ALTERMAN JULIA (US)
CONROY FAITH (US)
PFISTER EDITH (US)
ARONIN NEIL (US)
YAMADA KEN (US)
US20070259827A1 | 2007-11-08 | |||
US20160319278A1 | 2016-11-03 |
CLAIMS 1. A nucleic acid comprising: (a) a 5’ end and a 3’ end; (b) a seed region that is complementary to a region of a gene comprising an allelic polymorphism; (c) a single nucleotide polymorphism (SNP) position nucleotide at a position within the seed region, wherein the SNP position nucleotide is complementary to the allelic polymorphism; (d) a mismatch (MM) position nucleotide that is a mismatch with a nucleotide in the gene; and (e) at least one modified nucleotide (X) on either side of the SNP position nucleotide, wherein each X is located within four, three, or two nucleotides from the SNP position nucleotide. 2. A nucleic acid comprising: (a) a 5’ end and a 3’ end; (b) a seed region that is complementary to a region of a gene comprising an allelic polymorphism; (c) a single nucleotide polymorphism (SNP) position nucleotide at a position within the seed region, wherein the SNP position nucleotide is complementary to the allelic polymorphism; (d) a mismatch (MM) position nucleotide that is a mismatch with a nucleotide in the gene; and (e) at least one modified nucleotide (Y) on either side of the MM position nucleotide, wherein each Y is located within four, three or two nucleotides from the MM position nucleotide. 3. The nucleic acid of claim 1, wherein X comprises a sugar modification selected from the group consisting of 2’-O-methyl (2’-OMe), 2’-fluoro (2’-F), 2’-ribo, 2’-GHR[\ULER^^^ƍ-F-^ƍ- thioarabino (2’-F-ANA), 2’-O-(2-methoxyethyl) (2’-MOE), 4’-S-RNA, locked nucleic acid (LNA), 4’-S-F-ANA, 2’-O-allyl, 2’-O-ethylamine, 2’-O-cyanoethyl-RNA (CNet-RNA), tricyclo-DNA, cyclohexenyl nucleic acid (CeNA), arabino nucleic acid (ANA), and hexitol nucleic acid (HNA). 4. The nucleic acid of claim 2, wherein Y comprises a sugar modification selected from the group consisting of 2’-OMe, 2’-F, 2’-ribo, 2’-deoxyribo, 2’-F-ANA, 2’-MOE, 4’-S-RNA, LNA, 4’-S-F-ANA, 2’-O-allyl, 2’-O-ethylamine, CNet-RNA, tricyclo-DNA, CeNA, ANA, and HNA. 5. The nucleic acid of claim 1, wherein an X is positioned immediately 5’ to the SNP position nucleotide or immediately 3’ to the SNP position nucleotide. 6. The nucleic acid of claim 1, wherein an X is positioned immediately 5’ to the SNP position nucleotide and immediately 3’ to the SNP position nucleotide. 7. The nucleic acid of claim 2, wherein a Y is positioned immediately 5’ to the MM position nucleotide or immediately 3’ to the MM position nucleotide. 8. The nucleic acid of claim 2, wherein a Y is positioned immediately 5’ to the MM position nucleotide and immediately 3’ to the MM position nucleotide. 9. The nucleic acid of claim 1 or 2, wherein the SNP position nucleotide is present from position 2 to position 6 from the 5’ end. 10. The nucleic acid of claim 1 or 2, wherein the MM position nucleotide is located 2-11 nucleotides from the SNP position nucleotide. 11. The nucleic acid of claim 1 or 2, wherein the MM position nucleotide is located 2-6 nucleotides from the SNP position nucleotide. 12. A nucleic acid comprising: (a) a 5’ end and a 3’ end; (b) a seed region that is complementary to a region of a gene comprising an allelic polymorphism; (c) a single nucleotide polymorphism (SNP) position nucleotide at a position within the seed region, wherein the SNP position nucleotide is complementary to the allelic polymorphism; (d) a mismatch (MM) position nucleotide that is a mismatch with a nucleotide in the gene; (e) at least one modified nucleotide (X) on either side of the SNP position nucleotide, wherein each X is located within four, three or two nucleotides from the SNP position nucleotide; and (f) at least one modified nucleotide (Y) on either side of the MM position nucleotide, wherein each Y is located within four, three or two nucleotides from the MM position nucleotide. 13. The nucleic acid of claim 12, wherein X comprises a sugar modification selected from the group consisting of 2’-OMe, 2’-F, 2’-ribo, 2’-deoxyribo, 2’-F-ANA, 2’-MOE, 4’-S-RNA, LNA, 4’-S-F-ANA, 2’-O-allyl, 2’-O-ethylamine, CNet-RNA, tricyclo-DNA, CeNA, ANA, and HNA. 14. The nucleic acid of claim 12, wherein Y comprises a sugar modification selected from the group consisting of 2’-OMe, 2’-F, 2’-ribo, 2’-deoxyribo, 2’-F-ANA, 2’-MOE, 4’-S-RNA, LNA, 4’-S-F-ANA, 2’-O-allyl, 2’-O-ethylamine, CNet-RNA, tricyclo-DNA, CeNA, ANA, and HNA. 15. The nucleic acid of claim 12, wherein an X is positioned immediately 5’ to the SNP position nucleotide or immediately 3’ to the SNP position nucleotide. 16. The nucleic acid of claim 12, wherein an X is positioned immediately 5’ to the SNP position nucleotide and immediately 3’ to the SNP position nucleotide. 17. The nucleic acid of claim 12, wherein a Y is positioned immediately 5’ to the MM position nucleotide or immediately 3’ to the MM position nucleotide. 18. The nucleic acid of claim 12, wherein a Y is positioned immediately 5’ to the MM position nucleotide or immediately 3’ to the MM position nucleotide. 19. The nucleic acid of claim 12, wherein the SNP position nucleotide is present from position 2 to position 6 from the 5’ end. 20. The nucleic acid of claim 12, wherein the MM position nucleotide is located 2-11 nucleotides from the SNP position nucleotide. 21. The nucleic acid of claim 12, wherein the MM position nucleotide is located 2-6 nucleotides from the SNP position nucleotide. 22. The nucleic acid of claim 12, wherein X and Y comprise identical nucleotide modifications. 23. The nucleic acid of claim 12, wherein X and Y comprise different nucleotide modifications. 24. A nucleic acid comprising: (a) a 5’ end and a 3’ end; (b) a seed region that is complementary to a region of a gene comprising an allelic polymorphism; (c) a single nucleotide polymorphism (SNP) position nucleotide that is complementary to the allelic polymorphism; (d) a mismatch (MM) position nucleotide that is a mismatch with a nucleotide in the gene; (e) at least one 2’-fluoro-ribonucleotide on either side of the SNP position nucleotide, wherein each 2’-fluoro-ribonucleotide is located within four, three or two nucleotides from the SNP position nucleotide; and (f) at least one 2’-methoxy-ribonucleotide on either side of the MM position nucleotide, wherein each 2’-methoxy-ribonucleotide is located within four, three or two nucleotides from the MM position nucleotide. 25. The nucleic acid of claim 24, wherein a 2’-fluoro-ribonucleotide is positioned immediately 5’ to the SNP position nucleotide or a 2’-fluoro-ribonucleotide is positioned immediately 3’ to the SNP position nucleotide. 26. The nucleic acid of claim 24, wherein a 2’-fluoro-ribonucleotide is positioned immediately 5’ to the SNP position nucleotide and a 2’-fluoro-ribonucleotide is positioned immediately 3’ to the SNP position nucleotide. 27. The nucleic acid of claim 24, wherein a 2’-methoxy-ribonucleotide is positioned immediately 5’ to the MM position nucleotide or a 2’-methoxy-ribonucleotide is positioned immediately 3’ to the MM position nucleotide. 28. The nucleic acid of claim 24, wherein a 2’-methoxy-ribonucleotide is positioned immediately 5’ to the MM position nucleotide and a 2’-methoxy-ribonucleotide is positioned immediately 3’ to the MM position nucleotide. 29. The nucleic acid of claim 24, wherein the SNP position nucleotide is present in a seed region, and wherein the MM position nucleotide is located 2-11 nucleotides from the SNP position nucleotide. 30. The nucleic acid of claim 29, wherein the SNP position nucleotide is present from position 2 to position 6 from the 5’ end, and wherein the MM position nucleotide is located 2- 6 nucleotides from the SNP position nucleotide. 31. The nucleic acid of claim 24, comprising three, four, five or six 2’-fluoro- ribonucleotides. 32. The nucleic acid of claim 24, comprising three, four, five or six 2’-methoxy- ribonucleotides. 33. A nucleic acid comprising: (a) a 5’ end and a 3’ end; (b) a seed region that is complementary to a region of a gene comprising an allelic polymorphism; (c) a single nucleotide polymorphism (SNP) position nucleotide that is complementary to the allelic polymorphism; (d) a mismatch (MM) position nucleotide that is a mismatch with a nucleotide in the gene; (e) at least three 2’-fluoro-ribonucleotides located within four, three or two nucleotides from the SNP position nucleotide; and (f) at least three 2’-methoxy-ribonucleotides located within four, three or two nucleotides from the MM position nucleotide. 34. The nucleic acid of claim 33, wherein a 2’-fluoro-ribonucleotide is positioned immediately 5’ to the SNP position nucleotide or a 2’-fluoro-ribonucleotide is positioned immediately 3’ to the SNP position nucleotide. 35. The nucleic acid of claim 33, wherein a 2’-fluoro-ribonucleotide is positioned immediately 5’ to the SNP position nucleotide and a 2’-fluoro-ribonucleotide is positioned immediately 3’ to the SNP position nucleotide. 36. The nucleic acid of claim 33, wherein a 2’-methoxy-ribonucleotide is positioned immediately 5’ to the MM position nucleotide or a 2’-methoxy-ribonucleotide is positioned immediately 3’ to the MM position nucleotide. 37. The nucleic acid of claim 33, wherein a 2’-methoxy-ribonucleotide is positioned immediately 5’ to the MM position nucleotide and a 2’-methoxy-ribonucleotide is positioned immediately 3’ to the MM position nucleotide. 38. The nucleic acid of claim 33, wherein the SNP position nucleotide is present in a seed region, and wherein the MM position nucleotide is located 2-11 nucleotides from the SNP position nucleotide. 39. The nucleic acid of claim 38, wherein the SNP position nucleotide is present from position 2 to position 6 from the 5’ end, and wherein the MM position nucleotide is located 2- 6 nucleotides from the SNP position nucleotide. 40. An siRNA molecule comprising a sense strand having complementarity to a target gene and an antisense strand having complementarity to the sense strand, wherein the antisense strand comprises the nucleic acid of any one of claims 1-39. 41. The siRNA molecule of claim 40, wherein the sense strand has a length of from 13 nucleotides or nucleotide analogs to 17 nucleotides or nucleotide analogs. 42. The siRNA molecule of claim 40 or 41, wherein the antisense strand has a length of from 18 nucleotides or nucleotide analogs to 22 nucleotides or nucleotide analogs. 43. The siRNA molecule of any one of claims 40-42, wherein the sense strand has a length of 15 nucleotides or nucleotide analogs and the antisense strand has a length of 20 nucleotides or nucleotide analogs. 44. The siRNA molecule of any one of claims 40-42, wherein the sense strand has a length of 16 nucleotides or nucleotide analogs and the antisense strand has a length of 20 nucleotides or nucleotide analogs. 45. A branched oligonucleotide comprising two or more siRNA molecules covalently bound to one another, wherein each siRNA molecule is, independently, an siRNA molecule of any one of claims 40-44. 46. The branched oligonucleotide of claim 45, wherein the branched oligonucleotide comprises two siRNA molecules covalently bound to one another. 47. The branched oligonucleotide of claim 45 or 46, wherein the siRNA molecules are covalently bound to one another by way of a linker. 48. A double-stranded nucleic acid comprising: (a) a first strand of nucleotides comprising: (i) a 5’ end and a 3’ end; (ii) a seed region that is complementary to a region of a gene comprising an allelic polymorphism; (iii) a single nucleotide polymorphism (SNP) position nucleotide at a position within the seed region, wherein the SNP position nucleotide is complementary to the allelic polymorphism; (iv) a mismatch (MM) position nucleotide that is not complementary to a nucleotide in the gene; and (v) at least one modified nucleotide located on either side of the SNP position nucleotide, on either side of the MM position nucleotide, or a combination thereof; wherein each modified nucleotide is located within four, three, or two nucleotides from the SNP position nucleotide or from the MM position nucleotide, respectively; (b) a second strand of nucleotides that is complementary to the first strand of nucleotides. 49. The double-stranded nucleic acid of claim 48, wherein the modified nucleotide comprises a modification selected from the group consisting of 2’ -O-methyl (2’-OMe), 2’- fluoro (2’-F), 2’-ribo, 2’-deoxyribo, 2'-F-4'-thioarabino (2’-F-ANA), 2’-O-(2-methoxyethyl) (2’-MOE), 4’-S-RNA, locked nucleic acid (LNA), 4’-S-F-ANA, 2’-O-allyl, 2’-O-ethylamine, 2’-O-cyanoethyl-RNA (CNet-RNA), tricyclo-DNA, cyclohexenyl nucleic acid (CeNA), arabino nucleic acid (ANA), hexitol nucleic acid (HNA), and a combination thereof. 50. The nucleic acid of claim 48, wherein the modified nucleotide is positioned immediately 5’ to the SNP position nucleotide, immediately 3’ to the SNP position nucleotide, or a mixture thereof. 51. The nucleic acid of claim 48, wherein the modified nucleotide is positioned immediately 5’ to the MM position nucleotide, immediately 3’ to the MM position nucleotide., or a mixture thereof. 52. The nucleic acid of claim 48, wherein the SNP position nucleotide is present from position 2 to position 6 from the 5’ end of the first strand of nucleotides. 53. The nucleic acid of claim 48, wherein the MM position nucleotide is located 2-11 nucleotides from the SNP position nucleotide of the first strand of nucleotides. 54. The nucleic acid of claim 48, wherein the MM position nucleotide is located 2-6 nucleotides from the SNP position nucleotide of the first strand of nucleotides. 55. The nucleic acid of claim 48, wherein the modified nucleotides comprise identical nucleotide modifications, different nucleotide modifications, or a mixture thereof. 56. The nucleic acid of claim 48, wherein the first strand has a length of from 13-17 nucleotides. 57. The nucleic acid of claim 48, wherein the second strand has a length of from 18-22 nucleotides. 58. The nucleic acid of claim 48, wherein the first strand has a length of 15 nucleotides and the second strand has a length of 20 nucleotides. 59. The nucleic acid of claim 48, wherein the first strand has a length of 16 nucleotides and the second strand has a length of 20 nucleotides. 60. The nucleic acid of claim 48, wherein the first strand has 3-7 more nucleotides than the second strand. 61. A branched oligonucleotide comprising two or more siRNA molecules covalently bound to one another, wherein each siRNA molecule comprises a double-stranded nucleic acid comprising: (a) a first strand of nucleotides comprising: (i) a 5’ end, a 3’ end; (ii) a seed region that is complementary to a region of a gene comprising an allelic polymorphism; (iii) a single nucleotide polymorphism (SNP) position nucleotide at a position within the seed region, wherein the SNP position nucleotide is complementary to the allelic polymorphism; (iv) a mismatch (MM) position nucleotide that not complementary to a nucleotide in the gene; and (v) at least one modified nucleotide located on either side of the SNP position nucleotide, on either side of the MM position nucleotide, or a combination thereof; wherein each modified nucleotide is located within four, three, or two nucleotides from the SNP position nucleotide or from the MM position nucleotide, respectively; (b) a second strand of nucleotides that is complementary to the first strand of nucleotides. 62. The branched oligonucleotide of claim 61, wherein the branched oligonucleotide comprises two siRNA molecules covalently bound to one another. 63. The branched oligonucleotide of claim 61, wherein the siRNA molecules are covalently bound to one another by way of a linker. |
[0219] In another embodiment, the hydrophobic moiety is an omega-6 fatty acid. Non-limiting examples of omega-6 fatty acids include, but are not limited to: linoleic acid, gamma-linolenic acid (GLA), eicosadienoic acid, dihomo-gamma-linolenic acid (DGLA), arachidonic acid (AA), docosadienoic acid, adrenic acid, docosapentaenoic acid (osbond acid), tetracosatetraenoic acid, and tetracosapentaenoic acid.
[0220] In another embodiment, the hydrophobic moiety is an omega-9 fatty acid. Non-limiting examples of omega-9 fatty acids include, but are not limited to: oleic acid, eicosenoic acid, Mead acid, erucic acid, and nervonic acid.
[0221] In another embodiment, the hydrophobic moiety is a conjugated linolenic acid. Non- limiting examples of conjugated linolenic acids include, but are not limited to: a-calendic acid, β-calendic acid, jacaric acid, a-eleostearic acid, β-eleostearic acid, catalpic acid, and punicic acid.
[0222] In another embodiment, the hydrophobic moiety is a saturated fatty acid. Non-limiting examples of saturated fatty acids include, but are not limited to: caprylic acid, capri c acid, docosanoic acid, lauric acid, myristic acid, palmitic acid, stearic acid, arachidic acid, behenic acid, lignoceric acid, and cerotic acid.
[0223] In another embodiment, the hydrophobic moiety is an acid selected from the group consisting of: rumelenic acid, a-parinaric acid, β-parinaric acid, bosseopentaenoic acid, pinolenic acid, and podocarpic acid.
[0224] In another embodiment, the hydrophobic moiety is selected from the group consisting of: docosanoic acid (DCA), docosahexaenoic acid (DHA), and eicosapentaenoic acid (EPA). In a particular embodiment, the hydrophobic moiety is docosanoic acid (DCA) In another particular embodiment, the hydrophobic moiety is DHA. In another particular embodiment, the hydrophobic moiety is EPA.
[0225] In another embodiment, the hydrophobic moiety is a secosteroid. In a particular embodiment, the hydrophobic moiety is calciferol. In another embodiment, the hydrophobic moiety is a steroid other than cholesterol.
[0226] In a particular embodiment, the hydrophobic moiety is not cholesterol. [0227] In another embodiment, the hydrophobic moiety is an alkyl chain, a vitamin, a peptide, or a bioactive conjugate, including but not limited to: glycosphingolipids, polyunsaturated fatty acids, secosteroids, steroid hormones, or sterol lipids. [0228] In an embodiment, a double-stranded RNA provided herein comprises one or more chemically-modified nucleotides. In a particular embodiment, the double-stranded RNA comprises alternating 2’-methoxy-nucleotides and 2’-fluoro-nucleotides. In another particular embodiment, one or more nucleotides of the double-stranded RNA are connected to adjacent nucleotides via phosphorothioate linkages. In certain embodiments of the dsRNAs disclosed herein, the mismatch nucleotide and the nucleotide(s) adjacent to the mismatch nucleotide are 2’-methoxy-ribonucleotides. [0229] In another particular embodiment, the nucleotides at positions 1 and 2 from the 3’ end of the double-stranded RNAs provided herein are connected to adjacent nucleotides via phosphorothioate linkages. In yet another particular embodiment, the nucleotides at positions 1 and 2 from the 3’ end of the double-stranded RNAs and the nucleotides at positions 1 and 2 from the 5’ end of the double-stranded RNAs are connected to adjacent nucleotides via phosphorothioate linkages. [0230] In one embodiment of a double-stranded RNA, the first oligonucleotide comprises at least 16 contiguous nucleotides, a 5’ end, a 3’ end, and has complementarity to a target, wherein: (1) the first oligonucleotide comprises alternating 2’-methoxy-nucleotides and 2’- fluoro-nucleotides; (2) the nucleotides at positions 2 and 14 from the 5’ end are not 2’-methoxy- nucleotides; (3) the nucleotides are connected via phosphodiester or phosphorothioate linkages; and (4) the nucleotides at positions 1-6 from the 3’ end, or positions 1-7 from the 3’ end, are connected to adjacent nucleotides via phosphorothioate linkages. 7) Advanced Stabilization Pattern [0231] In one embodiment of the double-stranded RNAs provided herein: (1) the first oligonucleotide comprises alternating 2’-methoxy-ribonucleotides and 2’- fluoro-ribonucleotides, wherein each nucleotide is a 2’-methoxy-ribonucleotide or a 2’-fluoro- ribonucleotide; and the nucleotides at positions 2 and 14 from the 5’ end of the first oligonucleotide are not 2’-methoxy-ribonucleotides; (2) the second oligonucleotide comprises alternating 2’-methoxy-ribonucleotides and 2’-fluoro-ribonucleotides, wherein each nucleotide is a 2’-methoxy-ribonucleotide or a 2’- fluoro-ribonucleotide; and the nucleotides at positions 2 and 14 from the 5’ end of the second oligonucleotide are 2’-methoxy-ribonucleotides; (3) the nucleotides of the first oligonucleotide are connected to adjacent nucleotides via phosphodiester or phosphorothioate linkages, wherein the nucleotides at positions 1-6 from the 3’ end, or positions 1-7 from the 3’ end are connected to adjacent nucleotides via phosphorothioate linkages; and (4) the nucleotides of the second oligonucleotide are connected to adjacent nucleotides via phosphodiester or phosphorothioate linkages, wherein the nucleotides at positions 1 and 2 from the 3’ end are connected to adjacent nucleotides via phosphorothioate linkages. [0232] In one embodiment of the double-stranded RNAs, the first oligonucleotide has 3-7 more ribonucleotides than the second oligonucleotide. [0233] In one embodiment, the double-stranded RNA comprises 11-16 base pair duplexes, wherein the nucleotides of each base pair duplex have different chemical modifications (e.g., one nucleotide has a 2’-fluoro modification and the other nucleotide has a 2’-methoxy). [0234] In one embodiment of the double-stranded RNAs, the first oligonucleotide has 3-7 more ribonucleotides than the second oligonucleotide. In another embodiment. [0235] In one embodiment, the first oligonucleotide is the antisense strand and the second oligonucleotide is the sense strand. See PCT Pub. No. WO 2016/161388, which is incorporated herein by reference. [0236] In one embodiment, the first or second oligonucleotide comprises one or more VP intersubunit modifications having the following formula: . 8) Branched Oligonucleotides [0237] Two or more RNA silencing agents as disclosed above, for example oligonucleotide constructs such as siRNAs, may be connected to one another by one or more moieties independently selected from a linker, a spacer and a branching point, forming a branched oligonucleotide containing two or more RNA silencing agents. FIG. 31 illustrates an exemplary di-siRNA di-branched scaffolding for delivering two siRNAs. In representative embodiments, the nucleic acids of the branched oligonucleotide each comprise an antisense strand (or portions thereof), wherein the antisense strand has sufficient complementary to a heterozygous single nucleotide polymorphism to mediate an RNA-mediated silencing mechanism (e.g. RNAi). In other embodiments, there is provided a second type of branched oligonucleotides featuring nucleic acids that comprise a sense strand (or portions thereof) for silencing antisense transcripts, where the sense strand has sufficient complementarity to an antisense transcript to mediate an RNA-mediated silencing mechanism. In further embodiments, there is provided a third type of branched oligonucleotides including nucleic acids of both types, that is, a nucleic acid comprising an antisense strand (or portions thereof) and an oligonucleotide comprising a sense strand (or portions thereof). [0238] In exemplary embodiments, the branched oligonucleotides may have two to eight RNA silencing agents attached through a linker. The linker may be hydrophobic. In a particular embodiment, branched oligonucleotides of the present application have two to three oligonucleotides. In one embodiment, the oligonucleotides independently have substantial chemical stabilization (e.g., at least 40% of the constituent bases are chemically-modified). In a particular embodiment, the oligonucleotides have full chemical stabilization (i.e., all of the constituent bases are chemically-modified). In some embodiments, branched oligonucleotides comprise one or more single-stranded phosphorothioated tails, each independently having two to twenty nucleotides. In a particular embodiment, each single-stranded tail has eight to ten nucleotides. [0239] In certain embodiments, branched oligonucleotides are characterized by three properties: (1) a branched structure, (2) full metabolic stabilization, and (3) the presence of a single-stranded tail comprising phosphorothioate linkers. In a specific embodiment, branched oligonucleotides have 2 or 3 branches. It is believed that the increased overall size of the branched structures promotes increased uptake. Also, without being bound by a particular theory of activity, multiple adjacent branches (e.g., 2 or 3) are believed to allow each branch to act cooperatively and thus dramatically enhance rates of internalization, trafficking and release. [0240] Branched oligonucleotides are provided in various structurally diverse embodiments. As shown in FIG. 36, for example, in some embodiments nucleic acids attached at the branching points are single stranded and consist of miRNA inhibitors, gapmers, mixmers, SSOs, PMOs, or PNAs. These single strands can be attached at their 3’ or 5’ end. Combinations of siRNA and single stranded oligonucleotides could also be used for dual function. In another embodiment, short nucleic acids complementary to the gapmers, mixmers, miRNA inhibitors, SSOs, PMOs, and PNAs are used to carry these active single-stranded nucleic acids and enhance distribution and cellular internalization. The short duplex region has a low melting temperature (T m ~37 °C) for fast dissociation upon internalization of the branched structure into the cell. [0241] As shown in FIG. 37, Di-siRNA branched oligonucleotides may comprise chemically diverse conjugates. Conjugated bioactive ligands may be used to enhance cellular specificity and to promote membrane association, internalization, and serum protein binding. Examples of bioactive moieties to be used for conjugation include DHAg2, DHA, GalNAc, and cholesterol. These moieties can be attached to Di-siRNA either through the connecting linker or spacer, or added via an additional linker or spacer attached to another free siRNA end. [0242] The presence of a branched structure improves the level of tissue retention in the brain more than 100-fold compared to non-branched compounds of identical chemical composition, suggesting a new mechanism of cellular retention and distribution. Branched oligonucleotides have unexpectedly uniform distribution throughout the spinal cord and brain. Moreover, branched oligonucleotides exhibit unexpectedly efficient systemic delivery to a variety of tissues, and very high levels of tissue accumulation. [0243] Branched oligonucleotides comprise a variety of therapeutic nucleic acids, including ASOs, miRNAs, miRNA inhibitors, splice switching, PMOs, PNAs. In some embodiments, branched oligonucleotides further comprise conjugated hydrophobic moieties and exhibit unprecedented silencing and efficacy in vitro and in vivo. Linkers [0244] In an embodiment of the branched oligonucleotide, each linker is independently selected from an ethylene glycol chain, an alkyl chain, a peptide, RNA, DNA, a phosphate, a phosphonate, a phosphoramidate, an ester, an amide, a triazole, and combinations thereof; wherein any carbon or oxygen atom of the linker is optionally replaced with a nitrogen atom, bears a hydroxyl substituent, or bears an oxo substituent. In one embodiment, each linker is an ethylene glycol chain. In another embodiment, each linker is an alkyl chain. In another embodiment, each linker is a peptide. In another embodiment, each linker is RNA. In another embodiment, each linker is DNA. In another embodiment, each linker is a phosphate. In another embodiment, each linker is a phosphonate. In another embodiment, each linker is a phosphoramidate. In another embodiment, each linker is an ester. In another embodiment, each linker is an amide. In another embodiment, each linker is a triazole. In another embodiment, each linker is a structure selected from the formulas of FIG.37. 9) Compound of Formula (I) [0245] In another aspect, provided herein is a branched oligonucleotide compound of formula (I): [0246] wherein L is selected from an ethylene glycol chain, an alkyl chain, a peptide, RNA, DNA, a phosphate, a phosphonate, a phosphoramidate, an ester, an amide, a triazole, and combinations thereof, wherein formula (I) optionally further comprises one or more branch point B, and one or more spacer S; wherein B is independently for each occurrence a polyvalent organic species or derivative thereof; S is independently for each occurrence selected from an ethylene glycol chain, an alkyl chain, a peptide, RNA, DNA, a phosphate, a phosphonate, a phosphoramidate, an ester, an amide, a triazole, and combinations thereof; N is an RNA duplex comprising a sense strand and an antisense strand, wherein the antisense strand comprises a region of complementarity which is substantially complementary to a region of a gene comprising an allelic polymorphism, wherein the antisense strand comprises: a single nucleotide polymorphism (SNP) position nucleotide at a position 2 to 7 from the 5’ end that is complementary to the allelic polymorphism; and a mismatch (MM) position nucleotide located 2-11 nucleotides from the SNP position nucleotide that is a mismatch with a nucleotide in the gene. In exemplary embodiments, the SNP position nucleotide is at a position 2, 4 or 6 from the 5’ end and the mismatch (MM) position nucleotide is located 2-6 nucleotides from the SNP position nucleotide. [0247] The sense strand and antisense strand each independently comprise one or more chemical modifications; and n is 2, 3, 4, 5, 6, 7 or 8. [0248] In an embodiment, the compound of formula (I) has a structure selected from formulas (I-1)-(I-9) of Table 1. Table 1 [0249] In one embodiment, the compound of formula (I) is formula (I-1). In another embodiment, the compound of formula (I) is formula (I-2). In another embodiment, the compound of formula (I) is formula (I-3). In another embodiment, the compound of formula (I) is formula (I-4). In another embodiment, the compound of formula (I) is formula (I-5). In another embodiment, the compound of formula (I) is formula (I-6). In another embodiment, the compound of formula (I) is formula (I-7). In another embodiment, the compound of formula (I) is formula (I-8). In another embodiment, the compound of formula (I) is formula (I-9). [0250] In an embodiment of the compound of formula (I), each linker is independently selected from an ethylene glycol chain, an alkyl chain, a peptide, RNA, DNA, a phosphate, a phosphonate, a phosphoramidate, an ester, an amide, a triazole, and combinations thereof; wherein any carbon or oxygen atom of the linker is optionally replaced with a nitrogen atom, bears a hydroxyl substituent, or bears an oxo substituent. In one embodiment of the compound of formula (I), each linker is an ethylene glycol chain. In another embodiment, each linker is an alkyl chain. In another embodiment of the compound of formula (I), each linker is a peptide. In another embodiment of the compound of formula (I), each linker is RNA. In another embodiment of the compound of formula (I), each linker is DNA. In another embodiment of the compound of formula (I), each linker is a phosphate. In another embodiment, each linker is a phosphonate. In another embodiment of the compound of formula (I), each linker is a phosphoramidate. In another embodiment of the compound of formula (I), each linker is an ester. In another embodiment of the compound of formula (I), each linker is an amide. In another embodiment of the compound of formula (I), each linker is a triazole. In another embodiment of the compound of formula (I), each linker is a structure selected from the formulas of FIG.36 and FIG.38. [0251] In one embodiment of the compound of formula (I), B is a polyvalent organic species. In another embodiment of the compound of formula (I), B is a derivative of a polyvalent organic species. In one embodiment of the compound of formula (I), B is a triol or tetrol derivative. In another embodiment, B is a tri- or tetra-carboxylic acid derivative. In another embodiment, B is an amine derivative. In another embodiment, B is a tri- or tetra-amine derivative. In another embodiment, B is an amino acid derivative. In another embodiment of the compound of formula (I), B is selected from the formulas of FIG.38. [0252] Polyvalent organic species are moieties comprising carbon and three or more valencies (i.e., points of attachment with moieties such as S, L or N, as defined above). Non-limiting examples of polyvalent organic species include triols (e.g., glycerol, phloroglucinol, and the like), tetrols (e.g., ribose, pentaerythritol, 1,2,3,5-tetrahydroxybenzene, and the like), tri- carboxylic acids (e.g., citric acid, 1,3,5-cyclohexanetricarboxylic acid, trimesic acid, and the like), tetra-carboxylic acids (e.g., ethylenediaminetetraacetic acid, pyromellitic acid, and the like), tertiary amines (e.g., tripropargylamine, triethanolamine, and the like), triamines (e.g., diethylenetriamine and the like), tetramines, and species comprising a combination of hydroxyl, thiol, amino, and/or carboxyl moieties (e.g., amino acids such as lysine, serine, cysteine, and the like). [0253] In an embodiment of the compound of formula (I), each nucleic acid comprises one or more chemically-modified nucleotides. In an embodiment of the compound of formula (I), each nucleic acid consists of chemically-modified nucleotides. In certain embodiments of the compound of formula (I), >95%, >90%, >85%, >80%, >75%, >70%, >65%, >60%, >55% or >50% of each nucleic acid comprises chemically-modified nucleotides. [0254] In an embodiment, each antisense strand independently comprises a 5’ terminal group R selected from the groups of Table 2: Table 2 [0255] In one embodiment, R is R 1 . In another embodiment, R is R 2 . In another embodiment, R is R 3 . In another embodiment, R is R 4. In another embodiment, R is R 5. In another embodiment, R is R 6. In another embodiment, R is R 7. In another embodiment, R is R 8. Structure of Formula (II) [0256] In an embodiment, the compound of formula (I) the structure of formula (II): wherein X, for each occurrence, independently, is selected from adenosine, guanosine, uridine, cytidine, and chemically-modified derivatives thereof; Y, for each occurrence, independently, is selected from adenosine, guanosine, uridine, cytidine, and chemically-modified derivatives thereof; - represents a phosphodiester internucleoside linkage; = represents a phosphorothioate internucleoside linkage; and --- represents, individually for each occurrence, a base-pairing interaction or a mismatch. [0257] In certain embodiments, the structure of formula (II) does not contain mismatches. In one embodiment, the structure of formula (II) contains 1 mismatch. In another embodiment, the compound of formula (II) contains 2 mismatches. In another embodiment, the compound of formula (II) contains 3 mismatches. In another embodiment, the compound of formula (II) contains 4 mismatches. In an embodiment, each nucleic acid consists of chemically-modified nucleotides. [0258] In certain embodiments, >95%, >90%, >85%, >80%, >75%, >70%, >65%, >60%, >55% or >50% of X’s of the structure of formula (II) are chemically-modified nucleotides. In other embodiments, >95%, >90%, >85%, >80%, >75%, >70%, >65%, >60%, >55% or >50% of X’s of the structure of formula (II) are chemically-modified nucleotides. Structure of Formula (III) [0259] In an embodiment, the compound of formula (I) has the structure of formula (III): [0260] wherein X, for each occurrence, independently, is a nucleotide comprising a 2’-deoxy- 2’-fluoro modification; X, for each occurrence, independently, is a nucleotide comprising a 2’- O-methyl modification; Y, for each occurrence, independently, is a nucleotide comprising a 2’-deoxy-2’-fluoro modification; and Y, for each occurrence, independently, is a nucleotide comprising a 2’-O-methyl modification. [0261] In an embodiment, X is chosen from the group consisting of 2’-deoxy-2’-fluoro modified adenosine, guanosine, uridine or cytidine. In an embodiment, X is chosen from the group consisting of 2’-O-methyl modified adenosine, guanosine, uridine or cytidine. In an embodiment, Y is chosen from the group consisting of 2’-deoxy-2’-fluoro modified adenosine, guanosine, uridine or cytidine. In an embodiment, Y is chosen from the group consisting of 2’- O-methyl modified adenosine, guanosine, uridine or cytidine. [0262] In certain embodiments, the structure of formula (III) does not contain mismatches. In one embodiment, the structure of formula (III) contains 1 mismatch. In another embodiment, the compound of formula (III) contains 2 mismatches. In another embodiment, the compound of formula (III) contains 3 mismatches. In another embodiment, the compound of formula (III) contains 4 mismatches. Structure of Formula (IV) [0263] In an embodiment, the compound of formula (I) has the structure of formula (IV): wherein X, for each occurrence, independently, is selected from adenosine, guanosine, uridine, cytidine, and chemically-modified derivatives thereof; Y, for each occurrence, independently, is selected from adenosine, guanosine, uridine, cytidine, and chemically-modified derivatives thereof; - represents a phosphodiester internucleoside linkage; = represents a phosphorothioate internucleoside linkage; and --- represents, individually for each occurrence, a base-pairing interaction or a mismatch. [0264] In certain embodiments, the structure of formula (IV) does not contain mismatches. In one embodiment, the structure of formula (IV) contains 1 mismatch. In another embodiment, the compound of formula (IV) contains 2 mismatches. In another embodiment, the compound of formula (IV) contains 3 mismatches. In another embodiment, the compound of formula (IV) contains 4 mismatches. In an embodiment, each nucleic acid consists of chemically-modified nucleotides. [0265] In certain embodiments, >95%, >90%, >85%, >80%, >75%, >70%, >65%, >60%, >55% or >50% of X’s of the structure of formula (II) are chemically-modified nucleotides. In other embodiments, >95%, >90%, >85%, >80%, >75%, >70%, >65%, >60%, >55% or >50% of X’s of the structure of formula (II) are chemically-modified nucleotides. Structure of Formula (V) [0266] In an embodiment, the compound of formula (I) has the structure of formula (V): wherein X, for each occurrence, independently, is a nucleotide comprising a 2’-deoxy-2’-fluoro modification; X, for each occurrence, independently, is a nucleotide comprising a 2’-O-methyl modification; Y, for each occurrence, independently, is a nucleotide comprising a 2’-deoxy-2’- fluoro modification; and Y, for each occurrence, independently, is a nucleotide comprising a 2’-O-methyl modification. [0267] In certain embodiments, X is chosen from the group consisting of 2’-deoxy-2’-fluoro modified adenosine, guanosine, uridine or cytidine. In an embodiment, X is chosen from the group consisting of 2’-O-methyl modified adenosine, guanosine, uridine or cytidine. In an embodiment, Y is chosen from the group consisting of 2’-deoxy-2’-fluoro modified adenosine, guanosine, uridine or cytidine. In an embodiment, Y is chosen from the group consisting of 2’- O-methyl modified adenosine, guanosine, uridine or cytidine. [0268] In certain embodiments, the structure of formula (V) does not contain mismatches. In one embodiment, the structure of formula (V) contains 1 mismatch. In another embodiment, the compound of formula (V) contains 2 mismatches. In another embodiment, the compound of formula (V) contains 3 mismatches. In another embodiment, the compound of formula (V) contains 4 mismatches. Variable Linkers [0269] In an embodiment of the compound of formula (I), L has the structure of L1: . [0270] In an embodiment of L1, R is R 3 and n is 2. [0271] In an embodiment of the structure of formula (II), L has the structure of L1. In an embodiment of the structure of formula (III), L has the structure of L1. In an embodiment of the structure of formula (IV), L has the structure of L1. In an embodiment of the structure of formula (V), L has the structure of L1. In an embodiment of the structure of formula (VI), L has the structure of L1. In an embodiment of the structure of formula (VI), L has the structure of L1. [0272] In an embodiment of the compound of formula (I), L has the structure of L2: . [0273] In an embodiment of L2, R is R 3 and n is 2. In an embodiment of the structure of formula (II), L has the structure of L2. In an embodiment of the structure of formula (III), L has the structure of L2. In an embodiment of the structure of formula (IV), L has the structure of L2. In an embodiment of the structure of formula (V), L has the structure of L2. In an embodiment of the structure of formula (VI), L has the structure of L2. In an embodiment of the structure of formula (VI), L has the structure of L2. 10) Delivery System [0274] In a further aspect, provided herein is a delivery system for therapeutic nucleic acids having the structure of formula (VI): wherein L is selected from an ethylene glycol chain, an alkyl chain, a peptide, RNA, DNA, a phosphate, a phosphonate, a phosphoramidate, an ester, an amide, a triazole, and combinations thereof, wherein formula (VI) optionally further comprises one or more branch point B, and one or more spacer S; wherein B is independently for each occurrence a polyvalent organic species or derivative thereof; S is independently for each occurrence selected from an ethylene glycol chain, an alkyl chain, a peptide, RNA, DNA, a phosphate, a phosphonate, a phosphoramidate, an ester, an amide, a triazole, and combinations thereof; each cNA, independently, is a carrier nucleic acid comprising one or more chemical modifications; and n is 2, 3, 4, 5, 6, 7 or 8. [0275] In one embodiment of the delivery system, L is an ethylene glycol chain. In another embodiment of the delivery system, L is an alkyl chain. In another embodiment of the delivery system, L is a peptide. In another embodiment of the delivery system, L is RNA. In another embodiment of the delivery system, L is DNA. In another embodiment of the delivery system, L is a phosphate. In another embodiment of the delivery system, L is a phosphonate. In another embodiment of the delivery system, L is a phosphoramidate. In another embodiment of the delivery system, L is an ester. In another embodiment of the delivery system, L is an amide. In another embodiment of the delivery system, L is a triazole. [0276] In one embodiment of the delivery system, S is an ethylene glycol chain. In another embodiment, S is an alkyl chain. In another embodiment of the delivery system, S is a peptide. In another embodiment, S is RNA. In another embodiment of the delivery system, S is DNA. In another embodiment of the delivery system, S is a phosphate. In another embodiment of the delivery system, S is a phosphonate. In another embodiment of the delivery system, S is a phosphoramidate. In another embodiment of the delivery system, S is an ester. In another embodiment, S is an amide. In another embodiment, S is a triazole. [0277] In one embodiment of the delivery system, n is 2. In another embodiment of the delivery system, n is 3. In another embodiment of the delivery system, n is 4. In another embodiment of the delivery system, n is 5. In another embodiment of the delivery system, n is 6. In another embodiment of the delivery system, n is 7. In another embodiment of the delivery system, n is 8. [0278] In certain embodiments, each cNA comprises >95%, >90%, >85%, >80%, >75%, >70%, >65%, >60%, >55% or >50% chemically-modified nucleotides. [0279] In an embodiment, the compound of formula (VI) has a structure selected from formulas (VI-1)-(VI-9) of Table 3:
Table 3 [0280] In an embodiment, the compound of formula (VI) is the structure of formula (VI-1). In an embodiment, the compound of formula (VI) is the structure of formula (VI-2). In an embodiment, the compound of formula (VI) is the structure of formula (VI-3). In an embodiment, the compound of formula (VI) is the structure of formula (VI-4). In an embodiment, the compound of formula (VI) is the structure of formula (VI-5). In an embodiment, the compound of formula (VI) is the structure of formula (VI-6). In an embodiment, the compound of formula (VI) is the structure of formula (VI-7). In an embodiment, the compound of formula (VI) is the structure of formula (VI-8). In an embodiment, the compound of formula (VI) is the structure of formula (VI-9). [0281] In an embodiment, the compound of formulas (VI) (including, e.g., formulas (VI-1)- (VI-9), each cNA independently comprises at least 15 contiguous nucleotides. In an embodiment, each cNA independently consists of chemically-modified nucleotides. [0282] In an embodiment, the delivery system further comprises n therapeutic nucleic acids (NA), wherein each NA comprises a region of complementarity which is substantially complementary to a region of a gene comprising an allelic polymorphism, wherein the antisense strand comprises: a single nucleotide polymorphism (SNP) position nucleotide at a position 2 to 7 from the 5’ end that is complementary to the allelic polymorphism; and a mismatch (MM) position nucleotide located 2-11 nucleotide from the SNP position nucleotide that is a mismatch with a nucleotide in the gene. In exemplary embodiments, the SNP position nucleotide is at a position 2, 4 or 6 from the 5’ end and the mismatch (MM) position nucleotide is located 2-6 nucleotides from the SNP position nucleotide. Also, each NA is hybridized to at least one cNA. In one embodiment, the delivery system is comprised of 2 NAs. In another embodiment, the delivery system is comprised of 3 NAs. In another embodiment, the delivery system is comprised of 4 NAs. In another embodiment, the delivery system is comprised of 5 NAs. In another embodiment, the delivery system is comprised of 6 NAs. In another embodiment, the delivery system is comprised of 7 NAs. In another embodiment, the delivery system is comprised of 8 NAs. [0283] In an embodiment, each NA independently comprises at least 16 contiguous nucleotides. In an embodiment, each NA independently comprises 16-20 contiguous nucleotides. In an embodiment, each NA independently comprises 16 contiguous nucleotides. In another embodiment, each NA independently comprises 17 contiguous nucleotides. In another embodiment, each NA independently comprises 18 contiguous nucleotides. In another embodiment, each NA independently comprises 19 contiguous nucleotides. In another embodiment, each NA independently comprises 20 contiguous nucleotides. [0284] In an embodiment, each NA comprises an unpaired overhang of at least 2 nucleotides. In another embodiment, each NA comprises an unpaired overhang of at least 3 nucleotides. In another embodiment, each NA comprises an unpaired overhang of at least 4 nucleotides. In another embodiment, each NA comprises an unpaired overhang of at least 5 nucleotides. In another embodiment, each NA comprises an unpaired overhang of at least 6 nucleotides. In an embodiment, the nucleotides of the overhang are connected via phosphorothioate linkages. [0285] In an embodiment, each NA, independently, is selected from the group consisting of: DNA, siRNAs, antagomiRs, miRNAs, gapmers, mixmers, or guide RNAs. In one embodiment, each NA, independently, is a DNA. In another embodiment, each NA, independently, is a siRNA. In another embodiment, each NA, independently, is an antagomiR. In another embodiment, each NA, independently, is a miRNA. In another embodiment, each NA, independently, is a gapmer. In another embodiment, each NA, independently, is a mixmer. In another embodiment, each NA, independently, is a guide RNA. In an embodiment, each NA is the same. In an embodiment, each NA is not the same. [0286] In an embodiment, the delivery system further comprising n therapeutic nucleic acids (NA) has a structure selected from formulas (I), (II), (III), (IV), (V), (VI), and embodiments thereof described herein. In one embodiment, the delivery system has a structure selected from formulas (I), (II), (III), (IV), (V), (VI), and embodiments thereof described herein further comprising 2 therapeutic nucleic acids (NA). In another embodiment, the delivery system has a structure selected from formulas (I), (II), (III), (IV), (V), (VI), and embodiments thereof described herein further comprising 3 therapeutic nucleic acids (NA). In one embodiment, the delivery system has a structure selected from formulas (I), (II), (III), (IV), (V), (VI), and embodiments thereof described herein further comprising 4 therapeutic nucleic acids (NA). In one embodiment, the delivery system has a structure selected from formulas (I), (II), (III), (IV), (V), (VI), and embodiments thereof described herein further comprising 5 therapeutic nucleic acids (NA). In one embodiment, the delivery system has a structure selected from formulas (I), (II), (III), (IV), (V), (VI), and embodiments thereof described herein further comprising 6 therapeutic nucleic acids (NA). In one embodiment, the delivery system has a structure selected from formulas (I), (II), (III), (IV), (V), (VI), and embodiments thereof described herein further comprising 7 therapeutic nucleic acids (NA). In one embodiment, the delivery system has a structure selected from formulas (I), (II), (III), (IV), (V), (VI), and embodiments thereof described herein further comprising 8 therapeutic nucleic acids (NA). [0287] In one embodiment, the delivery system has a structure selected from formulas (I), (II), (III), (IV), (V), (VI), further comprising a linker of structure L1 or L2 wherein R is R3 and n is 2. In another embodiment, the delivery system has a structure selected from formulas (I), (II), (III), (IV), (V), (VI), further comprising a linker of structure L1 wherein R is R3 and n is 2. In another embodiment, the delivery system has a structure selected from formulas (I), (II), (III), (IV), (V), (VI), further comprising a linker of structure L2 wherein R is R3 and n is 2. Pharmaceutical Compositions and Methods of Administration [0288] In one aspect, provided herein is a pharmaceutical composition comprising a therapeutically effective amount of one or more compound, oligonucleotide, or nucleic acid as described herein, and a pharmaceutically acceptable carrier. In one embodiment, the pharmaceutical composition comprises one or more double-stranded, chemically-modified nucleic acid as described herein, and a pharmaceutically acceptable carrier. In a particular embodiment, the pharmaceutical composition comprises one double-stranded, chemically- modified nucleic acid as described herein, and a pharmaceutically acceptable carrier. In another particular embodiment, the pharmaceutical composition comprises two double-stranded, chemically-modified nucleic acids as described herein, and a pharmaceutically acceptable carrier. [0289] In a particular embodiment, the pharmaceutical composition comprises a double- stranded RNA molecule comprising about 15-35 nucleotides complementary to a region of a gene encoding a heterozygous SNP mutant protein, said region comprising an allelic polymorphism, and a second strand comprising about 15-35 nucleotides complementary to the first strand, wherein the dsRNA molecule comprises a mismatch that is not in the position of the allelic polymorphism; and the mismatch and the nucleotide corresponding to the polymorphism are not in the center of the dsRNA molecule. [0290] In an embodiment, the mismatch is 4 nucleotides upstream, 3 nucleotides upstream nucleotide corresponding to the allelic polymorphism, 2 nucleotides upstream nucleotide corresponding to the allelic polymorphism, 1 nucleotide upstream, 1 nucleotide downstream nucleotide corresponding to the allelic polymorphism, 2 nucleotides downstream nucleotide corresponding to the allelic polymorphism, 3 nucleotides downstream nucleotide corresponding to the allelic polymorphism, 4 nucleotides downstream nucleotide corresponding to the allelic polymorphism, or 5 nucleotides downstream nucleotide corresponding to the allelic polymorphism. In certain embodiments, the mismatch is not adjacent to the nucleotide corresponding to the allelic polymorphism. [0291] In another embodiment of the pharmaceutical composition, the double-stranded RNA comprises a nucleotide corresponding to the allelic polymorphism which is in position 2, 3, 4, 5, or 6 from the 5’ end. In an embodiment, the nucleotide corresponding to the allelic polymorphism is in position 2 from the 5’ end. In an embodiment, the nucleotide corresponding to the allelic polymorphism is in position 3 from the 5’ end. In an embodiment, the nucleotide corresponding to the allelic polymorphism is in position 4 from the 5’ end. In an embodiment, the nucleotide corresponding to the allelic polymorphism is in position 5 from the 5’ end. In an embodiment, the nucleotide corresponding to the allelic polymorphism is in position 6 from the 5’ end. [0292] In an embodiment of the pharmaceutical composition, the double-stranded RNA selectively silences a mutant allele having an allelic polymorphism, e.g., a heterozygous SNP. In an embodiment of the pharmaceutical composition, the double-stranded RNA silences a mutant allele having an allelic polymorphism and does not affect the wild-type allele of the same gene. In another embodiment of the pharmaceutical composition, the double-stranded RNA provided herein silences a mutant allele having an allelic polymorphism and silences the wild-type allele of the same gene to a lesser extent than the mutant allele. [0293] A pharmaceutical composition of the disclosure is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous (IV), intradermal, subcutaneous (SC or SQ), intraperitoneal, intramuscular, oral (e.g., inhalation), transdermal (topical), and transmucosal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. [0294] Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be desired to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin. [0295] Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, typical methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. [0296] The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds should typically lie within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the method of the disclosure, the therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the EC50 (i.e., the concentration of the test compound which achieves a half-maximal response) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography. Methods of Treatment [0297] The present disclosure provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disease or disorder caused, in whole or in part, by an allelic polymorphism (e.g., a heterozygous SNP). In one embodiment, the disease or disorder is a trinucleotide repeat disease or disorder. In another embodiment, the disease or disorder is a polyglutamine disorder. In an embodiment, the methods comprise administering a therapeutically effective amount of a double-stranded RNA molecule provided herein. In an embodiment, the disease or disorder is a disorder associated with the expression of huntingtin and in which alteration of huntingtin, especially the amplification of CAG repeat copy number, leads to a defect in the huntingtin gene (structure or function) or huntingtin protein (structure or function or expression), such that clinical manifestations include those seen in Huntington’s disease patients. [0298] In embodiments of the methods, the double-stranded RNAs disclosed herein are homologous to an allelic polymorphism except for one mismatched oligonucleotide at a particular position relative to the nucleotide corresponding to the allelic polymorphism. In certain embodiments, the mismatch is within about 6 nucleotides of the nucleotide corresponding to the allelic polymorphism, within about 5 nucleotides of the nucleotide corresponding to the allelic polymorphism, within about 4 nucleotides of the nucleotide corresponding to the allelic polymorphism within about 3 nucleotide of the nucleotide corresponding to the allelic polymorphism, within about 2 nucleotide of the nucleotide corresponding to the allelic polymorphism, or within about 1 nucleotides of the nucleotide corresponding to the allelic polymorphism. In particularly exemplary embodiments, the mismatch is not adjacent to the nucleotide corresponding to the allelic polymorphism. [0299] In another embodiment of the methods, the double-stranded RNA comprises a nucleotide corresponding to the allelic polymorphism which is in position 2, 3, 4, 5, or 6 from the 5’ end. In an embodiment, the nucleotide corresponding to the allelic polymorphism is in position 2 from the 5’ end. In an embodiment, the nucleotide corresponding to the allelic polymorphism is in position 3 from the 5’ end. In an embodiment, the nucleotide corresponding to the allelic polymorphism is in position 4 from the 5’ end. In an embodiment, the nucleotide corresponding to the allelic polymorphism is in position 5 from the 5’ end. In an embodiment, the nucleotide corresponding to the allelic polymorphism is in position 6 from the 5’ end. [0300] In an embodiment of the methods, the dsRNA comprises a nucleotide corresponding to a polymorphism at position 6 from the 5’end and a mismatch at position 11 from the 5’ end. In an embodiment of the methods, the dsRNA comprises a nucleotide corresponding to a polymorphism at position 4 from the 5’ end and a mismatch at position 7 from the 5’ end. [0301] In another embodiment of the methods, the double-stranded RNA selectively silences a mutant allele having an allelic polymorphism. In an embodiment, the double-stranded RNA silences a mutant allele having an allelic polymorphism and does not affect the wild-type allele of the same gene. In another embodiment, the double-stranded RNA silences a mutant allele having an allelic polymorphism and silences the wild-type allele of the same gene to a lesser extent than the mutant allele. [0302] In an embodiment of the methods, the dsRNA comprises one or more VP intersubunit linkage modifications wherein the intersubunit linkage has the following formula: . [0303] In additional embodiments, the dsRNA comprises one or more of the intersubunit linkage modifications depicted in FIG. 43. [0304] “Treatment,” or “treating,” as used herein, is defined as the application or administration of a therapeutic agent (e.g., a RNA agent or vector or transgene encoding same) to a patient, or application or administration of a therapeutic agent to an isolated tissue or cell line from a patient, who has the disease or disorder, a symptom of disease or disorder or a predisposition toward a disease or disorder, with the purpose to cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve or affect the disease or disorder, the symptoms of the disease or disorder, or the predisposition toward disease. [0305] In one aspect, the disclosure provides a method for preventing in a subject, a disease or disorder as described above, by administering to the subject a therapeutic agent (e.g., an RNAi agent or vector or transgene encoding same). Subjects at risk for the disease can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein. Administration of a prophylactic agent can occur prior to the manifestation of symptoms characteristic of the disease or disorder, such that the disease or disorder is prevented or, alternatively, delayed in its progression. [0306] Another aspect of the disclosure pertains to methods treating subjects therapeutically, i.e., alter onset of symptoms of the disease or disorder. In an exemplary embodiment, the modulatory method of the disclosure involves contacting a cell expressing a gain-of-function mutant with a therapeutic agent (e.g., a RNAi agent or vector or transgene encoding same) that is specific for one or more target sequences within the gene, such that sequence specific interference with the gene is achieved. These methods can be performed in vitro (e.g., by culturing the cell with the agent) or, alternatively, in vivo (e.g., by administering the agent to a subject). [0307] An RNA silencing agent modified for enhanced uptake into neural cells can be administered at a unit dose less than about 1.4 mg per kg of bodyweight, or less than 10, 5, 2, 1, 0.5, 0.1, 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, 0.00005 or 0.00001 mg per kg of bodyweight, and less than 200 nmole of RNA agent (e.g., about 4.4 x 10 16 copies) per kg of bodyweight, or less than 1500, 750, 300, 150, 75, 15, 7.5, 1.5, 0.75, 0.15, 0.075, 0.015, 0.0075, 0.0015, 0.00075 or 0.00015 nmole of RNA silencing agent per kg of bodyweight. The unit dose, for example, can be administered by injection (e.g., intravenous or intramuscular, intrathecally, or directly into the brain), an inhaled dose, or a topical application. In exemplary embodiments, dosages are less than 2, 1 or 0.1 mg/kg of body weight. [0308] Delivery of an RNA silencing agent directly to an organ (e.g., directly to the brain) can be at a dosage on the order of about 0.00001 mg to about 3 mg per organ, or about 0.0001- 0.001 mg per organ, about 0.03-3.0 mg per organ, about 0.1-3.0 mg per organ or about 0.3-3.0 mg per organ. The dosage can be an amount effective to treat or prevent a neurological disease or disorder (e.g., Huntington’s disease). In one embodiment, the unit dose is administered less frequently than once a day, e.g., less than every 2, 4, 8 or 30 days. In another embodiment, the unit dose is not administered with a frequency (e.g., not a regular frequency). For example, the unit dose may be administered a single time. In one embodiment, the effective dose is administered with other traditional therapeutic modalities. [0309] In one embodiment, a subject is administered an initial dose, and one or more maintenance doses of an RNA silencing agent. The maintenance dose or doses are generally lower than the initial dose, e.g., one-half less of the initial dose. A maintenance regimen can include treating the subject with a dose or doses ranging from 0.01 mg to 1.4 mg/kg of body weight per day, e.g., 10, 1, 0.1, 0.01, 0.001, or 0.00001 mg per kg of bodyweight per day. The maintenance doses are typically administered no more than once every 5, 10, or 30 days. Further, the treatment regimen may last for a period of time which will vary depending upon the nature of the particular disease, its severity and the overall condition of the patient. In particular embodiments, the dosage may be delivered no more than once per day, e.g., no more than once per 24, 36, 48 or more hours, e.g., no more than once every 5 or 8 days. Following treatment, the patient can be monitored for changes in his condition and for alleviation of the symptoms of the disease state. The dosage of the compound may either be increased in the event the patient does not respond significantly to current dosage levels, or the dose may be decreased if an alleviation of the symptoms of the disease state is observed, if the disease state has been ablated, or if undesired side-effects are observed. Huntington’s Disease [0310] In certain aspects of the disclosure, RNA silencing agents are designed to target polymorphisms (e.g., heterozygous single nucleotide polymorphisms) in the mutant human huntingtin protein (htt) for the treatment of Huntington’s disease. Accordingly, in another aspect, provided herein is a method of treating or managing Huntington’s disease comprising administering to a patient in need of such treatment or management a therapeutically effective amount of a compound, oligonucleotide, or nucleic acid as described herein, or a pharmaceutical composition comprising said compound, oligonucleotide, or nucleic acid. [0311] Huntington’s disease, inherited as an autosomal dominant disease, causes impaired cognition and motor disease. Patients can live more than a decade with severe debilitation, before premature death from starvation or infection. The disease begins in the fourth or fifth decade for most cases, but a subset of patients manifest disease in teenage years. The genetic mutation for Huntington’s disease is a lengthened CAG repeat in the huntingtin gene. The CAG repeat varies in number from 8 to 35 copies in normal individuals (Kremer et al., 1994). The genetic mutation (e.g., an increase in length of the CAG repeats from less than 36 in the normal huntingtin gene to greater than 36 in the disease) is associated with the synthesis of a mutant huntingtin protein, which has greater than 36 consecutive polyglutamine residues (Aronin et al., 1995). In general, individuals with 36 or more CAG repeats will get Huntington's disease. Prototypie for as many as twenty other diseases with a lengthened CAG as the underlying mutation, Huntington’s disease still has no effective therapy. A variety of interventions — such as interruption of apoptotic pathways, addition of reagents to boost mitochondrial efficiency, and blockade of NMD A receptors — have shown promise in cell cultures and mouse model of Huntington’s disease. However, at best these approaches reveal a short prolongation of cell or animal survival.
[0312] The disease gene linked to Huntington’s disease is termed Huntingtin or (htt) The huntingtin locus is large, spanning 180 kb and consisting of 67 exons. The huntingtin gene is widely expressed and is required for normal development. It is expressed as 2 alternatively polyadenylated forms displaying different relative abundance in various fetal and adult tissues. The larger transcript is approximately 13.7 kb and i s expressed predominantly in adult and fetal brain whereas the smaller transcript of approximately 10.3 kb is more widely expressed. The two transcripts differ with respect to their 3 ' untranslated regions (Lin et al. 1993). Both messages are predicted to encode a 348 kilodalton protein containing 3144 amino acids. The genetic defect leading to Huntington’s disease is believed to confer a new property on the mRNA or alter the function of the protein
[0313] Huntington’s disease complies with the central dogma of genetics: a mutant gene serves as a template for production of a mutant mRNA; the mutant rnRNA then directs synthesis of a mutant protein (Aronin et al., 1995; DiFiglia et al., 1997). Mutant huntingtin (protein) likely accumulates in selective neurons in the striatum and cortex, disrupts as yet determined cellular activities, and causes neuronal dysfunction and death (Aronin et al., 1999; Laforet et al., 2001). Because a single copy of a mutant gene suffices to cause Huntington’s disease, the most parsimonious treatment would render the mutant gene ineffective. Theoretical approaches might include stopping gene transcription of mutant huntingtin, destroying mutant mRNA, and blocking translation. Each has the same outcome —loss of mutant huntingtin.
Huntington SNPs
[0314] Exemplary SNPs in the huntingtin gene sequence suitable for targeting according to certain exemplary embodiments are disclosed in Table 4 below. Genomic sequence for each SNP site can be found in, for example, the publicly available “SNP Entrez” database maintained by the NCBI. The frequency of heterozygosity for each SNP site for HD patient and control DNA is further illustrated in Table 4. Targeting combinations of frequently heterozygous SNPs allows the treatment of a large percentage of the individuals in a HD population using a relatively small number of allele-specific RNA silencing agents. Table 4. htt SNPs. [0315] In one embodiment, RNA silencing agents of the disclosure are capable of targeting one or more of the SNP sites listed in Table 4. In one embodiment, RNA silencing agents of the disclosure are capable of targeting rs363125 SNP site of the Huntingtin mRNA. In another embodiment, RNA silencing agents of the disclosure are capable of targeting rs362273 SNP site of the Huntingtin mRNA. In another embodiment, RNA silencing agents of the disclosure are capable of targeting rs362307 SNP site of the Huntingtin mRNA. In another embodiment, RNA silencing agents of the disclosure are capable of targeting rs362336 SNP site of the Huntingtin mRNA. In another embodiment, RNA silencing agents of the disclosure are capable of targeting rs362331 SNP site of the Huntingtin mRNA. In another embodiment, RNA silencing agents of the disclosure are capable of targeting rs362272 SNP site of the Huntingtin mRNA. In another embodiment, RNA silencing agents of the disclosure are capable of targeting rs362306 SNP site of the Huntingtin mRNA. In another embodiment, RNA silencing agents of the disclosure are capable of targeting rs362268 SNP site of the Huntingtin mRNA. In another embodiment, RNA silencing agents of the disclosure are capable of targeting rs362267 SNP site of the Huntingtin mRNA. In another embodiment, RNA silencing agents of the disclosure are capable of targeting rs363099 SNP site of the Huntingtin mRNA. In some embodiments, SNP sites targeted by RNA silencing agents are associated with Huntington’s Disease. In particularly exemplary embodiments, SNP sites targeted by RNA silencing agents are significantly associated with Huntington’s Disease. [0316] In additional exemplary embodiments, the RNA silencing agents include one or more of the sequences of Tables 5-7: Table 5 Table 6 Table 7 [0317] In certain embodiments of Tables 5-7, a U nucleotide may be replaced with a T nucleotide. Methods of Delivering Nucleic Acids [0318] RNA silencing agents of the disclosure may be directly introduced into a cell (e.g., a neural cell) (i.e., intracellularly); or introduced extracellularly into a cavity, interstitial space, into the circulation of an organism, introduced orally, or may be introduced by bathing a cell or organism in a solution containing the nucleic acid. Vascular or extravascular circulation, the blood or lymph system, and the cerebrospinal fluid are sites where the nucleic acid may be introduced. [0319] The RNA silencing agents of the disclosure can be introduced using nucleic acid delivery methods known in art including injection of a solution containing the nucleic acid, bombardment by particles covered by the nucleic acid, soaking the cell or organism in a solution of the nucleic acid, or electroporation of cell membranes in the presence of the nucleic acid. Other methods known in the art for introducing nucleic acids to cells may be used, such as lipid-mediated carrier transport, chemical- mediated transport, and cationic liposome transfection such as calcium phosphate, and the like. The nucleic acid may be introduced along with other components that perform one or more of the following activities: enhance nucleic acid uptake by the cell or other-wise increase inhibition of the target gene. [0320] Physical methods of introducing nucleic acids include injection of a solution containing the RNA, bombardment by particles covered by the RNA, soaking the cell or organism in a solution of the RNA, or electroporation of cell membranes in the presence of the RNA. A viral construct packaged into a viral particle would accomplish both efficient introduction of an expression construct into the cell and transcription of RNA encoded by the expression construct. Other methods known in the art for introducing nucleic acids to cells may be used, such as lipid-mediated carrier transport, chemical-IS mediated transport, such as calcium phosphate, and the like. Thus, the RNA may be introduced along with components that perform one or more of the following activities: enhance RNA uptake by the cell, inhibit annealing of single strands, stabilize the single strands, or other-wise increase inhibition of the target gene. [0321] RNA may be directly introduced into the cell (i.e., intracellularly), or introduced extracellularly into a cavity, interstitial space, into the circulation of an organism, introduced orally, or may be introduced by bathing a cell or organism in a solution containing the RNA. Vascular or extravascular circulation, the blood or lymph system, and the cerebrospinal fluid are sites where the RNA may be introduced. [0322] The cell having the target gene may be from the germ line or somatic, totipotent or pluripotent, dividing or non-dividing, parenchyma or epithelium, immortalized or transformed, or the like. The cell may be a stem cell or a differentiated cell. Cell types that are differentiated include adipocytes, fibroblasts, myocytes, cardiomyocytes, endothelium, neurons, glia, blood cells, megakaryocytes, lymphocytes, macrophages, neutrophils, eosinophils, basophils, mast cells, leukocytes, granulocytes, keratinocytes, chondrocytes, osteoblasts, osteoclasts, hepatocytes, and cells of the endocrine or exocrine glands. [0323] Depending on the particular target gene and the dose of double-stranded RNA material delivered, this process may provide partial or complete loss of function for the target gene. A reduction or loss of gene expression in at least 50%, 60%, 70%, 80%, 90%, 95% or 99% or more of targeted cells is exemplary. Inhibition of gene expression refers to the absence (or observable decrease) in the level of protein and/or mRNA product from a target gene. Specificity refers to the ability to inhibit the target gene without manifest effects on other genes of the cell. The consequences of inhibition can be confirmed by examination of the outward properties of the cell or organism (as presented below in the examples) or by biochemical techniques such as RNA solution hybridization, nuclease protection, Northern hybridization, reverse transcription, gene expression monitoring with a microarray, antibody binding, enzyme linked immunosorbent assay (ELISA), Western blotting, radioimmunoassay (RIA), other immunoassays, fluorescence activated cell analysis (FACS) and the like. [0324] For RNA-mediated inhibition in a cell line or whole organism, gene expression is conveniently assayed by use of a reporter or drug resistance gene whose protein product is easily assayed. Such reporter genes include acetohydroxyacid synthase (AHAS), alkaline phosphatase (AP), beta galactosidase (LacZ), beta glucoronidase (GUS), chloramphenicol acetyltransferase (CAT), green fluorescent protein (GFP), horseradish peroxidase (HRP), luciferase (Luc), nopaline synthase (NOS), octopine synthase (OCS), and derivatives thereof. Multiple selectable markers are available that confer resistance to ampicillin, bleomycin, chloramphenicol, gentamycin, hygromycin, kanamycin, lincomycin, methotrexate, phosphinothricin, puromycin, and tetracycline. Depending on the assay, quantitation of the amount of gene expression allows one to determine a degree of inhibition which is greater than 10%, 33%, 50%, 90%, 95% or 99% as compared to a cell not treated according to the present disclosure. Lower doses of injected material and longer times after administration of RNAi agent may result in inhibition in a smaller fraction of cells (e.g., at least 10%, 20%, 50%, 75%, 90%, or 95% of targeted cells). Quantization of gene expression in a cell may show similar amounts of inhibition at the level of accumulation of target mRNA or translation of target protein. As an example, the efficiency of inhibition may be determined by assessing the amount of gene product in the cell. mRNA may be detected with a hybridization probe having a nucleotide sequence outside the region used for the inhibitory double-stranded RNA, or translated polypeptide may be detected with an antibody raised against the polypeptide sequence of that region. [0325] The RNA may be introduced in an amount which allows delivery of at least one copy per cell. Higher doses (e.g., at least 5, 10, 100, 500 or 1000 copies per cell) of material may yield more effective inhibition; lower doses may also be useful for specific applications. [0326] In a particular aspect, the efficacy of an RNAi agent of the disclosure (e.g., an siRNA targeting a polymorphism in a mutant gene) is tested for its ability to specifically degrade mutant mRNA (e.g., mutant htt mRNA and/or the production of mutant huntingtin protein) in cells, in particular, in neurons (e.g., striatal or cortical neuronal clonal lines and/or primary neurons). Also suitable for cell-based validation assays are other readily transfectable cells, for example, HeLa cells or COS cells. Cells are transfected with human wild-type or mutant cDNAs (e.g., human wild-type or mutant huntingtin cDNA). Standard siRNA, modified siRNA or vectors able to produce siRNA from U-looped mRNA are co-transfected. Selective reduction in mutant mRNA (e.g., mutant huntingtin mRNA) and/or mutant protein (e.g., mutant huntingtin) is measured. Reduction of mutant mRNA or protein can be compared to levels of normal mRNA or protein. Exogenously-introduced normal mRNA or protein (or endogenous normal mRNA or protein) can be assayed for comparison purposes. When utilizing neuronal cells, which are known to be somewhat resistant to standard transfection techniques, it may be desirable to introduce RNAi agents (e.g., siRNAs) by passive uptake. [0327] In certain exemplary embodiments, a composition that includes an RNA agent, e.g., a dsRNA agent, of the disclosure can be delivered to the nervous system of a subject by a variety of routes. Exemplary routes include intrathecal, parenchymal (e.g., in the brain), nasal, and ocular delivery. The composition can also be delivered systemically, e.g., by intravenous, subcutaneous or intramuscular injection, which is particularly useful for delivery of the RNA agents, e.g., dsRNA agents, to peripheral neurons. An exemplary route of delivery is directly to the brain, e.g., into the ventricles or the hypothalamus of the brain, or into the lateral or dorsal areas of the brain. The RNA agents, e.g., dsRNA agents, for neural cell delivery can be incorporated into pharmaceutical compositions suitable for administration. [0328] For example, compositions can include one or more species of an RNA agent, e.g., a dsRNA agent, and a pharmaceutically acceptable carrier. The pharmaceutical compositions of the present disclosure may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic, intranasal, transdermal), oral or parenteral. Parenteral administration includes intravenous drip, subcutaneous, intraperitoneal or intramuscular injection, intrathecal, or intraventricular (e.g., intracerebroventricular) administration. In certain exemplary embodiments, an RNA silencing agent of the disclosure is delivered across the Blood-Brain- Barrier (BBB) suing a variety of suitable compositions and methods described herein. [0329] The route of delivery can be dependent on the disorder of the patient. For example, a subject diagnosed with Huntington’s disease can be administered an anti-htt RNA agent, e.g., a dsRNA agent, of the disclosure directly into the brain (e.g., into the globus pallidus or the corpus striatum of the basal ganglia, and near the medium spiny neurons of the corpus striatum). In addition to an RNA silencing agent of the disclosure, a patient can be administered a second therapy, e.g., a palliative therapy and/or disease-specific therapy. The secondary therapy can be, for example, symptomatic (e.g., for alleviating symptoms), neuroprotective (e.g., for slowing or halting disease progression), or restorative (e.g., for reversing the disease process). For the treatment of Huntington’s disease, for example, symptomatic therapies can include the drugs haloperidol, carbamazepine, or valproate. Other therapies can include psychotherapy, physiotherapy, speech therapy, communicative and memory aids, social support services, and dietary advice. [0330] An RNA agent, e.g., a dsRNA agent, can be delivered to neural cells of the brain. Delivery methods that do not require passage of the composition across the blood-brain barrier can be utilized. For example, a pharmaceutical composition containing an RNA agent, e.g., a dsRNA agent, can be delivered to the patient by injection directly into the area containing the disease-affected cells. For example, the pharmaceutical composition can be delivered by injection directly into the brain. The injection can be by stereotactic injection into a particular region of the brain (e.g., the substantia nigra, cortex, hippocampus, striatum, or globus pallidus). The RNA agent, e.g., a dsRNA agent, can be delivered into multiple regions of the central nervous system (e.g., into multiple regions of the brain, and/or into the spinal cord). The RNA agent, e.g., a dsRNA agent, can be delivered into diffuse regions of the brain (e.g., diffuse delivery to the cortex of the brain). [0331] In one embodiment, the RNA agent, e.g., a dsRNA agent, can be delivered by way of a cannula or other delivery device having one end implanted in a tissue, e.g., the brain, e.g., the substantia nigra, cortex, hippocampus, striatum or globus pallidus of the brain. The cannula can be connected to a reservoir of RNA agent, e.g., dsRNA agent. The flow or delivery can be mediated by a pump, e.g., an osmotic pump or minipump, such as an Alzet pump (Durect, Cupertino, CA). In one embodiment, a pump and reservoir are implanted in an area distant from the tissue, e.g., in the abdomen, and delivery is affected by a conduit leading from the pump or reservoir to the site of release. Devices for delivery to the brain are described, for example, in U.S. Pat. Nos.6,093,180, and 5,814,014. [0332] An RNA agent, e.g., a dsRNA agent, of the disclosure can be further modified such that it is capable of traversing the blood brain barrier. For example, the RNA agent, e.g., a dsRNA agent, can be conjugated to a molecule that enables the agent to traverse the barrier. Such modified RNA agents, e.g., dsRNA agents, can be administered by any desired method, such as by intraventricular or intramuscular injection, or by pulmonary delivery, for example. [0333] In certain embodiments, exosomes are used to deliver an RNA agent, e.g., a dsRNA agent, of the disclosure. Exosomes can cross the BBB and deliver siRNAs, antisense oligonucleotides, chemotherapeutic agents and proteins specifically to neurons after systemic injection (See, Alvarez-Erviti L, Seow Y, Yin H, Betts C, Lakhal S, Wood MJ. (2011). Delivery of siRNA to the mouse brain by systemic injection of targeted exosomes. Nat Biotechnol. 2011 Apr;29(4):341-5. doi: 10.1038/nbt.1807; El-Andaloussi S, Lee Y, Lakhal- Littleton S, Li J, Seow Y, Gardiner C, Alvarez-Erviti L, Sargent IL, Wood MJ.(2011). Exosome-mediated delivery of siRNA in vitro and in vivo. Nat Protoc.2012 Dec;7(12):2112- 26. doi: 10.1038/nprot.2012.131; EL Andaloussi S, Mäger I, Breakefield XO, Wood MJ. (2013). Extracellular vesicles: biology and emerging therapeutic opportunities. Nat Rev Drug Discov. 2013 May;12(5):347-57. doi: 10.1038/nrd3978; El Andaloussi S, Lakhal S, Mäger I, Wood MJ. (2013). Exosomes for targeted siRNA delivery across biological barriers. Adv. Drug Deliv Rev.2013 Mar;65(3):391-7. doi: 10.1016/j.addr.2012.08.008). [0334] In certain embodiments, one or more lipophilic molecules are used to allow delivery of an RNA agent, e.g., a dsRNA agent, of the disclosure past the BBB (Alvarez-Ervit (2011)). The RNA silencing agent would then be activated, e.g., by enzyme degradation of the lipophilic disguise to release the drug into its active form. [0335] In certain embodiments, one or more receptor-mediated permeabilizing compounds can be used to increase the permeability of the BBB to allow delivery of an RNA silencing agent of the disclosure. These drugs increase the permeability of the BBB temporarily by increasing the osmotic pressure in the blood which loosens the tight junctions between the endothelial cells ((El-Andaloussi (2012)). By loosening the tight junctions normal intravenous injection of an RNA silencing agent can be performed. [0336] In certain embodiments, nanoparticle-based delivery systems are used to deliver an RNA agent, e.g., a dsRNA agent, of the disclosure across the BBB. As used herein, “nanoparticles” refer to polymeric nanoparticles that are typically solid, biodegradable, colloidal systems that have been widely investigated as drug or gene carriers (S. P. Egusquiaguirre, M. Igartua, R. M. Hernandez, and J. L. Pedraz, “Nanoparticle delivery systems for cancer therapy: advances in clinical and preclinical research,” Clinical and Translational Oncology, vol. 14, no. 2, pp. 83–93, 2012). Polymeric nanoparticles are classified into two major categories, natural polymers and synthetic polymers. Natural polymers for siRNA delivery include, but are not limited to, cyclodextrin, chitosan, and atelocollagen (Y. Wang, Z. Li, Y. Han, L. H. Liang, and A. Ji, “Nanoparticle-based delivery system for application of siRNA in vivo,” Current Drug Metabolism, vol. 11, no. 2, pp. 182–196, 2010). Synthetic polymers include, but are not limited to, polyethyleneimine (PEI), poly(dl-lactide-co- glycolide) (PLGA), and dendrimers, which have been intensively investigated (X. Yuan, S. Naguib, and Z. Wu, “Recent advances of siRNA delivery by nanoparticles,” Expert Opinion on Drug Delivery, vol.8, no. 4, pp. 521–536, 2011). For a review of nanoparticles and other suitable delivery systems, See Jong-Min Lee, Tae-Jong Yoon, and Young-Seok Cho, “Recent Developments in Nanoparticle-Based siRNA Delivery for Cancer Therapy,” BioMed Research International, vol. 2013, Article ID 782041, 10 pages, 2013. doi:10.1155/2013/782041 (incorporated by reference in its entirety.) [0337] An RNA agent, e.g., a dsRNA agent, of the disclosure can be administered ocularly, such as to treat retinal disorder, e.g., a retinopathy. For example, the pharmaceutical compositions can be applied to the surface of the eye or nearby tissue, e.g., the inside of the eyelid. They can be applied topically, e.g., by spraying, in drops, as an eyewash, or an ointment. Ointments or droppable liquids may be delivered by ocular delivery systems known in the art such as applicators or eye droppers. Such compositions can include mucomimetics such as hyaluronic acid, chondroitin sulfate, hydroxypropyl methylcellulose or poly(vinyl alcohol), preservatives such as sorbic acid, EDTA or benzylchronium chloride, and the usual quantities of diluents and/or carriers. The pharmaceutical composition can also be administered to the interior of the eye, and can be introduced by a needle or other delivery device which can introduce it to a selected area or structure. The composition containing the RNA silencing agent can also be applied via an ocular patch. [0338] In general, an RNA agent, e.g., a dsRNA agent, of the disclosure can be administered by any suitable method. As used herein, topical delivery can refer to the direct application of an RNA agent, e.g., a dsRNA agent, to any surface of the body, including the eye, a mucous membrane, surfaces of a body cavity, or to any internal surface. Formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, sprays, and liquids. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable. Topical administration can also be used as a means to selectively deliver the RNA agent, e.g., a dsRNA agent, to the epidermis or dermis of a subject, or to specific strata thereof, or to an underlying tissue. [0339] Compositions for intrathecal or intraventricular (e.g., intracerebroventricular) administration may include sterile aqueous solutions which may also contain buffers, diluents and other suitable additives. Compositions for intrathecal or intraventricular administration typically do not include a transfection reagent or an additional lipophilic moiety besides, for example, the lipophilic moiety attached to the RNA agent, e.g., a dsRNA agent. [0340] Formulations for parenteral administration may include sterile aqueous solutions which may also contain buffers, diluents and other suitable additives. Intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir. For intravenous use, the total concentration of solutes should be controlled to render the preparation isotonic. [0341] An RNA agent, e.g., a dsRNA agent, of the disclosure can be administered to a subject by pulmonary delivery. Pulmonary delivery compositions can be delivered by inhalation of a dispersion so that the composition within the dispersion can reach the lung where it can be readily absorbed through the alveolar region directly into blood circulation. Pulmonary delivery can be effective both for systemic delivery and for localized delivery to treat diseases of the lungs. In one embodiment, an RNA agent, e.g., a dsRNA agent, administered by pulmonary delivery has been modified such that it is capable of traversing the blood brain barrier. [0342] Pulmonary delivery can be achieved by different approaches, including the use of nebulized, aerosolized, micellular and dry powder-based formulations. Delivery can be achieved with liquid nebulizers, aerosol-based inhalers, and dry powder dispersion devices. Metered-dose devices are exemplary. One of the benefits of using an atomizer or inhaler is that the potential for contamination is minimized because the devices are self-contained. Dry powder dispersion devices, for example, deliver drugs that may be readily formulated as dry powders. An RNA silencing agent composition may be stably stored as lyophilized or spray- dried powders by itself or in combination with suitable powder carriers. The delivery of a composition for inhalation can be mediated by a dosing timing element which can include a timer, a dose counter, time measuring device, or a time indicator which when incorporated into the device enables dose tracking, compliance monitoring, and/or dose triggering to a patient during administration of the aerosol medicament. [0343] The types of pharmaceutical excipients that are useful as carriers include stabilizers such as human serum albumin (HSA), bulking agents such as carbohydrates, amino acids and polypeptides; pH adjusters or buffers; salts such as sodium chloride; and the like. These carriers may be in a crystalline or amorphous form or may be a mixture of the two. [0344] Bulking agents that are particularly valuable include compatible carbohydrates, polypeptides, amino acids or combinations thereof. Suitable carbohydrates include monosaccharides such as galactose, D-mannose, sorbose, and the like; disaccharides, such as lactose, trehalose, and the like; cyclodextrins, such as 2-hydroxypropyl-.beta.-cyclodextrin; and polysaccharides, such as raffinose, maltodextrins, dextrans, and the like; alditols, such as mannitol, xylitol, and the like. An exemplary group of carbohydrates includes lactose, trehalose, raffinose maltodextrins, and mannitol. Suitable polypeptides include aspartame. Amino acids include alanine and glycine, with glycine being exemplary. [0345] Suitable pH adjusters or buffers include organic salts prepared from organic acids and bases, such as sodium citrate, sodium ascorbate, and the like; sodium citrate is exemplary. [0346] An RNA agent, e.g., a dsRNA agent, of the disclosure can be administered by oral and nasal delivery. For example, drugs administered through these membranes have a rapid onset of action, provide therapeutic plasma levels, avoid first pass effect of hepatic metabolism, and avoid exposure of the drug to the hostile gastrointestinal (GI) environment. Additional advantages include easy access to the membrane sites so that the drug can be applied, localized and removed easily. In one embodiment, an RNA silencing agent administered by oral or nasal delivery has been modified to be capable of traversing the blood-brain barrier. [0347] In one embodiment, unit doses or measured doses of a composition that include RNA agents, e.g., dsRNA agents, are dispensed by an implanted device. The device can include a sensor that monitors a parameter within a subject. For example, the device can include a pump, such as an osmotic pump and, optionally, associated electronics. [0348] It will be readily apparent to those skilled in the art that other suitable modifications and adaptations of the methods described herein may be made using suitable equivalents without departing from the scope of the embodiments disclosed herein. Having now described certain embodiments in detail, the same will be more clearly understood by reference to the following examples, which are included for purposes of illustration only and are not intended to be limiting. EXAMPLES Example 1: SNP Discrimination Varies According to the Position of the Mismatch [0349] FIG. 46 is a flow chart illustrating a methodology for generating and selecting SNP- discriminating siRNAs that was implemented in the instance of HTT, but is also applicable to SNPs in other genes. A primary screen is conducted to determine which position the SNP is placed at causes the greatest discrimination. Then, the mismatch position(s) yielding best results are selected, and affinity for non-target alleles is further reduced in a secondary screening where chemical and structural optimizations to the siRNA molecule with improved selectivity and/or potency are selected. [0350] There are several SNPs within the HTT gene that have high rates of heterozygosity in HD patients (FIG. 45). For optimization of SNP-specific RNAi-mediated silencing of huntingtin, SNP rs362273 in exon 57 of HTT mRNA was used as model target for optimization of SNP selective silencing. This SNP heterozygosity occurs in 35% of the HD patient population. [0351] The psiCHECK reporter plasmid described herein contains SNP rs362273 and a partial flanking region from exon 57 of htt, within a Rluc 3’ UTR. The wild-type psiCHECK reporter plasmid contains the same region of htt without the SNP (FIG.1). [0352] Hydrophobically modified RNAs (hsiRNAs) designed to be complimentary to the Huntingtin (htt) mRNA containing the mutant SNP (2273-1 (A)) were screened for efficacy with the psiCheck reporter plasmid system. The number following SNP represents the position of the SNP in the siRNA (FIG.47). FIG. 2 shows that placing the SNP in position 2, 4 or 6 provided the greatest SNP discrimination, without losing efficacy against the mutant allele. HeLa cells transfected with one of two reporter plasmids were reverse transfected with 1.5 PM hsiRNAs by passive uptake, and treated for 72 hours. Luciferase activity was measured at 72 hours post transfection (FIG.2). [0353] The hsiRNAs were further tested for allelic discrimination in a dose response dual luciferase assay in HeLa cells (FIG.3). Multiple hsiRNAs preferentially silenced the reporter plasmid containing the mutant SNP as compared to the wild-type reporter plasmid. HeLa cells transfected with one of two reporter plasmids were reverse transfected with 1.5 mM hsiRNAs by passive uptake, and treated for 72 hours. Reporter plasmid expression was measured at 72 hours post transfection (FIG.3). Example 2: SNP Discrimination in the Endogenous Htt mRNA [0354] The hsiRNAs were tested for efficacy against the endogenous Huntingtin mRNA containing a homozygous rs362273 SNP. As HeLa cells are homozygous at rs362273, with an A on each allele, allelic discrimination was not assessed with this assay. Instead, FIG.4 shows that two hsiRNAs, SNP4-0 and SNP6-0, were highly effective at silencing the htt mRNA containing the correct SNP. The mRNA levels were measured using Quantigene 2.0 bDNA assay after treating HeLa cells with hsiRNAs via passive uptake for 72 hours. Human htt mRNA levels were normalized to human HPRT. Example 3: Designing hsiRNAs with a Second Mismatch for Greater Allelic Discrimination [0355] For each of the three hsiRNAs (SNP2-0, SNP4-0, and SNP6-0, also named mm2, mm4, and mm6, respectively) previously chosen for dose response, 16 new hsiRNAs were designed and synthesized with slight sequence modifications (FIG.34). These sequences introduced a single mismatch at every possible position along the original sequence, in order to test if the second mismatch impairs silencing of the off-target SNP more significantly than before, with little effect on silencing the target SNP. Antisense strand sequences shown 5’ to 3’, with the SNP site in red, and the new mismatch in blue (FIG.12). [0356] A primary screen of the efficacy of the hsiRNAs in FIG.12 showed that the position of the second mismatch, relative to the position of the nucleotide corresponding to the SNP, resulted in varying levels of SNP discrimination in HeLa cells. HeLa cells transfected with one of two psiCHECK reporter plasmids were reverse transfected with 1.5 PM hsiRNAs by passive uptake, and treated for 72 hours. Luciferase activity was measured at 72 hours post transfection. FIG.5 shows that multiple hsiRNAs discriminately silenced the reporter plasmid containing the SNP mutation as compared to the wild-type reporter plasmid. [0357] The most efficacious hsiRNAs, containing the second mismatch, were further tested in a dose response curve to verify improved SNP discrimination. HeLa cells transfected with one of two reporter plasmids were reverse transfected with hsiRNAs by passive uptake, and treated for 72 hours. Reporter expression measured with a dual-luciferase assay. FIGs.6-8 show the IC50 values of the hsiRNAs with two mismatches for silencing the reporter plasmid containing the SNP mutation versus the wild-type reporter plasmid. The SNP6-11 hsiRNA (hsiRNA molecule with the nucleotide corresponding to the polymorphism at position 6 from the 5’ end and the mismatch at position 11 from the 5’ end) and the SNP4-7 hsiRNA (hsiRNA molecule with the nucleotide corresponding to the polymorphism at position 4 from the 5’end and the mismatch at position 7 from the 5’ end) were shown to be the most efficacious (see FIGs. 7- 9). Surprisingly, altering the modification pattern around the SNP rescues efficacy lost by introducing the second mismatch without impairing discrimination. The SNP6-11 hsiRNA was altered so that it had 2’O-methyl modifications flanking the mismatch nucleotide (as well as the mismatch nucleotide itself having the 2’O-methyl modification) (see FIG.10). Example 4: Additional Modifications [0358] A variety of oligonucleotide types (e.g., gapmers, mixmers, miRNA inhibitors, splice- switching oligonucleotides (“SSOs”), phosphorodiamidate morpholino oligonucleotides (“PMOs”), peptide nucleic acids (“PNAs”) and the like) can be used in the oligonucleotides described herein, optionally utilizing various combinations of modifications (e.g., chemical modifications) and/or conjugations described herein and in, e.g., U.S. Serial No. 15/089,423; U.S. Serial No.15/236,051; U.S. Serial No.15/419,593; U.S. Serial No.15/697,120 and U.S. Patent No.9,809,817; and U.S. Serial No.15/814,350 and U.S. Patent No.9,862,350, each of which is incorporated herein by reference in its entirety for all purposes. [0359] For example, an oligonucleotide described herein may be designed as a di-siRNA (see, e.g., FIG. 14). An oligonucleotide described herein may include one or more different backbone linkages (see, e.g., FIG. 15). An oligonucleotide described herein may include a variety of sugar modifications (see, e.g., FIG. 16). An oligonucleotide described herein may include a variety of internucleotide bonds (see, e.g., FIG. 17). An oligonucleotide described herein may include one or more 5’ stabilization modifications (see, e.g., FIG. 18). An oligonucleotide described herein may include one or more conjugated moieties (see, e.g., FIG. 19). Illustrated in FIG.35 are a number of exemplary oligonucleotide backbone modifications. [0360] An oligonucleotide described herein can effectively be used to target a G at the SNP site simply by changing the base at the SNP position. As seen in FIG.33, compound SNP6- 11 was synthesized a second time, this time to target a G at the SNP site instead of an A. This allowed for selectively silencing either allele, a strategy that is very useful for patients with different heterozygosities at the same SNP site. [0361] In certain exemplary embodiments, one or more abasic nucleotides are utilized at an SNP position nucleotide, at a MM position nucleotide, at the 5' end, at the 3' end, or any combination of these. [0362] In certain exemplary embodiments, hsiRNAs are synthesized with varying sugar modifications around the mismatch to improve allele specificity, e.g., 2’FANA instead of 2’F; triple 2’F or triple 2’OMe around SNP/mismatch position. Example 5: HTT Mouse Model [0363] BAC97-HD refer to a transgenic mouse comprising a human bacterial artificial chromosome (BAC) transgenic insert containing the entire pathogenic 170 kb human Huntingtin (htt) genomic locus that was modified by replacing the human htt exon 1 with a loxP-flanked human mutant htt exon 1 sequence containing 97 mixed CAA-CAG repeats encoding a continuous polyglutamine (polyQ) stretch. [0364] Lead compound (SNP6-11) was synthesized into the di-branched chemical scaffold having the structure illustrated in FIG.31 and subsequently tested in vivo via 40 nmol bilateral intracerebroventricular (ICV) injection (20nmols to each side) in BAC97-HD female mice at 8 weeks of age. The mice had two copies of normal mouse htt gene with a G at SNP rs362273 and a transgenic insert of pathogenic human htt gene with an A at SNP rs362273A. A nonsense sequence with no target matches in the RNA transcriptome was also synthesized into the same di-branched scaffold and injected in the mice as a negative control (NTC). [0365] Several brain regions were collected from the mice for RNA and protein analysis 1 month post injection, and HTT protein levels were measured by western blot using Ab1 antibody. FIG.32A is a western blot performed on collected striatum tissue, and protein levels normalized to vinculin are presented in FIG.32B. Example 6: SNP Targeting is Sequence-Independent [0366] Whether SNP discrimination of lead compounds was sequence-dependent was assessed. Hydrophobically modified RNAs (hsiRNAs) designed to be complimentary to the Huntingtin (htt) mRNA containing a U to G mismatch or a C to A mismatch in rs362273 were used. Both the 6-11 hsiRNA complementary to a U to G mismatch and the 6-11 hsiRNA complementary to a C to A mismatch preferentially cleaved the target SNP (FIG.20). Example 7: Synthesis of Vinyl Phosphonate Modified Intersubunit Linkages [0367] Representative syntheses of the vinyl phosphinate modified intersubunit linkages discussed herein are illustrated in FIGS. 21 and 29. The synthetic procedure of FIG. 21 is detailed below. Synthesis of compound 3a [0368] Anhydrous solution of compound 2a (16.6 g, 20.8 mmol) in pyridine (100 mL) was added anhydrous DIPEA (6.5 mL, 37.4 mmol) and benzoyl chloride (3.6 mL, 31.2 mmol). After the mixture was stirred for 4 hours at room temperature, excess pyridine was evaporated and diluted with CH 2 Cl 2 . The organic solution was washed by sat. aq. NaHCO 3 . The organic layer was collected, dried over MgSO 4 , filtered and evaporated. Obtained crude material was purified by silica gel column chromatography (hexane-ethyl acetate, 4:1 to 1:1) yielding compound 3a as a slightly yellow foam (14.5 g, 78%); 1 H NMR (500 MHz, CDCl 3 ) d 7.88- 7.87 (m, 2H), 7.84 (d, 1H, J = 8.3 Hz), 7.67-7.58 (m, 5H), 7.48-7.45 (m, 4H), 7.39-7.32 (m, 4H), 7.25-7.23 (m, 3H), 7.18-7.17 (m, 2H), 7.12-7.07 (m, 4H), 6.80-6.75 (m, 4H), 6.08 (dd, 1H, J HH = 1.5 Hz, J HF = 15.2 Hz), 5.14, (d, 1H, J HH = 8.3 Hz), 4.59 (ddd, 1H, J HH = 3.7, 1.5 Hz, J HF = 51.9 Hz), 4.43 (ddd, 1H, J HH = 7.4, 4.0 Hz, J HF = 19.1 Hz), 4.24-4.23 (m, 1H), 3.79 (s, 6H), 3.62 (dd, 1H, J HH = 11.2, 2.0 Hz), 3.35 (dd, 1H, J HH = 11.1, 2.0 Hz), 1.00 (s, 9H); 13 C NMR (126 Hz, CDCl 3 ) d 168.4, 161.8, 158.72, 158.66, 148.9, 143.9, 139.4, 135.71. 135.70, 135.1, 134.8, 134.7, 132.3, 132.2, 131.3, 130.4, 130.2, 130.1, 129.1, 128.2, 128.0,127.91, 127.89, 127.2, 113.19, 113.16, 102.2, 92.5 (d, JCF = 194.4 Hz), 87.7 (d, J CF = 34.5 Hz), 87.2, 82.4, 70.0 (d, J CF = 15.4 Hz), 60.7, 60.4, 55.2, 26.6. Synthesis of compound 4a [0369] Compound 3a (14.5 g, 16.3 mmol) was dissolved into 3% trichloroacetic acid/ CH 2 Cl 2 solution (200 mL) containing triethylsilane (8.0 mL, 50.1 mmol) and stirred for 1 hour at room temperature. After the solution was washed by sat. aq. NaHCO 3 three times, collected organic layer was dried over MgSO 4 , filtered, and evaporated. Obtained crude material was purified by silica gel column chromatography (hexane/ethyl acetate, 4:1 to 3:7) yielding compound 4a as a white foam (8.67 g, 91%); 1 H NMR (500 MHz, CDCl 3 ) d 7.89-7.88 (m, 2H), 7.68-7.64 (6H, m), 7.51-7.45 (m, 4H), 7.42-7.38 (4H, m), 5.93 (dd, 1H, J HH = 2.9 Hz, J HF = 15.1 Hz), 5.73 (d, 1H, J HH = 8.2 Hz), 4.74 (ddd, 1H, J HH = 4.1, 3.2 Hz, J HF = 52.2 Hz), 4.31 (ddd, 1H, J HH = 5.8, 4.7, J HF = 15.4 Hz), 4.11-4.09 (m, 1H), 3.82-3.79 (m, 1H), 3.39 (ddd, 1H, J HH = 12.1, 5.6, 1.5 Hz), 1.64 (br, 1H), 1.11 (s, 9H); 13 C NMR (126 Hz, CDCl 3 ) d 168.3, 161.8, 149.0, 140.5, 135.7, 135.2, 132.8, 132.3, 131.3, 130.5, 130.4, 130.3, 129.2, 128.02, 127.96, 102.4, 91.8 (d, J CF = 91.8 Hz), 89.5 (d, J CF = 33.6 Hz), 69.5 (d, J CF = 69.5 Hz), 60.3, 26.8. Synthesis of compound 6a [0370] Anhydrous solution of compound 4a (6.5 g, 11.0 mmol) was added IBX (7.7 g, 27.6 mmol) and stirred for 2 hours at 85 º C. After cooling the mixture in an ice bath, the precipitate in the solution was filtered off through celite. Collected eluent was evaporated, co-evaporated with anhydrous CH 3 CN three times under argon atmosphere, and obtained compound 5a as a white foam was used without further purification. In a separate flask, anhydrous CH 2 Cl 2 (25 mL) solution containing CBr 4 (7.3 g, 22.1 mmol) was added PPh 3 (11.6 g, 44.2 mmol) at 0 º C and stirred for 0.5 h at 0 º C. To this solution, anhydrous CH 2 Cl 2 solution (25 mL) of compound 5a was added dropwise (10 min) at 0 º C and stirred for 2 h at 0 º C. After diluting with CH 2 Cl 2 , the organic solution was washed by aq. sat. NH 4 Cl, dried over MgSO 4 , filtered, and evaporated. Obtained material was dissolved into minimum amount of diethyl ether and added dropwise to excess diethyl ether solution under vigorously stirring at 0 º C. Precipitate in solution was filtered off through celite and eluents was evaporated. Obtained crude material was purified by silica gel column chromatography (hexane/ethyl acetate, 9:1 to 1:1) yielding compound 6a as a white foam (4.3 g, 52 %).1H NMR (500 MHz, CDCl 3 ) d 7.68-7.84 (m, 2H), 7.70-7.65 (m, 3H), 7.60-7.58 (m, 2H), 7.52-7.49 (m, 2H), 7.42-7.36 (m ,4H), 7.31-7.28 (m, 2H), 7.09 (d, 1H, J = 8.2 Hz), 6.25 (d, 1H, J = 8.9 Hz), 5.75 (dd, 1H, J HF = 8.24 Hz), 5.49 (dd, 1H, J HF = 21.4 Hz), 4.77 (t, 1H, J HH = 8.5 Hz, J HF = 8.5 Hz), 4.38 (dd, 1H, J HH = 4.1 Hz, J HF = 52.1 Hz), 4.25 (ddd, 1H, J HH = 8.1, 4.9 Hz, J HF = 19.4 Hz), 1.10 (s, 9H); 13 C NMR (126 Hz, CDCl 3 ) d 167.9, 161.6, 148.3, 141.4, 135.8, 134.7 (d, J C-Br = 139.0 Hz), 132.5, 132.2, 131.1, 130.5, 130.3, 130.2, 129.2, 127.9, 102.7, 97.3, 93.3 (d, J CF = 39.1 Hz), 91.5 (d, J CF = 190.7 Hz), 82.4, 73.9 (d, J CF = 16.4 Hz), 26.7. Synthesis of compound 7a-E and 7a-Z [0371] Anhydrous solution of compound 6a (4.2 g, 5.66 mmol) in DMF (25 mL) was added dimethylphosphite (2.09 mL, 22.6 mmol) and triethylamine (1.58 mL, 11.3 mmol) at 0 º C, and then stirred overnight at room temperature. After the solution was diluted with ethyl acetate, the organic solution was washed with aq. sat. NH 4 Cl and brine. Then the organic solution was dried over MgSO 4 , filtered and evaporated. Obtained crude material was purified repeatedly by silica gel column chromatography (hexane/ethyl acetate, 9:1 to 1:1) until all pure isomeric compound were collected separately, giving compound 7a-E (1.95 g, 52%); 1 H NMR (500 MHz, CDCl 3 ) d 7.87-7.85 (m, 2H), 7.89-7.85 (m, 3H), 7.61-7.59 (m, 2H), 7.52-7.48 (m, 2H), 7.45-7.32 (m, 6H), 7.08 (d, 1H, J HH = 8.2), 6.49 (d, 1H, J HH = 13.7), 5.99 (dd, 1H, J HH = 13.7 Hz, 8.1 Hz), 5.75 (d, 1H, J HH = 8.2), 5.63 (d, 1H, J HF = 19.8 Hz), 4.43 (dd, 1H, J HF = 52.6 Hz, J HH = 4.3 Hz), 4.42 (t, 1H, J HH = 8.0 Hz), 4.07 (ddd, J HH = 7.8, 4.7 Hz, J HF = 19.5 Hz), 1.08 (s, 9H); 13 C NMR (126 Hz, CDCl 3 ) d 148.4, 140.4, 135.8, 135.7, 135.3, 133.3, 132.3, 132.4, 132.1, 131.1, 130.5, 130.4, 130.3, 129.2, 127.95, 127.93, 112.4, 102.7, 91.7 (d, J CF = 36.3 Hz), 91.6 (d, J CF = 191.6 Hz), 82.8, 73.9 (d, J CF = 16.4 Hz), 26.7, 19.1; and 7a-Z (0.58 g, 15%); 1 H NMR (500 MHz, CDCl 3 ) d 7.87-7.85 (m, 2H), 7.68-7.65 (m, 3H), 7.61-7.59 (m, 2H), 7.52-7.48 (m, 2H), 7.42-7.39 (m, 2H), 7.34-7.29 (m, 4H), 7.12 (d, 1H, J HH = 8.2 Hz), 6.51 (d, 1H, J HH = 7.4 Hz), 5.96 (dd, 1H, J HH = 8.4 Hz, 7.4 Hz), 5.75 (d, 1H, J HH = 8.2 Hz), 5.57 (dd, 1H, J HH = 1.2 Hz, J HF = 20.6 Hz), 5.04 (dd, 1H, J HH = 8.2 Hz), 4.48 (J HH = 3.5 Hz, J HF = 53.1 Hz), 4.24 (ddd, 1H, J HH = 7.8, 4.9 Hz, J HF = 18.6 Hz), 1.09 (s, 9H); 13 C NMR (126 Hz, CDCl 3 ) d 168.0, 161.7, 148.4, 141.4, 135.9, 135.8, 135.2, 132.6, 132.5, 131.2, 130.6, 130.5, 130.2, 130.1, 129.2, 127.8, 127.7, 114.5, 102.6, 93.0 (d, J CF = 37.2 Hz), 91.6 (d, J CF =191.6 Hz), 80.3, 74.3 (d, J CF = 16.4 Hz), 26.7, 19.1. Synthesis of compound 9a [0372] Anhydrous compound 7a-E (1.95 g, 2.94 mmol) and Pd(OAc) 2 (125 mg, 0.59 mmol) [ 1,1' ~s(diphenylphosphino)ferrocene]dichloropalladium (II) (652 mg, 1.18 mmol) were purged with argon, and then dissolved into anhydrous THF (50 mL). After adding propylene oxide (2.06 mL, 29.4 mmol), compound 8a (2.07 g, 3.24 mmol) was added in one portion and stirred at for 4 h at 70 º C. After removing solvent under reduced pressure, the crude mixture was purified by silica gel column chromatography (hexane/ethyl acetate, 50:50 to 0:100) and obtained fractions containing compound 9a were further purified by silica gel column chromatography (CH 2 Cl 2 -MeOH, 0% to 5%) yielding compound 9a as a mixture of diastereo- isomers (2.04 g, 57%); 31 P NMR (202 MHz, CDCl 3 ) d 18.3. Synthesis of compound 10a [0373] Compound 9a (2.0 g, 1.64 mmol) in anhydrous THF (22.5 mL) was added 1.0 M TBAF-THF (2.5 mL, 2.5 mmol) and stirred at ambient temperature for 30 minutes. After diluting with CH 2 Cl 2 (120 mL), the organic layer was washed with brine, dried over MgSO 4 , filtered, and then evaporated. Obtained crude material was purified by silica gel column chromatography (1%TEA-CH 2 Cl 2 /MeOH, 0% to 6%) yielding compound 10a (1.52 g, 94%); 31 P NMR (202 MHz, CDCl 3 ) d 19.0, 18.7. Synthesis of compound 11a [0374] Compound 10a (589.7 mg, 0.6 mmol) was rendered anhydrous by repeated co- evaporation with anhydrous CH 3 CN and then dissolved into anhydrous CH 2 Cl 2 (6.0 mL). To this solution N,N-diisopropylethylamine (0.31 mL, 1.8 mmol) and 2-cyanoethyl N,N- diisopropylchlorophosphoramidite (0.16 mL, 0.72 mmol) were added at 0 °C. After stirring for 30 min at 0 °C, the reaction mixture was diluted with excess CH 2 Cl 2 . The organic layer was repeatedly washed with aq. sat. NaHCO 3 , dried over MgSO 4 , filtered, and evaporated. The obtained crude material was purified by silica gel column chromatography (1%TEA- CH 2 Cl 2 /MeOH, from 100% to 4%) yielding compound 11a as a white foam (570 mg, 80%); 31 P NMR (202 MHz, CDCl 3 ) d 150.3, 151.2, 151.1, 151.0, 18.72, 18.65, 18.55, 18.3. Synthesis of compound 4b [0375] Anhydrous solution of compound 3b (1.35 g, 2.0 mmol) in pyridine (10 mL) was added DIPEA (0.63 mL, 3.6 mmol) and benzoyl chloride (0.35 mL, 3.0 mmol), and stirred for 3 hours at room temperature. After diluting with excess CH 2 Cl 2 , the organic solution was washed with aq. sat. NaHCO 3 and brine. After drying over MgSO4, filtered and evaporating, obtained crude material was used for the next reaction without further purification. Obtained crude material containing compound 3b was added 3% trichloroacetic acid in CH 2 Cl 2 (25 mL) and triethylsilane (1 mL, 6.26 mmol), and stirred for 1 hour at room temperature. After the reaction mixture was diluted with CH 2 Cl 2 , the solution was washed with sat. NaHCO3 aq. three times, dried over MgSO 4 , filtered, then evaporated. Obtained crude material was purified by silica gel column chromatography (hexane/ethyl acetate, 4:1 to 1:4) yielding pure compound 4b (596.7 mg, 63% in 2 steps); 1 H NMR (500 MHz, DMSO-d6) d^8.13 (d, 1H, J HH = 8.2 Hz), 7.95 (d, 2H, J HH = 7.3 Hz), 7.81 (t, 1H, J HH = 7.5 Hz), 7.69-7.68 (m, 2H), 7.64-7.59 (m, 4H), 7.49- 7.42 (m, 6H), 5.93 (d, 1H, J HH = 4.6 Hz), 5.26 (t, 1H, J HH = 4.6 Hz), 4.36 (dd, 1H, J HH = 4.6, 4.6 Hz), 4.02-4.00 (m, 1H), 3.65-3.61 (m, 1H), 3.54 (dd, 1H, J HH = 4.6, 4.6 Hz), 3.09 (s, 3H), 1.03 (s, 9H); 13 C NMR (126 Hz, DMSO-d6) 169.8, 162.1, 149.5, 141.3, 136.1, 135.9, 135.8, 133.4, 133.2, 131.5, 130.7, 130.52, 130.48, 130.0, 128.4, 128.3, 102.1, 86.7, 85.6, 82.8, 79.7, 70.8, 60.2, 57.8, 27.2, 19.4; HRMS (ESI) m/z calcd for C 33 H 35 N 2 O 7 Si- [M - H]- m/z 599.2219, found m/z 599.2258. Synthesis of compound 6b [0376] Anhydrous solution of compound 4b (300.4 mg, 0.5 mmol) in CH 3 CN (5 mL) was added IBX (350 mg, 1.3 mmol) and stirred for 2 hours at 85 º C. After cooling the solution at 0 º C, the precipitate was filtered off by celite-filtration. Obtained eluent containing compound 5b was evaporated, rendered anhydrous by repeated co-evaporation with anhydrous CH 3 CN, and used for the next reaction without further purification. Separatory prepared anhydrous solution of CBr 4 (331.6 mg, 1.0 mmol) in CH 2 Cl 2 (5.0 mL) was added triphenylphosphine (524.6 mg, 2.0 mmol) at 0 º C in one portion and stirred at 0 º C for 30 minutes. To this solution, compound 5b in anhydrous CH 2 Cl 2 (1.5 mL) was added dropwise (10 min) at 0 º C and stirred for 2 h at 0 º C. The solution was then diluted with CH 2 Cl 2 and washed with sat. NaHCO 3 aq. and brine. After the organic solution was dried over MgSO 4 , filtered and evaporated, obtained crude material was purified by silica gel column chromatography (hexane/ethyl acetate, 9:1 to 4:6) yielding compound 6b (210.9 mg, 56%); 1 H NMR (500 MHz, CDCl 3 ) d 7.88 (d, 2H, J HH = 7.3 Hz), 7.70-7.62 (5H, m), 7.51-7.38 (m, 9H), 7.08 (d, 1H, J HH = 8.2 Hz), 6.26 (d, 1H, J HH = 8.6 Hz), 5.75 (d, 1H, J HH = 8.2 Hz), 5.68 (d, 1H, J HH = 0.8 Hz), 4.84 (dd, 1H, J HH = 8.6 Hz, 8.6 Hz), 3.86 (dd, 1H, J HH = 7.5 Hz, 5.0 Hz), 3.30 (s, 3H), 3.18 (br, 1H), 1.11 (s, 9H); 13 C NMR (126 Hz, CDCl 3 ) 168.3, 161.7, 148.6, 138.9, 135.9, 135.8, 134.3, 132.6, 132.4, 131.2, 130.5, 130.4, 130.3, 129.2, 128.0, 127.9, 102.4, 97.5, 90.0, 82.44, 82.39, 74.4, 58.2, 26.7, 19.1; HRMS (ESI) m/z calcd for C 34 H 33 Br 2 N 2 O 6 Si- [M - H]- m/z 751.0480 [M-H]-, found m/z 753.6495. Synthesis of 7b-E and 7b-Z [0377] Anhydrous solution of compound 6b (6.11 g, 8.1 mmol) in DMF (35 mL) was added dimethylphosphite (2.97 mL, 34.0 mmol) and triethylamine (2.26 mL, 17.0 mmol) at 0 º C, and then stirred overnight at room temperature. After the solution was diluted with ethyl acetate, the organic solution was washed with sat. NH4Cl aq. and brine. Then the organic solution was dried over MgSO 4 , filtered and evaporated, and obtained crude material was purified repeatedly by silica gel column chromatography (hexane/ethyl acetate, 9:1 to 1:1) until all pure isomeric compound were collected separately, giving compound 7b-E (3.0 g, 55%); 1 H NMR (500 MHz, CDCl 3 ) d 7.89-7.87 (m, 2H), 7.70-7.62 (m, 5H), 7.51-7.39 (m, 8H), 7.10 (d, 1H, J HH = 8.3 Hz), 6.47 (dd, 1H, J HH = 13.6, 0.8 Hz), 6.01 (dd, 1H, J HH = 13.6, 7.9 Hz), 5.76-5.74 (m, 2H), 4.51 (dd, 1H, J HH = 7.8, 7.8 Hz), 7.36 (dd, 1H, J HH = 7.8 Hz, 4.9 Hz), 3.34 (s, 3H), 3.17 (dd, 1H, J HH = 4.7, 1.2 Hz), 1.09 (s, 9H); 13 C NMR (126 Hz, CDCl 3 ) d 168.3, 161.7, 148.7, 138.4, 135.9, 135.8, 135.3, 133.8, 132.6, 132.4, 131.2, 130.5, 130.4, 130.3, 129.2, 128.0, 127.9, 112.1, 102.3, 88.9, 82.8, 82.6, 77.2, 74.2, 58.1, 26.8, 19.1; and 7b-Z (1.23 g, 22%); 1 H NMR (500 MHz, CDCl3) d 7.89-7.87 (m, 2H), 7.72-7.70 (m, 2H), 7.68-7.63 (m, 3H), 7.51-7.44 (m, 4H), 7.41- 7.37 (m, 4H), 7.16 (d, 1H, J – 8.2 Hz), 6.53 (dd, 1H, J HH = 7.4, 0.6 Hz), 6.03 (dd, 1H, J HH = 8.5, 7.4 Hz), 5.75-5.73 (m, 2H), 5.12 (t, 1H, J HH = 8.1 Hz), 3.93 (dd, 1H, J HH = 6.9, 5.0 Hz), 3.32 (br, 1H), 3.26 (s, 3H), 1.10 (s, 9H); 13 C NMR (126 Hz, CDCl 3 ) d 168.3, 161.8, 148.7, 139.3, 135.91, 135.85, 135.22, 132.74, 132.71, 131.2, 130.8, 130.5, 130.23, 130.16, 129.2, 127.78, 127.75, 114.6, 102.2, 90.1, 82.4, 80.6, 77.2, 74.8, 58.1, 26.8, 19.2. Synthesis of compound 8b [0378] Anhydrous 5'-O-DMTr-2'-deoxy-2'-fluoro-3'-[methyl-N,N-(diisopropyl)ami no] phosphor-amidite (4.26 g, 6.0 mmol) was dissolved in 0.45 M 1H-tetrazole/CH 3 CN solution (27 mL, 12 mmol) and stirred for 30 minutes at room temperature. To this solution, H 2 O (3.6 mL) was added and stirred for 30 minutes at room temperature. After diluting with ethyl acetate, the organic solution was washed with brine six times, dried over MgSO 4 , filtered and then evaporated. Obtained compound 8b with a slight amount of impurity was used for the next reaction without further purification; 31 P NMR (CDCl 3 , 202 MHz) d 8.92, 8.28. Synthesis of compound 9b [0379] Anhydrous compound 7b-E (2.84 g, 4.20 mmol) and Pd(OAc) 2 (188.6 mg, 0.84 mmol) and [ 1,1'is(diphenylphosphino)ferrocene]dichloropalladium (II) (931.4 mg, 1.68 mmol) were purged with argon, and then dissolved into anhydrous THF (50 mL). After adding propylene oxide (2.94 mL, 42.0 mmol), compound 9b (3.16 g, 5.04 mmol) was added in one portion and stirred at for 4 hours at 70 º C. After removing solvent under reduced pressure, the crude mixture was purified by silica gel column chromatography (hexane-ethyl acetate, 50:50 to 0:100) and obtained fractions containing compound 9b were further purified by silica gel column chromatography (1%TEA-CH 2 Cl 2 /MeOH, 0% to 5%) yielding compound 9b as a mixture of diastereoisomers (3.3 g, 64%); 31 P NMR (202 MHz, CDCl 3 ) d 19.31, 18.72. Synthesis of compound 10b [0380] Compound 9b (3.3 g, 2.70 mmol) in anhydrous THF (36.5 mL) was added 1.0 M TBAF-THF (4.05 mL, 4.05 mmol) and stirred at ambient temperature for 30 minutes. After diluting with CH 2 Cl 2 (150 mL), the organic layer was washed with brine, dried over MgSO 4 , filtered, and then evaporated. Obtained crude material was purified by silica gel column chromatography (1%TEA-CH 2 Cl 2 /MeOH, 0% to 8%) yielding compound 10b (1.25 g, 47%); 31 P NMR (202 MHz, CDCl 3 ) d 19.8, 19.1. Synthesis of compound 11b [0381] Compound 10b (393.2 mg, 0.4 mmol) was rendered anhydrous by repeated co- evaporation with anhydrous CH 3 CN and then dissolved into anhydrous CH 2 Cl 2 (4.0 mL). To this solution N,N-diisopropylethylamine (0.21 mL, 1.2 mmol) and 2-cyanoethyl N,N- diisopropylchlorophosphoramidite (0.11 mL, 0.48 mmol) were added at 0 °C. After stirring for 30 min at 0 °C, the reaction mixture was diluted with excess CH 2 Cl 2 . The organic layer was repeatedly washed with aq. sat. NaHCO 3 , dried over MgSO 4 , filtered, and evaporated. The obtained crude material was purified by silica gel column chromatography (1%TEA- CH 2 Cl 2 /MeOH, from 100% to 4%) yielding compound 11b as a white foam (319.6 mg, 68%); 31 P NMR (202 MHz, CDCl 3 ) d150.7, 150.4, 150.3, 19.9, 19.5, 19.4, 18.8. Example 8: Solid Support-Mediated Synthesis of Vinyl Phosphonate-Modified Oligonucleotides [0382] A representative synthesis of an oligonucleotide having a vinyl phosphinate modified intersubunit linkages is illustrated in FIG.22. Examples of VP-modified sequences that were synthesized can be found in FIGS.28A and 28B. Synthesis of inter-nucleotide (E)-vinyl phosphonate modified RNA oligonucleotides. [0383] The synthesis RNA oligonucleotides having one vinyl phosphonate linkage was performed on MerMade 12 automated RNA synthesizer (BioAutomation) using 0.1 M anhydrous CH 3 CN solution of 2'-modified (2'-fluoro, 2'-O-methyl) phosphonamidite and vinylphosphonate-linked dimer phosphoramidites. For the solid support, UnyLinker support (ChemGenes) was used. The synthesis was conducted by standard 1.0 m l scale RNA phosphoramidite synthesis cycle, which consists of (i) detritylation, (ii) coupling, (iii) capping, and (iv) iodine oxidation. 5-(Benzylthio)-1H-tetrazole in anhydrous CH 3 CN was used for phosphoramidite activating reagent, and 3% dichloroacetic acid in CH 2 Cl 2 was used for detritylation. 16% N-methylimidazole in tetrehydrofurane (Cap A) and 80:10:10 (v/v/v) tetrhydrofurane-Ac 2 O-2,6-lutidine (Cap B) were used for capping reaction.0.02 M I 2 in THF- pyridine-H 2 O (7:2:1, v/v/v) was used for oxidation and 0.1 M 3-[(Dimethylamino- methylidene)amino]-3H-1,2,4-dithiazole3-thione in pyridine:CH 3 CN (9:1, v/v) was used for sulfurizing. For 5'-terminal phosphorylation, bis(2-cyanoethyl)-N,N-diisopropyl phosphoramidite was used. For the 3'-cholesterol modified RNA oligonucleotide synthesis, cholesterol 3ƍ-lcaa CPG 500Å (ChemGenes) was used, and RNA synthesis was conducted in the same condition as the condition used for VP-modified RNAs. After the chemical chain elongation, deprotection and cleavage from the solid support were conducted by NH 4 OH-EtOH (3:1, v/v) for 48 hours at 26 º C. In the case of vinyl phosphonate modified RNA, RNA on solid support was first treated with TMSBr-pyridine-CH 2 Cl 2 (3:1:18, v/v/v) for 1 h at ambient temperature in RNA synthesis column. Solid support was then washed by water (1 mL x 3), CH 3 CN (1 mL x 3) and CH 2 Cl 2 (1 mL x 3) by flowing solution thorough synthesis column, and then dried under vacuum. After transferring the solid support to screw-capped sample tube, base treatment by NH 4 OH-EtOH (3:1, v/v) for 48 h at 26 º C was conducted. Crude RNA oligonucleotide without cholesterol conjugate was purified by standard anion exchange HPLC, whereas RNAs with cholesterol-conjugate were purified by reversed-phase HPLC. Obtained all purified RNAs were desalted by Sephadex G-25 (GE Healthcare) and characterized by electrospray ionization mass spectrometry (ESI-MS) analysis. Example 9: Silencing Efficacy [0384] FIGS. 23 and 24 provide visual representations of the VP-modified siRNA studied herein. FIG.25 exemplifies the effect that one or more vinyl phosphonate modifications in an intersubunit linkage at varying positions on the guide strand has on silencing. As can be seen from the data in FIG. 25, RISC is very sensitive to VP modification, and having a mismatch base pair at various positions can disrupt siRNA potency. [0385] FIGS, 26, 27A, and 27B also illustrate the ability of VP-modified siRNA to silence the mutant allele. As can be seen by FIGS. 27A and 27B, adding a mismatch in the siRNA sequence could improve allelic discrimination without affecting mutant allele silencing. FIG. 30 demonstrates that the introduction of a VP-modified linkage next to the SNP site significantly enhanced target/non-target discrimination of SNP-selective siRNAs. Compounds containing primary (position 6) and secondary (position 11) SNPs were synthesized with or without a VP-modification between positions 5 and 6 As can be seen in FIG. 30, the presence of a VP-modification had no impact on “on target” activity, but fully eliminated any detectable silencing for non-target mRNAs. The method for generating the data in FIGS. 25, 26, 27A, and 27B is described below. hsiRNA passive delivery.
[0386] Cells were plated in Dulbecco’s Modified Eagle's Medium containing 6% FBS at 8,000 cells per well in 96-well cell culture plates. hsiRNAs were diluted to twice the final concentration in OptiMEM (Carlsbad, CA; 31985-088), and 50 mL diluted hsiRNAs were added to 50 pL of cells, resulting in 3% FBS final. Cells were incubated for 72 hours at 37 °C and 5% CO 2 . The maximal dose in the in vitro dose response assays was 1.5 mM compound. Method for quantitative analysis of tar set mRNA.
[0387] mRNA was quantified from cells using the Qu anti Gene 2.0 assay kit (Affymetrix, QS0011). Cells were lysed in 250 mL diluted lysis mixture composed of one part lysis mixture (Affymetrix, 13228), two parts H 2 O and 0.167 mg/mL proteinase K (Affymetrix, QS0103) for 30 min at 55 °C. Cell lysates were mixed thoroughly, and 40 mL of each lysate was added per well of a capture plate with 20 pL diluted lysis mixture without proteinase K. Probe sets for human HTT and (Affymetrix; #SA-50339, SA-10030) were diluted and used according to the manufacturer's recommended protocol. Datasets were normalized to HPRT.
Method for Creating Bar Graph.
[0388] Data were analyzed using GraphPad Prism 7 software (GraphPad Software, Inc., San Diego, CA). Concentration-dependent IC 50 curves were fitted using a log(inhibitor) versus response - variable slope (four parameters). For each cell treatment plate, the level of knockdown at each dose was normalized to the mean of the control group (untreated group). The lower limit of the curve was set to less than 5, and the upper limit of the curve was set to greater than 95. To create the bar graph, the percent difference was calculated by subtracting the IC 50 value for each compound from the IC 50 value for each corresponding control compound, dividing by the IC 50 value for the control compound, and multiplying by 100. If the percent difference was less than -500%, the percent difference was artificially set to -500%. The lower limit of the graph was cut at -300%. [0389] The contents of all cited references (including literature references, patents, patent applications, and websites) that maybe cited throughout this application are hereby expressly incorporated by reference in their entirety for any purpose, as are the references cited therein. The disclosure will employ, unless otherwise indicated, conventional techniques of immunology, molecular biology and cell biology, which are well known in the art. [0390] The disclosure may be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting of the disclosure. Scope of the disclosure is thus indicated by the appended claims rather than by the foregoing description, and all changes that come within the meaning and range of equivalency of the claims are therefore intended to be embraced herein. Example 10: Primary screen yields multiple efficacious siRNA sequences for SNP rs362307 heterozygosity [0391] siRNAs designed to be complimentary to the HTT mRNA containing an alternative mutant SNP (rs362307) (FIG. 39) were all screened with reporter plasmids containing the target region for the SNP of interest (FIG.40). HeLa cells transfected with one of two reporter plasmids were reverse transfected with 1.5uM hsiRNAs by passive uptake, and treated for 72 hours. The number following SNP represents the position of the SNP in the siRNA. It was expected that this SNP would be more difficult to target based on the high G/C content of the region around it. It appears that placing the SNP in position 3 provided the most SNP discrimination, without losing efficacy against the mutant allele, showing that the best SNP position is sequence-specific (FIG. 41). This primary screening process may thus be carried out for selecting the best SNP position for any SNP. Example 11: When applied to SNP rs362307, a secondary mismatch continues to improve allelic discrimination [0392] As reported in FIG.42, primary screen of new sequences with mismatches introduced into all possible positions yields multiple efficacious hsiRNAs with increased SNP discrimination at position rs362307 as well. Introducing a mismatch at position 7 and 8 appeared to increase selectivity while preserving target silencing efficacy. Other secondary mismatches provided excellent discrimination, but less activity overall. Example 12: Measuring SNP discrimination in sequences including an SNP [0393] To measure SNP discrimination by each of the sequences disclosed in Tables 5-7 (i.e., each hsiRNA having a particular SNP position nucleotide and mismatch (MM) position nucleotide combination), psiCHECK reporter plasmids containing either a wild-type region of htt or the same region of htt with the SNP of the sequence are prepared and tested using a dual- luciferase. HeLa cells transfected with one of two reporter plasmids are reverse transfected with hsiRNAs by passive uptake, and treated for 72 hours. Luciferase activities are measured in the assays with or without the additional mismatch, and are then plotted in dose response curves and compared to reveal sequences yielding the best results in terms of discrimination and efficacy of silencing. Example 13: Synthesis of a Phosphinate-Modified Intersubunit Linkage [0394] A method for preparing a phosphinate-modified intersubunit linkage is summarized in FIGS. 44A-44C. This method involves Jones oxidation from a free alcohol to the corresponding ketone followed by a Wittig olefination to achieve the exomethylene moiety shown in intermediate compound 3. Protecting of the amide with BOM followed by hydroboration-oxidation results in the free alcohol intermediate 5. Mesylation followed by a modified Finkelstein reaction produces the iodinated intermediate 7, which then undergoes further functionalization to achieve the methyl phosphinate monomer 9. [0395] To achieve monomer 18, various protection and deprotection steps are employed to achieve intermediate 13. IBX oxidation produces the corresponding ketone followed by Wittig olefination to access the methylene. Once again, hydroboration-oxidation followed by mesylation and Finkelstein reaction results in monomer 18. [0396] Combining monomers 9 and 18 under basic conditions produces phosphinate-linked dimer 19. Acid-mediated and Pearlman’s catalyzed deprotection followed by further phosphanamine functionalization results in dimer 22. Example 14: Altering 2’-OMe / 2’-F content to modify efficacy and discrimination [0397] By altering the 2’-O-methyl/fluoro backbone modification pattern around the SNP and mismatch site, efficacy and discrimination of the siRNA was modified (FIG. 48A-48D). Heavy 2’-fluorination adjacent to the SNP position improved target binding, but decreased target discrimination. Subsequently adding heavy 2’-O-methylation around the mismatch rescued discrimination lost due to fluorination. Although the original chemical modification pattern described supra was beneficial for in vivo study, the technique described in this example can be used to fine-tune SNP-targeting compounds described herein, and to identify additional new SNP-targeting compounds.
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