wherein each R 1 is independently as described in the present disclosure. In some embodiments, each R 1 is independently R as described in the present disclosure. In some embodiments, each R is independently R, wherein R is optionally substituted aliphatic, aryl, heteroaliphatic, or heteroaryl as described in the present disclosure. In some embodiments, each R 1 is phenyl. In some embodiments, R 1 is -L-R\ In some embodiments, R 1 is -L-R’, wherein L is In some embodiments, a provided chiral reagent has the structure of

, wherein each

-CM, -OR, -Cl, -Br, or --F, and W is O or S. In some embodiments, a provided chiral reagent has the

structure wherein each X 1 is independently -H, an electron-withdrawing group,— N0 2 , CN, -OR, -Cl, -Br, or -F, and W is O or S. In some embodiments, each X 1 is independently -CN, -OR, -Cl, -Br, or -F, wherein R is not -H. In some embodiments, R is optionally substituted C L-6 aliphatic. In some embodiments, R is optionally substituted C - 6 alkyl. In some embodiments, R is -CH 3. In some embodiments, one or more X s are independently electron-withdrawing groups (e.g, -CN, -N0 2 , halogen, -C(0)R l , -C(0)0R\ -C(0)N(R’) ¾ - S(0)R\ -S(0) 2 R ] , ~ ¥(W)(R 1 ) 2 , -PtOXR 1 ^, -P(0)(0R’) 2 , -P(S)(R 5 ) 2 , etc ).

In some embodiments, a provided chiral reagent has the structure

wherein R 1 is as described in the present disclosure. In some embodiments, a provided chiral reagent has

the structure wherein R 1 is as described in the present disclosure. In some embodiments, R 1 is R as described in the present disclosure. In some embodiments, R 1 is R, wherein R is optionally substituted aliphatic, aryl, heteroaliphatic, or heteroaryl as described in the present disclosure. In some embodiments, R 1 is -L-R’. In some embodiments, R 1 is -L-R’, wherein L is -S-. or

-N(R’). In some embodiments, a provided chiral reagent has the structure

wherein X is -H, an electron-withdrawing group, ~ N0 2 , -CN, -OR, -Cl, -Br, or -F, and W is O or S. In some embodiments, a provided chiral reagent has the structure wherein

X 1 is -H, an electron-withdrawing group, -N0 2 , -CN, -OR, -Cl, -Br, or -F, and W is O or S. In some embodiments, X 1 is -CN, -OR, -Cl, -Br, or -F, wherein R is not -H. In some embodiments, R is optionally substituted C j-6 aliphatic. In some embodiments, R is optionally substituted C ]-6 alkyl. In some embodiments, R is ~ CH 3 . In some embodiments, X 1 is an electron-withdrawing group (e.g., -CN, -N0 2 , halogen, -C(0)R\ -C(0)0R\ -C(0)N(R’) 2 , -S(0)R\ ~ S(Q) 2 R s , -PfWXR^, -P(O)(R S ) 2 , -P(0)(OR’) 2 ,-P(S)(R 1 ) 2 , etc.). In some embodiments, X 1 is an electron-withdrawing group that is not -CN, -N0 2 , or halogen. In some embodiments, X 1 is not -H, -CN, -N0 2 , halogen, or (C 3 alkyloxy.

[00993] In some embodiments, G 2 is -CH(R 2i )-CH(R 22 )=C(R 23 )(R 4 ), wherein each of R 21 , R 22 ,

R 2 ’, and R 24 is independently R. In some embodiments, R 2 and R 3 are both R, and the two R groups are taken together with their intervening atoms to fonn an optionally substituted aryl or heteroarl ring as described herein. In some embodiments, one or more substituents are independently electron- withdrawing groups. In some embodiments, R 21 and R 24 are both R, and the two R groups are taken together with their intervening atoms to fonn an optionally substituted ring as described herein. In some embodiments, R 21 and R 24 are both R, and the two R groups are taken together with their intervening atoms to fonn an optionally substituted saturated or partially saturated ring as described herein. In some embodiments, R 22 and R z3 are both R, and the two R groups are taken together with their intervening atoms to form an optionally substituted aryl or heteroaryl ring as described herein, and R l and R 24 are both R, and the two R groups are taken together with their intervening atoms to form an optionally substituted partially saturated ring as described herein. In some embodiments, R zl is -H. In some embodiments, R z4 is -H. In some embodiments, G 2 is optionally substituted In some

embodiments, G 2 is optionally substituted , wherein each Ring

A 2 is independently a 3-15 membered monocyclic, bicyclic or polycyclic ring as described herein. In some embodiments, Ring A 2 is an optionally substituted 5-10 membered monocyclic aryl or heteroaryl ring having 1-5 heteroatoms as described herein. In some embodiments, Ring A is an optionally- substituted phenyl ring as described herein in some embodiments, In some embodiments, G 2 is optionally substituted . In some embodiments, In some

embodiments, ,

100994] Certain useful example compounds for chiral auxiliaries are presented in, e.g.. Tables

CA-1 to CA-13. In some embodiments, a useful compound is an enantiomer of a compound in, e.g.. Tables CA-1 to CA-13. In some embodiments, a useful compound is a diastereomer of a compound in, e.g.. Tables CA-1 to CA-13. In some embodiments, a compound useful for chiral auxiliaries for removal under basic conditions (e.g., by a base under an anhydrous condition) is a compound of Tables CA-1 to CA-13, or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-1 or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-2 or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-3 or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-4 or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-5 or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-6 or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-7 or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-8 or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of " fable CA-9 or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-10 or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-l l or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-12 or an enantiomer or a diastereomer thereof. In some embodiments, such a compound is a compound of Table CA-13 or an enantiomer or a diastereomer thereof.

100995] In some embodiments, when contacted with a base, a chiral auxiliary' moiety, e.g., of an internucleotidic linkage, whose corresponding compound is a compound of Formula 3-1 or 3-AA may be released as an aikene, which has the same structure as a product fonned by elimination of a water molecule from the corresponding compound (elimination of -W 2 -H = -OH and an alpha-H of G 2 ). In some embodiments, such an aikene has the structure of (electron-withdrawing group) 2 =C(R 1 )-L-N(R 5 )(R°), (electron-withdrawing group)H=C(R 1 )-L-N(R 5 )(R 6 ),

CH(--L”--R’)===C(R i )---L-N(R 5 )(R 0 ) wherein the CH group is optionally substituted, or C X =C(R 1 ) L N(R 5 )(R°), wherein C x is optionally substituted , and may be optionally fused with one or more optionally substituted rings, and each other variable is independently as described herein. In

some embodiments, C x is optionally substituted In some embodiments. C x is . In some embodiments, such an alkene is . In some

, , . , „ .

embodiments, such an alkene is In some embodiments such an alkene is

100996] In some embodiments, a chiral reagent is an aminoalcohol. In some embodiments, a chtral reagent is an aminothiol. In some embodiments, a chiral reagent is an aminophenol. In some embodiments, a chiral reagent is (S)- and (A)~2-methylamino-l-phenylethanoi, (!R, 25)-ephedrine, or (12?, 25)-2-methyl amino- 1 ,2 -diphenylethanol .

00997] In some embodiments of the disclosure, a chiral reagent is a compound of one of the following formulae:

Formula 0 Formula P Formula Q Formula R

DPSE.

[00998] In some embodiments, a useful chiral reagent is a compound selected from the compounds below, or its related stereoisomer, particularly enantiomer (e.g., WV-CA-237 is a related stereoisomer of WV-CA-236 (a related diastereomer, having the same constitution, the same configuration at one chiral center but not the other); WV-CA-108 is a related enantiomer of WV-CA-236 (mirror image of each other));

Table CA-l . Example chiral auxiliaries.

[00999] In some embodiments, a provided compound is an enantiomer of a compound selected from Table CA-1 or a salt thereof. In some embodiments, a provided compound is a diastereomer of a compound selected from Table CA-1 or a salt thereof.

[001000] In some embodiments, a useful chiral reagent is a compound selected from the compounds below, or its related stereoisomer, particularly enantiomer:

Table CA-2. Example chiral auxiliaries.

[001001] In some embodiments, a provided compound is an enantiomer of a compound selected from Table CA-2 or a salt thereof. In some embodiments, a provided compound is a diastereomer of a compound selected from Table CA-2 or a salt thereof.

[001002] In some embodiments, a useful chiral reagent is a compound selected from the compounds below, or its related stereoisomer, particularly enantiomer:

Table CA-3. Example chiral auxiliaries.

[001003] In some embodiments, a provided compound is an enantiomer of a compound selected from Table CA-3 or a salt thereof. In some embodiments, a provided compound is a diastereomer of a compound selected from Table CA-3 or a salt thereof

[001004] In some embodiments, a useful chiral reagent is a compound selected from the compounds below, or its related stereoisomer, particularly enantiomer:

Table CA-4. Example chiral auxiliaries.

[001005] In some embodiments, a provided compound is an enantiomer of a compound selected from Table CA-4 or a salt thereof. In some embodiments, a provided compound is a diastereomer of a compound selected from Table CA-4 or a salt thereof.

[001006] In some embodiments, a useful chiral reagent is a compound selected from the compounds below, or its related stereoisomer, particularly enantiomer:

Table CA-5. Example chiral auxiliaries.

[001007] In some embodiments, a provided compound is an enantiomer of a compound selected from Table CA-5 or a salt thereof. In some embodiments, a provided compound is a diastereomer of a compound selected from Table CA-5 or a salt thereof

[001008] In some embodiments, a useful chiral reagent is a compound selected from the compounds below, or its related stereoisomer, particularly enantiomer:

Table CA-6. Example chiral auxiliaries.

[001009] In some embodiments, a provided compound is an enantiomer of a compound selected from Table CA-6 or a salt thereof. In some embodiments, a provided compound is a diastereomer of a compound selected from Table CA-6 or a salt thereof

[001010] In some embodiments, a useful chiral reagent is a compound selected from the compounds below, or its related stereoisomer, particularly enantiomer:

Table CA-7. Example chiral auxiliaries.

[001011] In some embodiments, a provided compound is an enantiomer of a compound selected from Table CA-7 or a salt thereof. In some embodiments, a provided compound is a diastereomer of a compound selected from Table CA-7 or a salt thereof.

[001012] In some embodiments, a useful chiral reagent is a compound selected from the compounds below, or its related stereoisomer, particularly enantiomer:

Table CA-8 Example chiral auxiliaries.

[001017] In some embodiments, a provided compound is an enantiomer of a compound selected from Table CA-!O or a salt thereof. In some embodiments, a provided compound is a diastereomer of a compound selected from Table CA-10 or a salt thereof.

[001018] In some embodiments, a useful chiral reagent is a compound selected from the compounds below, or its related stereoisomer, particularly enantiomer:

Table CA-1 1. Example chiral auxiliaries.

[001019] In some embodiments, a provided compound is an enantiomer of a compound selected from Table CA-11 or a salt thereof. In some embodiments, a provided compound is a diastereomer of a compound selected from Table CA-11 or a salt thereof.

[001020] In some embodiments, a useful chiral reagent is a compound selected from the compounds below, or its related stereoisomer, particularly enantiomer:

Table CA-12. Example chiral auxiliaries.

[001021] In some embodiments, a provided compound is an enantiomer of a compound selected from Table CA-12 or a salt thereof. In some embodiments, a pro vided compound is a diastereomer of a compound selected from Table CA-12 or a salt thereof.

[001022] In some embodiments, a useful chiral reagent is a compound selected from the compounds below, or its related stereoisomer, particularly enantiomer:

Table CA-13. Example chiral auxiliaries.

[001023] In some embodiments, a provided compound is an enantiomer of a compound selected from Table CA-13 or a salt thereof. In some embodiments, a pro vided compound is a diastereomer of a compound selected from Table CA-13 or a salt thereof.

[001024] As appreciated by those skilled in the art, chiral reagents are typically stereopure or substantially stereopure, and are typically utilized as a single stereoisomer substantially free of other stereoisomers. In some embodiments, compounds of the present disclosure are stereopure or substantially stereopure.

[001025] As demonstrated herein, when used for preparing a chiral intemucleotidic linkage, to obtain stereoselectivity generally stereochemically pure chiral reagents are utilized. Among other things, the present disclosure provides stereochemically pure chiral reagents, including those having structures described.

[001026] The choice of chiral reagent, for example, the isomer represented by Formula Q or its stereoisomer, Formula R, permits specific control of chirality at a linkage phosphorus. Thus, either an Rp or ,Sp configuration can be selected in each synthetic cycle, permitting control of the overall three dimensional structure of a chirally controlled oligonucleotide. In some embodiments, a chirally controlled oligonucleotide has all Rp stereocenters. In some embodiments of the disclosure, a chirally controlled oligonucleotide has all Sp stereocenters. In some embodiments of the disclosure, each linkage phosphorus in the chirally controlled oligonucleotide is independently Rp or Sp. in some embodiments of the disclosure, each linkage phosphorus in the chirally controlled oligonucleotide is independently Rp or Sp, and at least one is Rp and at least one is Sjp. In some embodiments, the selection of Rp and Sp centers is made to confer a specific three dimensional superstructure to a chirally controlled oligonucleotide. Examples of such selections are described in further detail herein.

[001027] In some embodiments, a provided oligonucleotide comprise a chiral auxiliary moiety, e.g., in an internucleoiidic linkage. In some embodiments, a chiral auxiliary is connected to a linkage phosphorus. In some embodiments, a chiral auxiliary is connected to a linkage phosphorus through W 2 . In some embodiments, a chiral auxiliary is connected to a linkage phosphorus through W 2 , wherein W 2 is O Optionally, W 5 , e.g., when W 1 is -NG 5 -, is capped during oligonucleotide synthesis. In some embodiments, W 1 in a chiral auxiliary in an oligonucleotide is capped, e.g., by a capping reagent during oligonucleotide synthesis. In some embodiments, W 1 may be purposeful capped to modulate oligonucleotide property. In some embodiments, W 1 is capped with -R l . In some embodiments, R 1 is -C(0)R’. In some embodiments, R’ is optionally substituted C w aliphatic. In some embodiments, R’ is methyl.

[001028] In some embodiments, a chiral reagent for use in accordance with the present disclosure is selected for its ability to be removed at a particular step in the above-depicted cycle. For example, in some embodiments it is desirable to remove a chiral reagent during the step of modifying the linkage phosphorus. In some embodiments, it is desirable to remove a chiral reagent before the step of modifying the linkage phosphorus. In some embodiments, it is desirable to remove a chiral reagent after the step of modifying the linkage phosphorus. In some embodiments, it is desirable to remove a chiral reagent after a first coupling step has occurred hut before a second coupling step has occurred, such that a chiral reagent is not present on the growing oligonucleotide during the second coupling (and likewise for additional subsequent coupling steps). In some embodiments, a chiral reagent is removed during the‘deblock” reaction that occurs after modification of the linkage phosphorus but before a subsequent cycle begins. Example methods and reagents for removal are described herein.

[001029] In some embodiments, removal of chiral auxiliary is achieved when performing the modification and/or deblocking step, as illustrated in Scheme I. It can be beneficial to combine chiral auxiliary removal together with other transformations, such as modification and deblocking. A person of ordinary skill in the art would appreciate that the saved steps/transformation could improve the overall efficiency of synthesis, for instance, with respect to yield and product purity, especially for longer oligonucleotides. One example wherein the chiral auxiliary is removed during modification and/or deblocking is illustrated m Scheme I.

[001030] In some embodiments, a chiral reagent for use in accordance with methods of the present disclosure is characterized in that it is removable under certain conditions. For instance, in some embodiments, a chiral reagent is selected for its ability to be removed under acidic conditions. In certain embodiments, a chiral reagent is selected for its ability to be removed under mildly acidic conditions. In certain embodiments, a chiral reagent is selected for its ability' to be removed by way of an El elimination reaction (e.g., removal occurs due to the formation of a cation intermediate on the chiral reagent under acidic conditions, causing the chiral reagent to cleave from the oligonucleotide). In some embodiments, a chirai reagent is characterized in that it has a structure recognized as being able to accommodate or facilitate an El elimination reaction. One of skill in the relevant arts will appreciate which structures would be envisaged as being prone toward undergoing such elimination reactions.

|001031] In some embodiments, a chiral reagent is selected for its ability to be removed with a nucleophile. In some embodiments, a chiral reagent is selected for its ability to be removed with an amine nucleophile. In some embodiments, a chiral reagent is selected for its ability to be removed with a nucleophile other than an amine.

[001032] In some embodiments, a chiral reagent is selected for its ability to be removed with a base. In some embodiments, a chiral reagent is selected for its ability to be removed with an amine. In some embodiments, a chiral reagent is selected for its ability to be removed with a base other than an amine.

[001033] In some embodiments, chirally pure phosphoramidites comprising chiral auxiliaries may be isolated before use. In some embodiments, chirally pure phosphoramidites comprising chiral auxiliaries may be used without isolation - some embodiments, they may be used directly after formation.

Activation

[001034] As appreciated by those skilled in the art, oligonucleotide preparation may use various conditions, reagents, etc. to active a reaction component, e.g., during phosphoramidite preparation, during one or more steps during in the cycles, during post-cycle cleavage/deprotection, etc. Various technologies for activation can be utilized in accordance with the present disclosure, including but not limited to those described in US 9695211, US 9605019, US 9598458, US 2013/0178612, US 20150211006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, WO 2017/210647, WO 2018/223056, WO 2018/237194, and/or WO 2019/05595 !, the activation technologies of each of which are incorporated by reference. Certain activation technologies, e.g., reagents, conditions, methods, etc. are illustrated in the Examples.

Coupling

|001035] In some embodiments, cycles of the present disclosure comprise stereoselective condensation/coupling steps to form chirally controlled intemucleotidic linkages. For condensation, often an activating reagent is used, such as 4,5-dicyanoimidazole (DCI), 4,5-dichloroimidazole, 1- phenylimidazolium Inflate (PhIMT), benzimidazolium triflate (BIT), benztriazole, 3 -nitro-1, 2, 4-triazole (NT), tetrazole, 5-ethylthiotetrazole (ETT), 5-benzylthiotetrazole (BTT), 5-(4-nitropheny])tetrazole, N- cyanornethylpyrrolidinium triflate (CMPT), V-cyanomethylpiperidinium triflate, N- cyanomethyldimethylammonium inflate, etc. Suitable conditions and reagents, including chiral phosphoramidites, include those described in US 9695211, US 9605019, US 9598458, US 2013/0178612, US 20150211006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, WO 2017/210647, WO 2018/223056, WO 2018/237194, and/or WO 2019/055951, the condensation reagents, conditions and methods of each of which are incorporated by reference. Certain coupling technologies, e.g., reagents, conditions, methods, etc. are illustrated in the Examples.

[001036] In some embodiments, a phosphoramidite for coupling has the structure of

, wherein each variable is independently as described in the present disclosure. In some embodiments, each R is independently optionally substituted C 6 aliphatic. A person skill in the art will appreciate that two R groups in any structure or formula can either be the same or different. In some embodiments, each R is independently optionally substituted Ci -6 alkyl. In some embodiments, each R is independently optionally substituted C - 6 alkenyl. In some embodiments, each R is independently optionally substituted C.- 6 alkynyl. In some embodiments, each R is indenpendtly isopropyl. In some embodiments, -X-L-R 1 comprises an optionally substituted triazole group. In some embodiments, X is a covalent bond. In some embodiments, L is a covalent bond. In some embodiments, -X-L-R 1 is R 1 . In some embodiments, R 1 comprise an optionally substituted ring. In some embodiments, R 1 is R as described herein. In some embodiments, R 1 is optionally substituted

HN In some embodiments, R 1 is In some embodiments. R 1 is .In some

embodiments, R 1 In some embodiments, -L- comprises Ci_ 6 alkylene. In some embodiments, -L- comprises C ]-6 alkenylene. In some embodiments, -L- comprises . In some embodiments, R 1 is R as described herein. In some embodiments, -L- is and R 1 is

H. In some embodiments, -L-R 1 is . In some embodiments, -X-L-R 1 . In some embodiments, -X-L-R 1 is -OCH 2 CH 2 CN.

001037] In some embodiments, a chiral phosphoramidite for coupling has the structure of

, wherein each variable is independently as described in the present disclosure. In some embodiments, chiral phosphoramidite for coupling has the structure

In some embodiments, a chiral

phosphoramidite for coupling has the structure of

wherein each variable is independently as described in the present disclosure. In some embodiments, G ! or G 2 comprises an electron -withdrawing group as described in the present disclosure. In some embodiments, a chiral phosphoramidite for

coupling has the structure

wherein each variable is independently as described in the present disclosure. In some embodiments, R ! is R as described in the present disclosure. In some embodiments, R 1 is R as described in the present disclosure. In some embodiments, R is optionally substituted phenyl as described in tire present disclosure. In some embodiments, R is phenyl. In some embodiments, R is 4-methyl phenyl. In some embodiments, R is 4-methoxy phenyl. In some embodiments, R is optionally substituted C._ 6 aliphatic as described in the present disclosure. In some embodiments, R is optionally substituted C._ 6 alkyl as described in the present disclosure. For example, in some embodiments, R is methyl; in some embodiments, R is isopropyl; in some embodiments, R is t-butyl; etc.

[001038] In some embodiments, R I. is R’O-. In some embodiments, R O is DMTrQ-. In some embodiments, R 4s is -H. In some embodiments, R 4s and R" are taken together to form a bridge -L-O- as described in the present disclosure. In some embodiments, the -O- is connected to the carbon at the 2’ position. In some embodiments, L is -CH 2 -. In some embodiments, L is -CH(Me)-. In some embodiments, L is -(R)-CH(Me)-. In some embodiments, L is (,$) ~ CH(Me)-. In some embodiments, R ¾ is -H. In some embodiments, R zs is -F. In some embodiments, R 2s is --OR’. In some embodiments, R ¾ is -OMe. In some embodiments, R ¾ is -MOE. As appreciated by those skilled in the art, BA may be suitably protected during synthesis.

[001039] In some embodiments, an internucleotidic linkage formed in a coupling step has the structure of formula I or a salt form thereof. In some embodiments, P L is P. In some embodiments,

wherein each variable is independently in accordance with the present disclosure. In some embodiments, X I . R 1 is

Cl 1 ( 1 i c\

[001040] In some embodiments, a coupling forms an intemucleotidic linkage with a stereoselectivity of 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more. In some embodiments, the stereoselectivity is 85% or more. In some embodiments, the stereoselectivity is 85% or more. In some embodiments, the stereoselectivity is 90% or more in some embodiments, the stereoselectivity is 91% or more. In some embodiments, the stereoselectivity is 92% or more. In some embodiments, the stereoselectivity is 93% or more. In some embodiments, the stereoselectivity is 94% or more. In some embodiments, the stereoselectivity is 95% or more. In some embodiments, the stereoselectivity is 96% or more. In some embodiments, the stereoselectivity is 97% or more. In some embodiments, the stereoselectivity is 98% or more. In some embodiments, the stereoselectivity is 99% or more.

Capping

[001041] If the final nucleic acid is larger than a dimer, the unreacted -OH moiety is generally capped with a blocking/capping group. Chiral auxiliaries in oligonucleotides may also be capped with a blocking group to form a capped condensed intermediate. Suitable capping technologies (e.g., reagents, conditions, etc.) include those described in US 9695211, US 9605019, US 9598458, US 2013/0178612, US 20150211006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, WO 2017/210647, WC) 2018/223056, WO 2018/237194, and/or WO 2019/055951, the capping technologies of each of which are incorporated by reference. In some embodiments, a capping reagent is a carboxylic acid or a derivate thereof. In some embodiments, a capping reagent is R COOH. In some embodiments, a capping step introduces R COO- to unreacted S’- OH group and/or amino groups in chiral auxiliaries. In some embodiments, a cycle may comprise two or more capping steps. In some embodiments, a cycle comprises a first capping before modification of a coupling product (e.g., converting P(II1) to P(V)), and another capping after modification of a coupling product. In some embodiments, a first capping is performed under an amidation condition, e.g., which comprises an acylatmg reagent (e.g., an anhydride having the structure of (RC(0)) 2 0, (e.g., Ac 2 0)) and a base (e.g., 2,6-lutidine). In some embodiments, a first capping caps an amino group, e.g., that of a chiral auxiliary in an internucleotidic linkage. In some embodiments, an internucleotidic linkage fonned in a coupling step has the structure of formula I or a salt form thereof. In some embodiments, is P. In

, wherem each variable is independently in accordance with the present disclosure. In some embodiments, R ! is R-C(O)-. in some embodiments, R is CH 3- . In some embodiments, each chiral!y controlled coupling (e.g., using a chiral auxiliary') is followed with a first capping. Typically, cycles for non-chirally controlled coupling using traditional phosphoramidite to construct natural phosphate linkages do not contain a first capping. In some embodiments, a second capping is performed, e.g., under an esterification condition (e.g., capping conditions of traditional phosphoramidite oligonucleotide synthesis) wherein free 5’-OH are capped.

[001042] Certain capping technologies, e.g., reagents, conditions, methods, etc. are illustrated in the Examples.

Modifying

[001043] In some embodiments, an internucleotidic linkage wherein its linkage phosphorus exists as P(II1) is modified to form another modified internucleotidic linkage (e.g., one of formula 1, I -a. I-b, I- c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, III, or a salt form thereof) or a natural phosphate linkage. In many embodiments, P(IH) is modified by reaction with an electrophile. Various types of reactions suitable for P(ITI) may be utilized in accordance with the present disclosure. Suitable modifying technologies (e.g., reagents (e.g., sulfurization reagent, oxidation reagent, etc.), conditions, etc.) include those described in US 9695211, US 9605019, US 9598458, US 2013/0178612, US 2015021 1006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, WO 2017/210647, WO 2018/223056, WO 2018/237194, and/or WO 2019/055951, the modifying technologies of each of which are incorporated by reference.

[001044] In some embodiments, as illustrated in the Examples, the present disclosure provides modifying reagents for introducing non-negativeiy charged intemucleotidic linkages including neutral intemucleotidic linkages.

[001045] In some embodiments, modifying is within a cycle. In some embodiments, modifying can be outside of a cycle. For example, in some embodiments, one or more modifying steps can be performed after the oligonucleotide chain has been reached to introduce modifications simultaneously at one or more intemucleotidic linkages and/or other locations.

[001046] In some embodiments, modifying comprises use of click chemistry, e.g , wherein an alkyne group of an oligonucleotide, e.g., of an intemucleotidic linkage, is reacted with an azide. Various reagents and conditions for click chemistry can be utilized in accordance with the present disclosure in some embodiments, an azide has the structure of R ! -N 3 , wherein R ! is as described in the present disclosure. In some embodiments, R 1 is optionally substituted C, 6 alkyl. In some embodiments, R 1 is isopropyl.

[001047] In some embodiments, as demonstrated m the examples, a P(III) linkage can be converted into a non-negativeiy charged intemucleotidic linkage by reacting the P(III) linkage with an azide or an

azido imidazolinium salt (e.g., a compound comprising some embodiments, referred to as an azide reaction) under suitable conditions. In some embodiments, an azido imidazolinium salt is a salt

of PF ft . In some embodiments an azido imidazolinium salt is a salt In some

embodiments, a useful reagent, e.g., an azido imidazolinium salt, is a salt some

embodiments, a useful reagent is a salt some embodiments, a useful reagent is a

salt of . , u u g Such reagents comprising nitrogen cations also contain counter anions (e.g., Q as described in the present disclosure), which are widely known the art and are contained m various chemical reagents hr some

embodiments, a useful reagent is Q Q . wherein

is a counter anion. In some embodiments, Q is

, . In

some embodiments, . In some embodiments, As appreciated by those skilled in the art, in a compound having the structure of Q Q , typically the number of positive charges in Q equals the number of negative charges in Q . In some embodiments, Q is a monovalent cation and Q is a monovalent anion. In some embodiments, Q is F , Cf , Br , BFty, PF 6 , TfO , Tf 2 N , AsFty, C IO. . or SbF 6 . In some embodiments, Q is PF 6 . Those skilled in the art readily appreciate that many other types of counter anions are available and can be utilized in accordance with the present disclosure. In some embodiments, an azido imidazolinium salt is 2-azido-l,3-

dimethylimidazolinium hexafluorophosphate . In some embodiments, an azide is In

N 3 some embodiments, an azido imidazolinium salt is . In some embodiments, an azido

imidazolinium salt is . In some embodiments, an azide is

In some embodiments, an azide is . In some embodiments, an azide is . In some embodiments, an azido imidazolinium salt In

some embodiments, an azido imidazolinium salt is ^ ^ . In some embodiments, an azido

imidazolinium salt is ^ ^ In some embodiments, an azido imidazolinium

salt

[001048] In some embodiments, a P(III) linkage is reacted with an electrophile having the structure of R-G z , wherein R is as described in the present disclosure, and is a leaving group, e.g., -Cl, -Br, -I, -OTf, Oms, -OTosyl, etc. In some embodiments, R is -CH 3 . In some embodiments, R is -CH 2 CH 3 . In some embodiments, R is -CH 2 CH 2 CH 3 . In some embodiments, R is -CH 2 OCH 3 . In some embodiments, R is CH 3 CH 2 OCH 2 -. In some embodiments, R is PhCH 2 OCH 2 - In some embodiments, R is HC= : C-CH 2 - j n some embodiments, R is H 3 c~ -C= C' ~~CH 2 ~~ y n SO me embodiments, R is CH 2 =CHCH 2- . In some embodiments, R is CH 3 SCH 2- . In some embodiments, R is -CH 2 COOCH 3 . In some embodiments, R is -CH 2 COOCH 2 CH 3 . In some embodiments, R is -CH 2 CONHCH 3 .

[001049] In some embodiments, after a modifying step, a P(iil) linkage phosphorus is converted into a P(V) intemucleotidic linkage. In some embodiments, a P(ffl) linkage phosphorus is converted into a P(V) intemucleotidic linkage, and all groups bounded to the linkage phosphorus remain unchanged. In some embodiments, a linkage phosphorus is converted from P into P( :=: 0). In some embodiments, a linkage phosphorus is converted from P into P(=S). In some embodiments, a linkage phosphorus is converted from P into P(=N-L-R 5 ). In some embodiments, a linkage phosphorus is converted from P wherein each variable is independently as described in the present disclosure. In some embodiments, P is pi

converted into . . In some

embodiments, P is converted into In some embodiments, P is converted into

in some embodiments, P is converted into As appreciated by those skilled in the art, for each cation there typically exists a counter anion so that the total number of positive charges equals the total number of negative charges in a system (e g., compound, composition, etc ). In some embodiments, a counter anion is Q ~ as described in the present disclosure (e.g., F ~ , CF, Br , BF « , PF 6 , TfO , TtVN , AsF 6 , C10 4 , SbF 6 , etc.). In some embodiments, an intemucieotidic linkage having the structure of formula I, I- a, I-b, I-c, I-n-1, I n - i n-3. 1-n-4, II, I I -a- 1. II-a-2, II-b-1, I J-b-2. II-c-1, II-c~2, II-d-1, II-d-2, or a salt form thereof, wherein P L is P, is converted into an intemucieotidic linkage having the structure of formula I, I-a, I-b, I-c, I-n-1, 1-n-2, 1-n-3, 1-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, ll-d-l, II-d-2, III, or a salt form thereof, wherein P L is P(=W) or P B(R’) 3 or P . In some embodiments, an intemucieotidic linkage having the structure of formula I, I-a, I-b, I-c, I-n-1, i n-2. 1-n-

3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof, wherein P L is P, is converted into an intemucieotidic linkage having the structure of formula I, I-a, I-b, I-c, I-n-1, 1- n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, U-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof, wherein P L is P(=W) or P B(R’) 3 . In some embodiments, a linkage phosphorus P, which is P L in an intemucieotidic linkage having the structure of formula I, I-a, I-b, I-c, I-n-1, 1-n-2, I-n-3, I-n-4, II, Il-a- 1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof is converted into P L which is P(=W) or P B(R’) 3 . In some embodiments, a linkage phosphorus P, which is P L in an intemucieotidic linkage having the structure of formula I or a salt fonn thereof is converted into P L which is P(=W) or P-->B(R/) 3 . In some embodiments, W is O (e.g., for an oxidation reaction). In some embodiments, W is S (e.g., for a sulfurization reaction). In some embodiments, W is =N-L-R S (e.g., for an azide reaction). In some embodiments, an intemucleotidic linkage having the structure of formula I or a salt form thereof (e.g., wherein P is P) is converted into an intemucleotidic linkage having the structure of formula III or a salt form thereof:

!-Y- -Z-f-

III

wherein:

Q is an anion, and

each other variables is independently as described in the present disclosure.

In some embodiments, P N is P(=N-L-R 5 ). In some embodiments,

In some embodiments, P N is In

some embodiments, P N is In some embodiments, intemucleotidic linkages of the present disclosure may exist in a salt form. In some embodiments, intemucleotidic linkages of formula III may exist in a salt form. In some embodiments, in a salt fonn of an intemucleotidic linkage of formula In some embodiments, P N is P=W . wherein

W N is as described herein.

[001051] In some embodiments, Y, Z, and -X-L-R 1 remains the same during the conversion. In some embodiments, each of X, Y and Z is independently -Q-. hi some embodiments, as described herein, -X-L-R 1 is of such a structure that H-X-L-R 1 is a chiral reagent described herein, or a capped chiral reagent described herein wherein an ammo group of the chiral reagent (typically of -W 1 -!! or -W 2 -H, which comprises an amino group -NHG ' -) is capped, e.g., with -C(0)R’ (replacing a -H, e.g.,

, wherein each variable is independently in accordance with the present disclosure. In some embodiments, wherein R ! is -C(0)R. In some embodiments, R 1 is CH 3 C(0)-. In some embodiments, as described herein, G 2 comprises an electron -withdrawing group. In some embodiments, G 2 is -CH 2 S0 2 Ph.

[001052] In some embodiments, an intemucleotidic linkage (e.g., a modified intemucleotidic linkage, a chiral intemucleotidic linkage, a cfairally controlled intemucleotidic linkage, a non-negatively charged intemucleotidic linkage, a neutral intemucleotidic linkage, etc.) has the structure of fonnula I, I- a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, II-d-2, or a salt form thereof, wherein P L is P(==N-L-R), or of formula III or a salt form thereof. In some embodiments, such an intemucleotidic linkage is chirally controlled. In some embodiments, ail such internucleotidic linkages are chirally controlled in some embodiments, linkage phosphorus of at least one of such intemucleotidic linkages is Rp. In some embodiments, linkage phosphorus of at least one of such intemucleotidic linkages is Sp. In some embodiments, linkage phosphorus of at least one of such intemucleotidic linkages is Rp, and linkage phosphorus of at least one of such internucleotidic linkages is 5p. in some embodiments, oligonucleotides of the present disclosure comprises one or more (e.g., 1-5, 1- 10, 1-15, 1-20, 1-25, 1-30, 1-40, 1-50, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, etc.) such intemucleotidic linkages. In some embodiments, such oligonucleotide further comprise one or more oilier types of intemucleotidic linkages, e.g., one or more natural phosphate linkages, and/or one or more phosphorothioate intemucleotidic linkages (e.g., m some embodiments, one or more of which are independently chirally controlled; in some embodiments, each of which is independently chirally controlled; in some embodiments, at least one is Rp: some embodiments, at least one is Sp; in some embodiments, at least one is Rp and at least one is Sp etc.) In some embodiments, such oligonucleotides are stereopure (substantially free of other stereoisomers). In some embodiments, the present disclosure provides chirally controlled oligonucleotide compositions of such oligonucleotides. In some embodiments, the present disclosure provides chirally pure oligonucleotide compositions of such oligonucleotides.

[001053] In some embodiments, modifying proceeds with a stereoselectivity of 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more. In some embodiments, the stereoselectivity is 85% or more. In some embodiments, the stereoselectivity is 85% or more. In some embodiments, the stereoselectivity is 90% or more. In some embodiments, the stereoselectivity is 91% or more. In some embodiments, the stereoselectivity is 92% or more. In some embodiments, the stereoselectivity is 93% or more hi some embodiments, the stereoselectivity is 94% or more hi some embodiments, the stereoselectivity is 95% or more. In some embodiments, the stereoselectivity is 96% or more. In some embodiments, the stereoselectivity is 97% or more. In some embodiments, the stereoselectivity is 98% or more. In some embodiments, the stereoselectivity is 99% or more. In some embodiments, modifying is stereospecific.

Deblocking

[001054] In some embodiments, a cycle comprises a cycle step. In some embodiments, the 5’ hydroxyl group of the growing oligonucleotide is blocked (i.e., protected) and must be deblocked in order to subsequently react with a nucleoside coupling partner.

[001055] In some embodiments, acidification is used to remove a blocking group. Suitable deblocking technologies (e.g., reagents, conditions, etc.) include those described in US 9695211, US 9605019, US 9598458, US 2013/0178612, US 20150211006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, WO 2017/210647, WO 2018/223056, WO 2018/237194, and/or WO 2019/055951, the deblocking technologies of each of which are incorporated by reference. Certain deblocking technologies, e.g., reagents, conditions, methods, etc. are illustrated in the Examples.

Cleavage and Deprotection

[001056] At certain stage, e.g., after the desired oligonucleotide lengths have been achieved, cleavage and/or deprotection are performed to deprotect blocked nucleobases etc. and cleave the oligonucleotide products from support. In some embodiments, cleavage and deprotection are performed separately. In some embodiments, cleavage and deprotection are performed in one step, or in two or more steps but without separation of products in between. In some embodiments, cleavage and/or deprotection utilizes basic conditions and elevated temperature. In some embodiments, for certain chiral auxiliaries, a fluoride condition is required (e.g., TBAF, HF-ET 3 N, etc., optionally with additional base). Suitable cleavage and deprotection technologies (e.g., reagents, conditions, etc.) include those described in US 9695211, US 9605019, IJS 9598458, US 2013/0178612, US 20150211006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, WO 2017/210647, WO 2018/223056, WO 2018/237194, and/or WO 2019/055951, the cleavage and deprotection technologies of each of winch are incorporated by reference. Certain cleavage and deprotection technologies, e.g., reagents, conditions, methods, etc. are illustrated in the Examples.

[001057] In some embodiments, certain chiral auxiliaries are removed under basic conditions. In some embodiments, oligonucleotides are contacted with a base, e.g., an amine having the structure of N(R)3, to remove certain chiral auxiliaries (e.g., those comprising an electronic -withdrawing group in G z as described in the present disclosure). In some embodiments, a base is NHR 2 . In some embodiments, each R is independently optionally substituted Ci 6 aliphatic. In some embodiments, each R is independently optionally substituted C 1-6 alkyl. In some embodiments, an amine is DEA. In some embodiments, an amine is TEA. In some embodiments, an amine is provided as a solution, e.g., an acetonitrile solution. In some embodiments, such contact is performed under anhydrous conditions. In some embodiments, such a contact is performed immediately after desired oligonucleotide lengths are achieved (e.g., first step post synthesis cycles). In some embodiments, such a contact is performed before removal of chiral auxiliaries and/or protection groups and/or cleavage of oligonucleotides from a solid support. In some embodiments, contact with a base may remove cyanoethyl groups utilized in standard oligonucleotide synthesis, providing an natural phosphate linkage which may exist in a salt form (with the cation being, e.g., an ammonium salt). In some embodiments, contact with a base provides an intern ucleotidic linkage of formula I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II- c-2, Il-d-1, or II-d-2, or a salt form thereof. In some embodiments, contact with a base removes a chiral auxiliary from an intemucleotidic linkage of formula I, I-a, I-b, I-c, I-n-1, I-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1 , II-c-2, II-d-1, or II-d-2, or a salt form thereof. In some embodiments, contact with a base removes a chiral auxiliary (e.g., -X-L-R 1 ) from an intemucleotidic linkage of formula I or a salt fomi thereof (e.g., wherein P L is P(=N-L-R’)). In some embodiments, contact with a base removes a chiral auxiliary (e.g., -X-L-R 1 ) from an intemucleotidic linkage of formula III or a salt form thereof. In some embodiments, In some embodiments, contact with a base converts an intemucleotidic linkage of formula I or a salt form thereof (e.g., wherein is P(=N-L-R 5 )), or of formula III or a salt form thereof, into an intemucleotidic linkage of formula II-n-1, l-n-2, I-n-3, I-n-4, II, II-a-1, II-a-2, II-b-1, II-b-2, II-c-1, II-c-2, II-d-1, or II-d-2, or a salt form thereof

Cycles

[001058] Suitable cycles for preparing oligonucleotides of the present disclosure include those described in US 9695211, US 9605019, US 9598458, US 2013/0178612, US 20150211006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741 , WO 2017/192664, WO 2017/192679, WO 2017/210647 (e.g.. Schemes I, I-b, I-c, I-d, I-e, I-f, etc.), WO 2018/223056, WO 2018/237194, and/or WO 2019/055951, the cycles of each of which are incorporated by reference. For example, in some embodiments, an example cycle is Scheme I-f Certain cycles are illustrated the Examples (e.g., for preparation of natural phosphate linkages, utilizing other chiral auxiliaries, etc.). Scheme I-e. Example cycle using DPSE chiral auxiliary'.

[001059] In some embodiments, R s is H or -OR 1 , wherein R 1 is not hydrogen. In some embodiments, R 2s is H or -OR 1 , wherein R l is optionally substituted C s-6 alkyl. In some embodiments, R 2S is H. In some embodiments, R 2s is -OMe. In some embodiments, R 2s is -OCH CH 2 OCH 3 . In some embodiments, R 2s is -F. In some embodiments, R 4s is -H. In some embodiments, R 4 " and R 2s are taken together to form a bridge -L-O- as described in the present disclosure. In some embodiments, the ~ 0 ~ is connected to the carbon at the Y position. In some embodiments, L is -CH 2 ~ . In some embodiments, L is -CH(Me)-. In some embodiments, L is -(R)-CH(Me)-. In some embodiments, L is

Purification and Characterization

[001060] Various purification and/or characterization technologies (methods, instruments, protocols, etc.) can be utilized to purify and/or characterize oligonucleotides and oligonucleotide compositions in accordance with the present disclosure. In some embodiments, purification is performed using various types of HPLC/UPLC technologies. In some embodiments, characterization comprises MS, NMR, UV, etc. In some embodiments, purification and characterization may be performed together, e.g.„ HPLC-MS, UPLC-MS, etc. Example purification and characterization technologies include those described in US 969521 1 , US 9605019, US 9598458, US 2013/0178612, US 2015021 1006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, WO 2017/210647, WO 2018/223056, WO 2018/237194, and/or WO 2019/055951, tire purification and characterization technologies of each of which are incorporated by reference.

[001061 j In some embodiments, the present disclosure provides methods for preparing provided oligonucleotide and oligonucleotide compositions. In some embodiments, a provided method comprises providing a provided chiral reagent having the structure of formula 3-1 or 3-AA. In some embodiments, a provided method comprises providing a provided chiral reagent having the structure of , wherein W is -NG , W is O, each of G and G is independently hydrogen or an optionally substituted group selected from C MO aliphatic, heterocyclyl, heteroaryl and aryl, G 2 is -C(R) 2 Si(R)3, and G 4 and G s are taken together to form an optionally substituted saturated, partially unsaturated or unsaturated heteroatom-containing ring of up to about 20 ring atoms which is monocyclic or polycyclic, fused or unfused, wherein each R is independently hydrogen, or an optionally substituted group selected from C r- C 6 aliphatic, carbocycly!, aryl, heteroaryl, and heterocyclyl. In some

embodiments, a provided chiral reagent has the structure of , ^ ^ or , wherein each variable is independently as described in the present disclosure. In some embodiments, a provided methods comprises providing a phosphoramidite comprising a moiety from a

chiral reagent having the structure

, wherein -W H and -W Z H, or the hydroxyl and amino groups, form bonds with the phosphorus atom of the phosphoramidite. In some embodiments, -W ! H and -W 2 H, or the hydroxyl and

ammo groups, form bonds with the phosphorus atom of the phosphoramidite,

wherein B r is BA as described in the present disclosure, and each other variable is as described in the present disclosure. In some embodiments, B is a protected nudeobase. In some embodiments, B u is protected A, T, G, C, U or a tautomers thereof. In some embodiments, R is a protection group. In some embodiments, R is DMTr.

[001062] In some embodiments, G 2 is -C(R) 2 Si(R) 3 , wherein -C(R) 2- i s optionally substituted -CH 2- , and each R of -Si(R) 3 is independently an optionally substituted group selected from C ]-]0 aliphatic, heterocyclyl, heteroaryl and aryl. In some embodiments, at least one R of -Si(R) 3 is independently optionally substituted C HO alkyl. In some embodiments, at least one R of -Si(R) 3 is independently optionally substituted phenyl. In some embodiments, one R of -Si(R) 3 is independently optionally substituted phenyl, and each of the other two R is independently optionally substituted C HO alkyl. In some embodiments, one R of -Si(R) 3 is independently optionally substituted C HO alkyl, and each of the other two R is independently optionally substituted phenyl. In some embodiments, G 2 is optionally substituted -CH 2 Si(Ph)(Me) 2 . In some embodiments, G 2 is optionally substituted -CH 2 Si(Me)(Ph) 2 . In some embodiments, G 2 is ---CH 2 Si(Me)(Ph) 2. In some embodiments, G 2 is -CH 2 SiMe 3 . In some embodiments, G 2 is -CH 2 Si(?Pr) 3 . In some embodiments, G 4 and G 2 are taken together to form an optionally substituted saturated 5-6 membered ring containing one nitrogen atom (to which G 5 is attached). In some embodiments, G and G 5 are taken together to form an optionally substituted saturated 5-membered ring containing one nitrogen atom. In some embodiments, G 1 is hydrogen. In some embodiments, G’ is hydrogen. In some embodiments, both G ! and G 3 are hydrogen. In some embodiments, both G 1 and G 3 are hydrogen, G 2 is -C(R) 2 Si(R) 3 , wherein -C(R) 2 - is optionally substituted -CH 2- , and each R of -Si(R) 3 is independently an optionally substituted group selected from C HO aliphatic, heterocyclyl, heteroaryl and aryl, and G 4 and G 5 are taken together to form an optionally substituted saturated 5-membered ring containing one nitrogen atom. In some embodiments, a provided method further comprises providing a fluoro-containing reagent. In some embodiments, a provided fluoro-containing reagent removes a chiral reagent, or a product formed from a chiral reagent, from oligonucleotides after synthesis. Various known fluoro-containing reagents, including those F ~ sources for removing -SiR 3 groups, can be utilized in accordance with the present disclosure, for example, TBAF, HF 3 -Et 3 N etc. In some embodiments, a fluoro-containing reagent provides better results, for example, shorter treatment time, lower temperature, less de-sulfurization, etc, compared to traditional methods, such as concentrated ammonia. In some embodiments, for certain fluoro-containing reagent, the present disclosure provides linkers for improved results, for example, less cleavage of oligonucleotides from support during removal of chiral reagent (or product formed therefrom during oligonucleotide synthesis). In some embodiments, a provided linker is an SP linker. In some embodiments, the present disclosure demonstrated that a HF-base complex can be utilized, such as HF-NR 3 , to control cleavage during removal of chiral reagent (or product formed therefrom during oligonucleotide synthesis). In some embodiments, HF-NR 3 is HF-NEt 3 . In some embodiments, HF-NR 3 enables use of traditional linkers, e.g., suecinyl linker.

[001063] In some embodiments, as described herein, G 2 comprises an electron-withdrawing group, e.g., at its a position. In some embodiments, G 2 is methyl substituted with one or more electron- withdrawing groups. In some embodiments, an electronic -withdrawing group comprises and/or is connected to the carbon atom through, e ., -S(O)-, -S(0) 2- , -P(0)(R 5 )--, -P(S)R i -, or -C(O)-. In some embodiments, an electron-withdrawing group is -CN, -N0 2 , halogen, --C(0)R 1 , -C(0)OR’, C(( ) )\( R -S(0)R ] , S(0) . -R '. FiWH R/ ) ·. -P(0)(R l ) 2 , -P(0)(OR\} 2 , or -P(S)(R l ) 2 . In some embodiments, an electron-withdrawing group is aryl or heteroaryl, e ., phenyl, substituted with one or more of -CN, -N0 2 , halogen, -C(0)R\ -C(0)OR\ -C(0)N(R’) 2 , -S(0)R\ ~ S(0) 2 R 1 , ~ P(W)(R i ) 2 , -P(0)(R 1 ) 2 , -P(0)(OR’) 2 , or -P(S)(R 1 ) 2 . In some embodiments, G 2 is -CH 2 S(0)R’. In some embodiments, G 2 is -CH 2 S(0) 2 R\ In some embodiments, G 2 is --CH 2 P(0)(R’) 2 . Additional example embodiments are described, eg., as for chiral reagents/auxiliaries.

|001064] Confirmation that a stereocontrolled oligonucleotide (e.g., one prepared by a method described herein or in the art) comprises the intended stereocontrolled (chirally controlled) internucleotidic linkage can be performed using a variety of suitable technologies. A stereocontrolled (chirally controlled) oligonucleotide comprises at least one stereocontrolled internucleotidic linkage, which can be, e.g., a stereocontrolled internucleotidic linkage comprising a phosphorus, a stereocontrolled phosphorothioate internucleotidic linkage (PS) in the Rp configuration, a PS in the Sp configuration, etc. Useful technologies include, as non-limiting examples: NMR (e ., ID (one-dimensional) and/or 2D (two-dimensional)’H- 31 ? HETCOR (heteronuclear correlation spectroscopy)), HPLC, RP-HPLC, mass spectrometry, LC-MS, and/or stereospecific nucleases. In some embodiments, stereospecific nucleases include: benzonase, micrococcal nuclease, and svPDE (snake venornc phosphodiesterase), which are specific for intemucleotidic linkages in the Rp configuration (e.g., a PS in the Rp configuration); and nuclease PI, mung bean nuclease, and nuclease Si, which are specific for intemucleotidic linkages in the Sp configuration (e.g., a PS in the Sp configuration).

|001065] In some embodiments, tire present disclosure pertains to a method of confirming or identifying the stereochemistry pattern of the backbone of an oligonucleotide and/or stereochemistry of particular intemucleotidic linkages. In some embodiments, an oligonucleotide comprises a stereocontrolled intemucleotidic linkage comprising a phosphorus, a stereocontrolled phosphorothioate (PS) in the Rp configuration, or a PS in the Sp configuration. In some embodiments, an oligonucleotide comprises at least one stereocontrolled intemucleotidic linkage and at least one intemucleotidic linkage which is not stereocontrolled. hi some embodiments, a method comprises digestion of an oligonucleotide with a stereospecific nuclease. In some embodiments, a stereospecific nuclease is selected from: benzonase, micrococcal nuclease, and svPDE (snake venom phosphodiesterase), which are specific for intemucleotidic linkages in the Rp configuration (e.g., a PS in the Rp configuration); and nuclease PI, mung bean nuclease, and nuclease SI, which are specific for intemucleotidic linkages m the Sp configuration (e.g., a PS in the Sp configuration). In some embodiments, an oligonucleotide or fragments thereof produced by digestion with a stereospecific nuclease are analyzed. In some embodiments, an oligonucleotide or fragments thereof (e.g., produced by digestion with a stereospecific nuclease) are analyzed by NMR, ID (one-dimensional) and/or 2D (two-dimensional) ΐΐ- 31 ? HETCOR (heteronuclear correlation spectroscopy), HPLC, RP-HPLC, mass spectrometry, LC-MS, UPLC, etc. In some embodiments, an oligonucleotide or fragments thereof are compared with chemically synthesized fragments of the oligonucleotide having a known pattern of stereochemistry.

[001066] Without wishing to be bound by any particular theory, the present disclosure notes that, in at least some cases, stereospecificity of a particular nuclease may be altered by a modification (e.g., 2’- modification) of a sugar, by a base sequence, or by a stereochemical context. For example, in some embodiments, benzonase and micrococcal nuclease, which are specific for Rp intemucleotidic linkages, were both unable to cleave an isolated PS Rp intemucleotidic linkage flanked by PS Sp intemucleotidic linkages.

[001067] Various techniques and materials can be utilized. In some embodiments, the present disclosure provides useful combinations of technologies. For example, some embodiments, stereochemistry of one or more particular intemucleotidic linkages of an oligonucleotide can be confirmed by digestion of the oligonucleotide with a stereospecific nuclease and analysis of the resultant fragments (e.g., nuclease digestion products) by any of a variety of techniques (e.g., separation based on mass-to-charge ratio, NMR, HPLC, mass spectrometry, etc.). In some embodiments, stereochemistr ' of products of digesting an oligonucleotide with a stereospecific nuclease can be confirmed by comparison (e.g., NMR, HPLC, mass spectrometry, etc.) with chemically synthesized fragments (e.g., dimers, trimers, tetramers, etc.) produced, e.g., via technologies that control stereochemistry .

[001068] In one example, an oligonucleotide was confirmed to have the designed and intended pattern of stereochemistry in the backbone. The tested oligonucleotide comprises a core comprising 2 deoxy nucleosides, wherein all of the internucleotidic linkages were PS in the Sp configuration except for one PS in the Rp configuration; and two wings, each of which comprising 2’-OMe nucleosides, wherein all the internucleotidic linkages in each wing were phosphodiester (PO) except for one PS in the Sp configuration in each wing. The oligonucleotide was digested with a stereospecific nuclease (e.g., nuclease PI). The various fragments were analyzed (e.g., by LC-MS and by comparison with chemically synthesized fragments of known stereochemistry). It was confirmed that the oligonucleotide had the intended patern of stereochemistry in its backbone.

[001069] In another example, an oligonucleotide having a different sequence was confirmed to have the intended pattern of stereochemistry in its backbone, using digestion with a stereospecific nuclease and analysis of the resultant fragments. This oligonucleotide comprises a core comprising 2 - deoxy nucleotides, wherein all of the internucleotidic linkages were PS in the Sp configuration except for one PS in the Rp configuration; and two wings, each of which comprising 2’-OMe nucleotides, wherein all the internucleotidic linkages in each wing were phosphodiester (PO) except for one PS in the Sp configuration in each wing.

[001070] In yet another example, a different oligonucleotide was tested to confirm that the internucleotidic linkages were in the intended configurations. The oligonucleotide is capable of skipping exon 51 of DMD; the majority of the nucleotides in the oligonucleotide were 2’-F and the remainder were 2’-OMe; the majority of the internucleotidic linkages in the oligonucleotide were PS in the Sp configuration and the remainder were PO. This oligonucleotide w¾s tested by digestion with stereospecific nucleases, and the resultant digestion fragments were analyzed (e.g., by LC-MS and by comparison with chemically synthesized fragments of known stereochemistry). The results confirmed that the oligonucleotide had tire intended pattern of stereocontrolled internucleotidic linkages.

[001071] In some embodiments, NMR is useful for characterization and/or confirming stereochemistry . In a set of example experiments, a set of oligonucleotides comprising a stereocontrolled CpG motif were tested to confirm the intended stereochemistry of the CpG motif. Oligonucleotides of the set comprise a motif having the structure of pCpGp, wherein C is Cytosine, G is Guanine, and p is a phosphorothioate winch is stereorandom or stereocontrolled (e.g., in the Rp or Sp configuration). For exampl e, one oligonucleotide comprises a pCpGp structure, wherein the pattern of stereochemistry of the phosphorothioates (e.g., the ppp) was RRR; in another oligonucleotide, the pattern of stereochemistry of the ppp was RSS; in another oligonucleotide, the pattern of stereochemistry of the ppp was RSR; etc. In the set, all possible patterns of stereochemistry of the ppp were represented. In the portion of the oligonucleotide outside the pCpGp structure, all the intemucleotidic linkages were PO; all nucleosides in the oligonucleotides were 2’~deoxy. These various oligonucleotides were tested in NMR, without digestion with a stereospecific nuclease, and distinctive patterns of peaks were observed, indicating that each PS which was Rp or Sp produced a unique peak, and confirming that the oligonucleotides comprised stereocontrolled PS intemucleotidic linkages of the intended stereochemistry.

[001072] Stereochemistry pattern s of the intemucleotidic linkages of various other stereocontrolled oligonucleotides were confirmed, wherein the oligonucleotides comprise a variety of chemical modifications and patterns of stereochemistry.

[001073] As those skilled in the art will appreciate, in some embodiments, a product oligonucleotide of a step, cycle or preparation is an oligonucleotide comprising O P , O p , * PD , * FD S, * PD R, * N , * N S and/or * N R as described herein, which oligonucleotide is optionally linked to a support (e.g., CPG) optionally via a linker (e.g., a CAN linker). For example, in some embodiments, after coupling

and/or pre -modification capping and before modification, 0 5P is -sugar

5'-sugar 5'-sugar

3‘-sugar 3 -sugar or a saj f 0!Tn thereof. In some embodiments , after modification 0 3p is L P0 , L PA , L PB , or a salt form thereof.

Metabolites

[001074] in some embodiments, a DMD oligonucleotide corresponds to a fragment of a different, longer DMD oligonucleotide. In some embodiments, a DMD oligonucleotide corresponds to a metabolite produced by cleavage (e.g, enzymatic cleavage by a nuclease) of a longer DMD oligonucleotide, which produces a fragment or portion of the longer DMD oligonucleotide. In some embodiments, the present disclosure pertains to an DMD oligonucleotide winch corresponds to a metabolite produced by the cleavage of a DMD oligonucleotide described herein. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which corresponds to a portion, or fragment of a DMD oligonucleotide disclosed herein.

[001075] Several experiments were performed wherein a DMD oligonucleotide was incubated in vitro in the presence of any of various substances comprising nucleases. In various experiments, such substances include brain homogenatem, cerebrospinal fluid or plasma from Sprague-Dawley rat or Cynomolgus monkey. Plasma was heparinized. Oligonucleotides were incubated for various time points (e.g., 0, 1, 2, 3, 4 or 5 days for brain tissue homogenate, with a pre-incubation period of 0, 1 or 2 days; 0, 1, 2, 4, 8, 16, 24 or 48 hrs for cerebrospinal fluid; or 0, 1, 2, 4, 8, 16 or 24 hrs for plasma). Pre -incubation indicates that the homogenate is incubated at 37 degrees °C for 0, 24 or 48 hrs to activate the enzymes before adding the oligonucleotide. Final concentration and volume of oligonucleotides was 20 mM in 200 mΐ. Products produced by cleavage of the oligonucleotides were analyzed by LC/MS

[001076] For one DMD oligonucleotide, which is 20 bases long, tested in rat brain homogenate, the major metabolites represented the 3’ end of the oligonucleotide, which were truncated by 4, 10, 11, 12, or 13 bases.

[001077] One test DMD oligonucleotide has a length of 20 bases and was tested in rat brain homogenate, yielding major metabolites winch were truncated at the 5’ end by 4, 10, 11, 12, or 13 bases, leaving metabolites representing the 3’ end of the oligonucleotide and which were 16, 10, 9, 8 or 7 bases long, respectively. This oligonucleotide also produced a metabolite which was a 5’ fragment which was 12 bases long (truncated at the 3’ end by 8 bases).

[001078] A second test oligonucleotide has a length of 20 bases and was tested in rat brain homogenate, yielding major metabolites which wore truncated at the 3’ end by 4, 8, 9 or 10 bases, leaving metabolites representing the 5’ end of the oligonucleotide and which were 16, 12, 11 or 10 bases long, respectively.

[001079] The two tested oligonucleotides comprise intemucleotidic linkages which are phosphodiesters, phosphorothioate in the Rp configuration, and phosphorothioates in the Sp configuration. In some embodiments, phosphodiesters were more labile than the phosphorothioate in the Rp configuration or the phosphorothioate in the Sp configuration. In some cases, a metabolite of an oligonucleotide represents a product of a cleavage at a phosphodiester.

[001080] In some embodiments, the present disclosure pertains to a DMD oligonucleotide which corresponds to a metabolite of a DMD oligonucleotide disclosed herein. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, or more bases shorter than a DMD oligonucleotide disclosed herein. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which has a base sequence which is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, or more bases shorter than that of a DMD oligonucleotide disclosed herein.

[001081] In some embodiments, a metabolite is designated as 3’-N-#, or 5’-N-#, wherein the # indicates the number of bases removed, and the 3 or 5 indicates which end of the molecule from which the bases were deleted. For example, 3’-N-l indicates a fragment or metabolite wherein 1 base was removed from the 3’ end.

[001082] In some embodiments, the present disclosure perhaps to an oligonucleotide which corresponds to a fragment or metabolite of a DMD oligonucleotide disclosed herein, wherein the fragment or metabolite can be described as corresponding to 3’-N-l, 3’-N~2, 3’-N-3, 3’-N-4, 3’-N-5, 3’- N-6, 3’-N-7, 3’-N-8, 3’-N-9, 3’-N-10, 3 --N -- 1 ! . 3’-N-12, 5’-N-l, 5’-N-2, 5’-N-3, 5 -N-4, 5’-N-5, 5’-N-6, 5’-N-7, 5 -N-8, 5’-N-9, 5’-N-10, 5’-N-l l, or 5’-N-12 of a DMD oligonucleotide described herein.

[001083] In some embodiments, the present disclosure pertains to a DMD oligonucleotide which is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,1 1, 12, 13, or more bases shorter on the 5’ end than a DMD oligonucleotide disclosed herein. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which has a base sequence which is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, or more bases shorter on the 5 end than that of a DMD oligonucleotide disclosed herein. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, or more bases shorter on the 3’ end than a DMD oligonucleotide disclosed herein. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which has a base sequence which is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, or more bases shorter on the 3’ end than that of a DMD oligonucleotide disclosed herein.

[001084] In some embodiments, the present disclosure pertains to a DMD which corresponds to a metabolite of a DMD oligonucleotide, wherein the metabolite is truncated on the 5" and/or 3’ end relative to the DMD oligonucleotide disclosed herein. In some embodiments, the present disclosure pertains to a DMD which corresponds to a metabolite of a DMD oligonucleotide, wherein the metabolite is truncated on both the 5’ and 3’ end relative to the DMD oligonucleotide disclosed herein. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, or more total bases shorter on the 5’ and/or 3’ end than a DMD oligonucleotide disclosed herein. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which has a base sequence which is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, or more bases total shorter on the 5’ and/or 3’ end than that of a DMD oligonucleotide disclosed herein.

[001085] In some embodiments, the present disclosure pertains to a DMD oligonucleotide which would be represented by a product of cleavage of a DMD oligonucleotide disclosed herein, which is cleaved at a phosphodiester linkage. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which would be represented by a product of cleavage of a DMD oligonucleotide disclosed herein, if such an oligonucleotide were cleaved at a phosphorothioate linkage in the Rp configuration. In some embodiments, the present disclosure pertains to a DMD oligonucleotide which would be represented by a product of cleavage of a DMD oligonucleotide disclosed herein, if such an oligonucleotide w¾re cleaved at one or more phosphodiester linkages and/or phosphorothioate linkages in the Rp configuration. Biological Applications, Example Use, and Dosing Regimens

[001086] As described herein, provided compositions and methods are useful for various purposes, e.g., those described in US 969521 1, US 9605019, US 9598458, US 2013/0178612, US 20150211006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, and/or WO 2017/210647. Among other things, provided technologies can function and/or provide various benefits through a number of chemical and/or biological mechanisms, pathways, etc (e.g., RNase H, RNAi, splicing modulation (exon skippmg(e.g., for DMD DMD subjects/samples), exon inclusion (e.g., for SMN2 in SMA subjects/samples)), etc). In some embodiments, provided technologies reduce levels, activities, expressions, etc. of a nucleic acid and/or a product thereof. For example, in some embodiments, provided technologies reduce levels and/or activities of target transcripts and/or products encoded thereby (without the intention to be limited by any particular theory, in some embodiments, via RNase H pathway). In some embodiments, provided technologies increase levels and/or activities of target transcripts and/or products encoded thereby (without the intention to be limited by any particular theory, in some embodiments, via exon skipping) A number of oligonucleotides comprising various types of modified internucleotidic linkages, including many comprising non-negatively charged intemuc!eotidic linkages (e.g., nOOl ), which have various base sequences and/or target various nucleic acids (e.g., transcripts of various genes) were prepared, and various useful properties, activities, and/or advantages were demonstrated. Certain such oligonucleotides, including many comprising non- negatively charged internucleotidic linkages, target transcripts of PNPLA3, C9orf72, SMN2, etc. and have demonstrated various activities and/or benefits. Example oligonucleotides comprising non-negatively charged internucleotidic linkages and targeting various genes, and compositions and uses thereof, include those described in WO 2018/223056, WO 2019/032607, PCT/US 18/55653, and WO 2019/032612, each of which is independently incorporated herein by reference.

[001087] In some embodiments, the present disclosure provides methods for modulating level of a transcript or a product encoded thereby in a system, comprising administering an effective amount of a provided oligonucleotide or a composition thereof. In some embodiments, the present disclosure provides methods for modulating level of a transcript or a product encoded thereby in a system, comprising contacting the transcript a provided oligonucleotide or a composition thereof. In some embodiments, a system is an in vitro system. In some embodiments, a system is a cell. In some embodiments, a system is a tissue. In some embodiments, a system is an organ. In some embodiments, a system is an organism. In some embodiments, a system is a subject. In some embodiments, a system is a human. In some embodiments, modulating level of a transcript decreases level of the transcript. In some embodiments, modulating level of a transcript increases level of the transcript.

[001088] In some embodiments, the present disclosure provides methods for preventing or treating a condition, disease, or disorder associated with a nucleic acid sequence or a product encoded thereby, comprising administering to a subject suffering therefrom or susceptible thereto an effective amount of a provided oligonucleotide or composition thereof, wherein the oligonucleotide or composition thereof modulate level of a transcript of the nucleic acid sequence. In some embodiments, a nucleic acid sequence is a gene in some embodiments, modulating level of a transcript decreases level of the transcript. In some embodiments, modulating level of a transcript increases level of the transcript.

[001089] In some embodiments, change of the level of a modulated transcript, e.g., through knock down, exon skipping, etc., is at least 1.1, 1.2, 1.3, 1.4, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 100, 200, 500, or 1000 fold.

[001090] In some embodiments, provided oligonucleotides and oligonucleotide compositions modulate splicing. In some embodiments, provided oligonucleotides and oligonucleotide compositions promote exon skipping, thereby produce a level of a transcript which has increased beneficial functions that the transcript prior to exon skipping. In some embodiments, a beneficial function is encoding a protein that has increased biological functions. In some embodiments, the present disclosure provides methods for modulating splicing, comprising administering to a splicing system a provided oligonucleotide or oligonucleotide composition, wherein splicing of at least one transcript is altered . In some embodiments, level of at least one splicing product is increased at least 1.1, 1.2, 1.3, 1.4, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 100, 200, 500, or 1000 fold. In some embodiments, the present disclosure provides methods for modulating DMD splicing, comprising administering to a splicing system a provided DMD oligonucleotide or composition thereof.

[001091] In some embodiments, the present disclosure provides methods for preventing or treating DMD, comprising administering to a subject susceptible thereto or suffering therefrom a pharmaceutical composition comprising an effective amount of a provided oligonucleotide or oligonucleotide composition.

[001092] In some embodiments, provided compositions and methods provide improved splicing patterns of transcripts compared to a reference pattern, which is a pattern from a reference condition selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof. An improvement can be an improvement of any desired biological functions. In some embodiments, for example, in DMD, an improvement is production of an mR A from which a dystrophin protein with improved biological activities is produced.

[001093] In some embodiments, particularly useful and effective are chirally controlled oligonucleotides and chirally controlled oligonucleotide compositions, wherein the oligonucleotides (or oligonucleotides of a plurality in chirally controlled oligonucleotide compositions) optionally comprises one or more non-negatively charged intemucleotidic linkages. Among other things, such oligonucleotides and oligonucleotide compositions can provide greatly improved effects, better delivery, lower toxicity, etc.

[001094] For Duchenne muscular dystrophy, example mutations and/or suitable DMD exons for skipping are widely known in the art, including but not limited to those described in US Patent No. 8,759,507, US Patent No. US 8,486,907, and reference cited therein.

[001095] In some embodiments, one or more skipped exons are selected from exon 2, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59 and 60. In some embodiments, exon 2 of DMD is skipped. In some embodiments, exon 29 of DMD is skipped. In some embodiments, exon 40 of DMD is skipped hi some embodiments, exon 41 of DMD is skipped. In some embodiments, exon 42 of DMD is skipped. In some embodiments, exon 43 of DMD is skipped. In some embodiments, exon 44 of DMD is skipped. In some embodiments, exon 45 of DMD is skipped. In some embodiments, exon 46 of DMD is skipped. In some embodiments, exon 47 of DMD is skipped. In some embodiments, exon 48 of DMD is skipped. In some embodiments, exon 49 of DMD is skipped hi some embodiments, exon 50 of DMD is skipped. In some embodiments, exon 51 of DMD is skipped. In some embodiments, exon 52 of DMD is skipped. In some embodiments, exon 53 of DMD is skipped. In some embodiments, exon 54 of DMD is skipped. In some embodiments, exon 50 of DMD is skipped. In some embodiments, exon 55 of DMD is skipped. In some embodiments, a skipped exon is any exon whose inclusion decreases a desired function of DMD. hi some embodiments, a skipped exon is any exon whose skipping increased a desired function of DMD.

|001096] In some embodiments, more than one exon of DMD is skipped. In some embodiments, two or more exons of DMD are skipped. In some embodiments, two or more adjacent exons of DMD are skipped.

[001097] In some embodiments, for exon skipping of DMD transcript, or for treatment of DMD, a sequence of a provided plurality of oligonucleotides comprises a DMD sequence list herein. In some embodiments, a sequence comprises one of SEQ ID Nos 1-30 of US Patent No. 8,759,507. In some embodiments, a sequence comprises one of SEQ ID Nos 1-211 of US Patent No. US 8,486,907. In some embodiments, for exon skipping of DMD transcript, or for treatment of DMD, a sequence of a provided plurality of oligonucleotides is a DMD sequence disclosed herein. In some embodiments, a sequence is one of SEQ ID Nos 1-30 of US Patent No. 8,759,507. In some embodiments, a sequence is one of SEQ ID Nos 1-211 of US Patent No. US 8,486,907. In some embodiments, a sequence is, comprises or comprises at least 15 consecuti ve bases of the sequence of any oligonucleotide list herein, e.g., Table Al. In some embodiments, a sequence is one described in Kemaiadewi, et al., Dual exon skipping in myostatin and dystrophin for Duchenne muscular dystrophy, BMC Med Genomics. 201 1 Apr 20;4:36. doi: 10.1186/1755-8794-4-36; or Malerba et al., Dual Myostatin and Dystrophin Exon Skipping by Morpholine Nucleic Acid Oligomers Conjugated to a Cell-penetrating Peptide Is a Promising Therapeutic Strategy for the Treatment of Duchenne Muscular Dystrophy, Mol Ther Nucleic Acids. 2012 Dec 18;l :e62. doi: 10.!038/mtna.2G 12.54.

[001098] In some embodiments, a provided oligonucleotide composition is administered at a dose and/or frequency lower than that of an otherwise comparable reference oligonucleotide composition with comparable effect in altering the splicing of a target transcript. In some embodiments, a stereocontrolled (chirally controlled) oligonucleotide composition is administered at a dose and/or frequency lower than that of an otheiwise comparable stereorandom reference oligonucleotide composition with comparable effect in altering the splicing of the target transcript. If desired, a provided composition can also be administered at higher dose/frequency due to its lower toxicities.

[001099] In some embodiments, provided oligonucleotides, compositions and methods have low toxicities, e.g., when compared to a reference composition. As widely known in the art, oligonucleotides can induce toxicities when administered to, e.g. , cells, tissues, organism, etc. hi some embodiments, oligonucleotides can induce undesired immune response. In some embodiments, oligonucleotide can induce complement activation. In some embodiments, oligonucleotides can induce activation of the alternative pathway of complement. In some embodiments, oligonucleotides can induce inflammation. Among other things, the complement system has strong cytolytic activity that can damages cells and should therefore be modulated to reduce potential injuries. In some embodiments, oligonucleotide- induced vascular injury is a recurrent challenge in the development of oligonucleotides for e.g., pharmaceutical use. In some embodiments, a primary source of inflammation when high doses of oligonucleotides are administered involves activation of the alternative complement cascade. In some embodiments, complement activation is a common challenge associated with phosphorothioate- eontaining oligonucleotides, and there is also a potential of some sequences of phosphorothioates to induce innate immune cell activation. In some embodiments, cytokine release is associated with administration of oligonucleotides. For example, in some embodiments, increases in interleukin-6 (IL-6) monocyte chemoattractant protein (MCP-1) and/or interleukin- 12 (IL-12) is observed. See, e.g., Frazier, Antisense Oligonucleotide Therapies: The Promise and the Challenges from a Toxicologic Pathologist’s Perspective. Toxicol Pathol., 43: 78-89, 2015; and Engelhard!, et al., Scientific and Regulatory Policy Committee Points-to-consider Paper: Drug -induced Vascular Injury' Associated with Nonsmall Molecule Therapeutics in Preclinical Development: Part 2. Antisense Oligonucleotides. Toxicol Pathol. 43: 935- 944, 2015.

[001100] Oligonucleotide compositions as provided herein can be used as agents for modulating a number of cellular processes and machineries, including but not limited to, transcription, translation, immune responses, epigenetics, etc. In addition, oligonucleotide compositions as provided herein can be used as reagents for research and/or diagnostic purposes. One of ordinary skill in the art will readily recognize that the present disclosure disclosure herein is not limited to particular use but is applicable to any situations where the use of synthetic oligonucleitides is desirable. Among other things, provided compositions are useful in a variety of therapeutic, diagnostic, agricultural, and/or research applications.

[001101] Various dosing regimens can be utilized to administer .provided chirally controlled oligonucleotide compositions, e.g., those described in in US 9695211, US 9605019, US 9598458, US 2013/0178612, US 20150211006, US 20170037399, WO 2017/015555, WO 2017/062862, WO 2017/160741, WO 2017/192664, WO 2017/192679, and/or WO 2017/210647, the dosing regimens of each of which is incorporated herein by reference.

[001102] In some embodiments, with their low toxicity , provided oligonucleotides and compositions can be administered in higher dosage and/or with higher frequency. In some embodiments, with their improved delivery (and other properties), provided compositions can be administered in lower dosages and/or with lower frequency to achieve biological effects, for example, clinical efficacy.

[001103] A single dose can contain various amounts of oligonucleotides. In some embodiments, a single dose can contain various amounts of a type of chirally controlled oligonucleotide, as desired suitable by the application in some embodiments, a single dose contains about 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300 or more (e.g., about 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000 or more) mg of a type of chirally controlled oligonucleotide. In some embodiments, a chirally controlled oligonucleotide is administered at a lower amount in a single dose, and/or in total dose, than a chirally uncontrolled oligonucleotide. In some embodiments, a chirally controlled oligonucleotide is administered at a lower amount in a single dose, and/or in total dose, than a chirally uncontrolled oligonucleotide due to improved efficacy. In some embodiments, a chirally controlled oligonucleotide is administered at a higher amount in a single dose, and/or in total dose, than a chirally uncontrolled oligonucleotide. In some embodiments, a chirally controlled oligonucleotide is administered at a higher amount in a single dose, and/or in total dose, than a chirally uncontrolled oligonucleotide due to improved safety.

001104] When used as therapeutics, a provided oligonucleotide or oligonucleotide composition described herein is administered as a pharmaceutical composition. In some embodiments, the pharmaceutical composition comprises a therapeutically effective amount of a provided oligonucleotides, or a pharmaceutically acceptable salt thereof, and at least one pharmaceutically acceptable inactive ingredient selected from pharmaceutically acceptable diluents, pharmaceutically acceptable excipients, and pharmaceutically acceptable carriers. In some embodiments, in provided compositions provided oligonucleotides may exist as salts, preferably pharmaceutically acceptable salts, e.g, sodium salts, ammonium salts, etc. In some embodiments, a salt of a provided oligonucleotide comprises two or more cations, for example, in some embodiments, up to the number of negatively charged acidic groups {e.g., phosphate, phosphorothioate, etc.) in an oligonucleotide. As appreciated by those skilled in the art, oligonucleotides described herein may be provided and/or utilized in a salt form, particularly a pharmaceutically acceptable salt form.

1001105] In some embodiments, the present disclosure provides salts of provided oligonucleotides, e.g., chirally controlled oligonucleotides, and pharmaceutical compositions thereof. In some embodiments, a salt is a pharmaceutically acceptable salt. In some embodiments, each hydrogen ion that may be donated to a base (e.g., under conditions of an aqueous solution, a pharmaceutical composition, etc.) is replaced by a non-H + cation. For example, in some embodiments, a pharmaceutically acceptable salt of an oligonucleotide is an all-metal ion salt, wherein each hydrogen ion (for example, of -OH, -SH, etc., acidic enough m water) of each internucieotidic linkage (e.g., a natural phosphate linkage, a phosphorothioate diester linkage, etc.) is replaced by a metal ion. In some embodiments, a provided salt is an all-sodium salt. In some embodiments, a provided pharmaceutically acceptable salt is an all -sodium salt. In some embodiments, a provided salt is an ail-sodium salt, wherein each internucieotidic linkage which is a natural phosphate linkage (acid form -Q-P(Q)(QH)-Q-), if any, exists as its sodium salt form (-0-P(0)(0Na)-0-), and each internucieotidic linkage which is a phosphorothioate diester linkage (phosphorothioate internucieotidic linkage; acid form -0-P(0)(SH)-0-), if any, exists as its sodium salt form (-0-P(0)(SNa)-0-).

[001106] In some embodiments, the pharmaceutical composition is formulated for intravenous injection, oral administration, buccal administration, inhalation, nasal administration, topical administration, ophthalmic administration or otic administration. In some embodiments, the pharmaceutical composition is a tablet, a pill, a capsule, a liquid, an inhalant, a nasal spray solution, a suppository, a suspension, a gel, a colloid, a dispersion, a suspension, a solution, an emulsion, an ointment, a lotion, an eye drop or an ear drop.

[001107] In some embodiments, the present disclosure provides a pharmaceutical composition comprising chirally controlled oligonucleotide, or composition thereof, in admixture with a pharmaceutically acceptable excipient. One of skill in tire art will recognize that tire pharmaceutical compositions include the pharmaceutically acceptable salts of the chirally controlled oligonucleotide, or composition thereof, described above.

[001108] A variety of supramolecuiar nanocarriers can be used to deliver nucleic acids. Example nanocarriers include, but are not limited to liposomes, cationic polymer complexes and various polymeric. Complexation of nucleic acids with various polycations is another approach for intracellular delivery; this includes use of PEGlyated polycations, polyethyleneamine (PEI) complexes, cationic block co-polymers, and dendrimers. Several cationic nanocarriers, including PEI and polyamidoamine dendrimers help to release contents from endosomes. Other approaches include use of polymeric nanoparticles, polymer micelles, quantum dots and lipoplexes. In some embodiments, an oligonucleotide is conjugated to another molecular

[001109] Additional nucleic acid deliver}' strategies are known in addition to the example delivery strategies described herein.

[001110] In therapeutic and/or diagnostic applications, the compounds of the disclosure can be fonnulated for a variety of modes of administration, including systemic and topical or localized administration. Techniques and formulations generally may be found in Remington, The Science and Practice of Pharmacy, (20th ed. 2000).

[001111] Provided oligonucleotides, and compositions thereof, are effective over a wide dosage range. For example, in the treatment of adult humans, dosages from about 0.01 to about 1000 mg, from about 0.5 to about 100 mg, from about 1 to about 50 mg per day, and from about 5 to about 100 mg per day are examples of dosages that may be used " lire exact dosage will depend upon the route of administration, the form in which the compound is administered, the subject to be treated, tire body weight of the subject to be treated, and the preference and experience of the attending physician.

[001112] Pharmaceutically acceptable salts are generally well known to those of ordinary skill in the art, and may include, by way of example but not limitation, acetate, benzene sulfonate, besylate, benzoate, bicarbonate, bitartrate, bromide, calcium edetate, camsylate, carbonate, citrate, edetate, edisylate, estoiate, esylate, fiimarate, giuceptate, gluconate, glutamate, glycollylarsanilate, hexy!resorcinate, hydrabamine, hydrobromide, hydrochloride, hydroxynaphthoate, iodide, isethionate, lactate, lactobionate, malate, maleate, mandelate, mesylate, mucate, napsylate, nitrate, pamoate (embonate), pantothenate, phosphate/diphosphate, polygalacturonate, salicylate, stearate, subacetate, succinate, sulfate, tannate, tartrate, or teoclate. Other pharmaceutically acceptable salts may be found in, for example, Remington, The Science and Practice of Pharmacy (20th ed. 2000). Preferred pharmaceutically acceptable salts include, for example, acetate, benzoate, bromide, carbonate, citrate, gluconate, hydrobromide, hydrochloride, maleate, mesylate, napsylate, parnoate (embonate), phosphate, salicylate, succinate, sulfate, or tartrate.

[001113] As appreciated by a person having oridinary skill in the art, oligonucleotides may be formulated as a number of salts for, e.g., pharmaceutical uses. In some embodiments, a salt is a metal cation salt and/or ammonium salt. In some embodiments, a salt is a metal cation salt of an oligonucleotide. In some embodiments, a salt is an ammonium salt of an oligonucleotide. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. In some embodiments, a salt is a sodium salt of an oligonucleotide. In some embodiments, pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed with oligonucleotides. As appreciated by a person having oridinary skill in the art, a salt of an oligonucleotide may contain more than one cations, e.g , sodium ions, as there may be more than one anions within an oligonucleotide.

[001114] Depending on the specific conditions being treated, such agents may be formulated into liquid or solid dosage forms and administered systemical!y or locally. The agents may be delivered, for example, in a timed- or sustained- low release form as is known to those skilled in the art. Techniques for formulation and administration may be found in Remington, The Science and Practice of Pharmacy (20th ed. 2000). Suitable routes may include oral, buccal, by inhalation spray, sublingual, rectal, transdermal, vaginal, transmucosal, nasal or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intra- articullar, intra-stemal, intra-synovial, intra-hepatic, intralesional, intracranial, intraperitoneal, intranasal, or intraocular injections or other modes of delivery.

[001115] For injection, the agents of the disclosure may be formulated and diluted in aqueous solutions, such as m physiologically compatible buffers such as Hank's solution, Ringer's solution, or physiological saline buffer. For such transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.

[001116] Use of pharmaceutically acceptable inert carriers to formulate the compounds herein disclosed for the practice of the disclosure into dosages suitable for systemic administration is within the scope of the disclosure. With proper choice of carrier and suitable manufacturing practice, the compositions of the present disclosure, in particular, those formulated as solutions, may be administered parenterally, such as by intravenous injection.

[001117] Compounds, e.g., oligonucleotides, can be formulated readily using pharmaceutically acceptable carriers well known in the art into dosages suitable for oral administration. Such carriers enable the compounds of the disclosure to be formulated as tablets, pills, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a subject (e.g., patient) to be treated. [001118] For nasal or inhalation delivery, tire agents of tire disclosure may also be formulated by methods known to those of skill in the art, and may include, for example, but not limited to, examples of solubilizing, diluting, or dispersing substances such as, saline, preservatives, such as benzyl alcohol, absorption promoters, and fluorocarbons.

[001119] In certain embodiments, oligonucleotides and compositions are delivered to the CNS. In certain embodiments, oligonucleotides and compositions are delivered to the cerebrospinal fluid. In certain embodiments, oligonucleotides and compositions are administered to the brain parenchyma. In certain embodiments, oligonucleotides and compositions are delivered to an animal/subject by intrathecal administration, or intracerebroventricular administration. Broad distribution of oligonucleotides and compositions, described herein, within the central nervous system may be achieved with imtraparenchymai administration, intrathecal administration, or intracerebroventricular administration.

[001120] In certain embodiments, parenteral administration is by injection, by, e.g., a syringe, a pump, etc. In certain embodiments, the injection is a bolus injection. In certain embodiments, the injection is administered directly to a tissue, such as striatum, caudate, cortex, hippocampus and cerebellum.

[001121] In certain embodiments, methods of specifically localizing a pharmaceutical agent, such as by bolus injection, decreases median effective concentration (EC50) by a factor of 20, 25, 30, 35, 40, 45 or 50. In certain embodiments, the targeted tissue is brain tissue. In certain embodiments the targeted tissue is striatal tissue. In certain embodiments, decreasing EC50 is desirable because it reduces the dose required to achieve a pharmacological result in a patient in need thereof.

1001122] In certain embodiments, an oligonucleotide is delivered by injection or infusion once every month, every two months, every 90 days, every 3 months, every' 6 months, twice a year or once a year.

[001123] Pharmaceutical compositions suitable for use in the present disclosure include compositions wherein the active ingredients are contained in an effective amount to achieve its intended purpose. Determination of the effective amounts is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein.

[001124] In addition to the active ingredients, these pharmaceutical compositions may contain suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of an active compound into preparations which can be used pharmaceutically. The preparations formulated for oral administration may be in the form of tablets, dragees, capsules, or solutions.

j 001125] Pharmaceutical preparations for oral use can be obtained by combining an active compound with solid excipients, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol: cellulose preparations, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, grim tragacanth, methyl cellulose, hydroxypropyl methyl -cellulose, sodium carboxymethyl-cellulose (CMC), and/or polyvinylpyrrolidone (PVP: povidone). If desired, disintegrating agents may be added, such as the cross- linked polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.

[001126] Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol (PEG), and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dye-stuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.

[001127] Pharmaceutical preparations that can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin, and a plasticizer, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, an active compound may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols (PEGs). In addition, stabilizers may be added.

[001128] In some embodiments, any DMD oligonucleotide, or combination thereof, described herein, or any composition comprising a DMD oligonucleotide described herein, can he combined with any pharmaceutical preparation described herein or known in the art.

Certain Embodiments of Conjugates and Additional Chemical Moieties

[001129] In some embodiments, provided oligonucleotides comprise one or more additional chemical moieties (e.g., other than typical moieties of nudeobases, sugars and/or intemucleotidic linkages, etc.), optionally through a linker. In some embodiments, a chemical moiety is a lipid moiety. In some embodiments, a chemical moiety is a carbohydrate moiety. In some embodiments, a chemical moiety is a targeting moiety. In some embodiments, a chemical moiety is a moiety of a ligand. In some embodiments, a chemical moiety can increase delivery of oligonucleotides to certain organelles, cells, tissues, organs, and/or organisms. In some embodiments, a chemical moiety enhances one or more of desired properties and/or activities. Certain example chemical moieties utilized in certain oligonucleotides are presented in the Tables (e.g., various Mod in Table Al). In some embodiments, a chemical moiety comprises one or more sugar moieties or derivatives thereof, e.g., glucose, mannose, etc. In some embodiments, a chemical moiety is or comprises a lipid moiety. In some embodiments, a chemical moiety is or comprises a vitamin E moiety. In some embodimen