NOVEL INHIBITORS OF RETROVIRAL REVERSE TRANSCRIPTASE

GRANT STATEMENT

[0001 ] This invention was made in part from government support under Grant No. AI 62513 from the National Institutes of Health. The U.S. Government has certain rights in the present disclosure.

RELATED APPLICATION INFORMATION

[0002] This application claims the benefit of U.S. Patent Application Serial No. 61/128,478, filed May 22, 2008, the disclosure of which is herein incorporated by reference in its entirety.

TECHNICAL FIELD

[0003] The present invention relates to the field of oligonucleotide chemistry and more specifically to novel oligonucleotide molecules and their use as anti-viral agents.

BACKGROUND

[0004] Aptamers are oligonucleic acid or peptide molecules that are characterized by specific binding to a target molecule. The specific binding underlies the ability of aptamers to act as potent modifiers of protein function. Although they are now known to occur naturally in riboswitches, aptamers as originally described are engineered molecules produced through iterative selection processes drawing from a large random sequence pool. Aptamers are useful in basic research and hold special promise for clinical applications as macromolecular drugs. [0005] A nucelic acid aptamer is essentially a single-stranded oligonucleotide (DNA or RNA), or a series thereof. Selection processes for producing nucleic acid aptamers include a combinatorial technique known as SELEX ("Systematic Evolution of Ligands by Exponential Enrichment"; Tuerk C. & Gold L., SCIENCE (1990), 249 (4968): 505-510), and the process known as in vitro selection in which RNA ligands are selected against various organic dyes (Ellington A.D. & Szostak J.W., NATURE (1990), 346: 818-822). In any case, the resulting aptamers bind tightly and selectively to their ligands and may potentially be employed in targeted molecular therapies.

[0006] Certain aptamers and their molecular ligands have been tested for potential therapeutic applications. In particular, the FDA has approved clinical trials for

Macugen™(pegaptinib sodium), an aptamer with application in ophthalmic pathologies. DNA

and RNA aptamers also have been generated against HIV-I proteins to target viral enzymes (Reverse Transcriptase, Protease, Integrase) or viral expression (Rev, Tat), packaging and entry (Gag, nucleocapsid, gpl20). For example, certain RNA aptamers against HIV-I Reverse Transcriptase have been isolated and tested in vitro and in vivo, and some single-stranded DNA aptamers against HIV-I Reverse Transcriptase have also been described. [0007] A "G-quadruplex" (also known as a G-tetrad or G4-DNA) is a four-stranded nucleic acid structure formed from a sequence that is guanine -rich and thus capable of forming a square arrangement of guanines (a tetrad), which is stabilized by Hoogsteen hydrogen bonding and further stabilized by the existence of a monovalent cation (especially potassium) in the center of the tetrads. A G-quadruplex can be formed of DNA, RNA, LNA and PNA, and may be intramolecular, bimolecular or tetramolecular. Depending on the direction of the strands or parts of a strand that form the tetrads, structures may be described as parallel or antiparallel. Potential quadruplex sequences have been identified in eukaryotic telomeres. Recently, non-telomeric quadruplexes have been identified, e.g. in the proto-oncogene c-myc _^ H-ras, N-ras promoter regions. Thus, quadruplex structures may be a common control element of gene expression. Increasing interest exists in finding and identifying small molecules and naturally occurring proteins that may be control targets of G-quadruplex structures and thus may be candidates for specific therapeutic interventions. The SELEX technique for generating aptamers has been used to generate a few sequence variants that produce variants of the G -quadruplex structure. [0008] G-rich oligonucleotides (GRO), a novel class of antiproliferative agents, have also been described. The DNA aptamer AGROlOO is an experimental anticancer drug that has entered human clinical trials. It is a non-antisense, guanosine-rich phosphodiester oligodeoxynucleotide that also forms stable G-quadruplex structures. The biological activity of GROs results from their specific binding to specific cellular proteins as aptamers. Nucleolin has is an important target protein of GROs, and is a multifunctional protein expressed at high levels by cancer cells.

[0009] Certain DNA oligomers having G-quadruplex structures have been described as inhibitors of certain retroviral functions. For example, the DNA oligomers Zintevir™ , 93del, and 112 del are different G-quadruplex aptamers possessing anti-HIV activity. Zintevir™ is a unimolecular 17-mer ODN-derived aptamer (ARl 77, T30177, and T30695) which prevents the binding of HIV gpl20 to CD4 cells and inhibits HIV integrase, and is among the first

oligonucleotides to enter human clinical trials. 93 del and 112 del are dimeric DNA G- quadruplex aptamers (shorter DNA aptamers derived from ODN93 and ODNl 12) originally selected as inhibitors against RNaseH activity).

[0010] Thus, the quadruplex structure may be important structural component of new antiviral and ant-cancer drugs, and may be useful in the development of strategies for designing new anti-viral and anti-cancer drugs, particularly for combating the immunodeficiency viruses including HIV-I, HIV-2 and SIV. Consequently, there is a need in the art for methods that allow the identification of aptamers that inhibit proteins that are critical to HIV-I, HIV-2 and SIV replication, as well as specific aptamers that recognize these molecules.

SUMMARY

[0011] In one aspect, the present disclosure relates to an isolated nucleic acid molecule comprising a double-helical domain and a G-quadruplex domain coupled by a linker domain. [0012] In another aspect the present disclosure relates to an isolated nucleic acid molecule having a sequence selected from the group consisting of SEQ ID NOS. 15-56 and SEQ ID NOS. 59-63.

[0013] In another aspect the present disclosure relates to a method of binding a nucleic acid molecule to a primate lentiviral reverse transcriptase polypeptide comprising combining the nucleic acid molecule and the lentiviral reverse transcriptase polypeptide for a time and under conditions effective to allow the nucleic acid molecule to bind to the lentiviral reverse transcriptase polypeptide such that said binding occurs, wherein the lentiviral reverse transcriptase polypeptide has at least 60% sequence identity with SEQ ID. NO: 1, and the isolated nucleic acid molecule comprises a double-helical domain and a G-quadruplex domain coupled by a linker domain.

[0014] In another aspect the present disclosure relates to a method of preparing an isolated nucleic acid molecule that binds a primate lentiviral reverse transcriptase polypeptide, the method including identifying a first nucleotide sequence that provides a double-helical domain, identifying a second nucleotide sequence that provides a G-quadruplex domain, identifying a linker domain; and identifying an aptamer sequence for the isolated nucleic acid molecule that comprises the double helical domain coupled to the G-quadruplex domain by the linker domain. [0015] In another aspect the present disclosure relates to a kit for inhibiting a primate lentiviral reverse transcriptase, the kit comprising at least one nucleic acid molecule as provided

above, and written material describing methods for its use to inhibit a primate lentiviral reverse transcriptase.

BRIEF DESCRIPTION OF THE FIGURES

[0016] Figure 1 shows the scheme two variants of the invented inhibitory structure. The difference is in the localization of the terminal ends. Q-quadruplex structure; HF-double helical fragment; IL-inter-module linker/bridge; TL-terminal loop; The quadruplex linkers/loops are not marked.

[0017] Figure 2 shows the inhibition of HIV- 1 (HXB2) RT polymerization using ssDNA molecules. RT6(80) - ssDNA aptamer (Schneider D., et. al, Biochemistry (1995), 34:9599- 9610); RlT is a nucleic acid molecule in which intervening bases in the quadruplex domain are single Ts; RlC - a nucleic acid molecule in which the intervening bases in the quadruplex domain are single Cs; RlA - a nucleic acid molecule in which the intervening bases in the quadruplex domain are single As. The increasing final concentrations of inhibitor in the reactions were as follows: 10, 30 and 100 nM; N - the control reaction, without RT protein; K- the control reaction, without any inhibitor.

[0018] Figure 3 shows the inhibition of HIV- 1 (HXB2) RT polymerization using ssDNA molecules. RlT - the nucleic acid molecule in which the intervening bases in the quadruplex domain are single Ts; HF -the double helical domain only; Q -the quadruplex domain only; M - a mix of HF and Q in ratio, 1 :1, but lacking a physical connection; DNA- random fragment of DNA molecule (increasing final concentrations of inhibitor in reactions as follows: 10, 30 and 100 nM for RlT and 10, 30 and 100 μM for HF, Q, M and DNA; N - the control reaction, without any RT protein; K- the control reaction, without any inhibitor).

[0019] Figure 4A shows the inhibition of HIV- 1 (HXB2) RT polymerization using ssDNA molecules in standard assay buffer (K+). RlT - the nucleic acid molecule in which the intervening bases in the quadruplex domain are single Ts; SN (Supernova) - the nucleic acid molecule in which the intervening bases in the quadruplex domain are replaced by Sp- C 18(HEG); Vor ("RT6-B")- a nucleic acid molecule in which ATC is deleted from the 3' end of the RT-6 "full-length" apatmer starting sequence (increasing final concentrations of inhibitor in reactions as follows: 10, 30 and 100 nM; N - the control reaction, without RT protein; K- the control reaction, without any inhibitor).

[0020] Figure 4B shows the inhibition of HIV- 1 (HXB2) RT polymerization using ssDNA molecules in buffer with Na+ as the only monovalent ion. RlT - the nucleic acid molecule in which the intervening bases in the quadruplex domain are single Ts; SN (Supernova)- the nucleic acid in which the intervening bases in the quadruplex domain are replaced by Sp- C 18(HEG); Vor ("RT6-B")- a nucleic acid molecule in which ATC is deleted from the 3' end of the RT-6 "full-length" apatmer starting sequence (increasing final concentrations of inhibitor in reactions as follows: 10, 30 and 100 nM; N - the control reaction, without RT protein; K- the control reaction, without any inhibitor).

[0021] Figure 5 shows the inhibition of HIV-I (HXB2) RT polymerization using ssDNA molecules. R4T - the nucleic acid molecule in the intervening bases in the quadruplex domain are single Ts (increasing final concentrations of inhibitor in reactions are following: 0.3, 1, 3, 10, 30, 100 and 300 nM); R8T - the nucleic acid molecule in the intervening bases in the quadruplex domain are eight Ts (increasing final concentrations of inhibitor in reactions as follows: 0.3, 1, 3, 10, 30, 100 and 300 nM; N - the control reaction, without RT protein; K- the control reaction, without any inhibitor).

[0022] Figure 6 shows the inhibition of HIV-I (HXB2) RT polymerization using ssDNA molecules. RlT-HEG - the nucleic acid molecule in which the intervening bases in the quadruplex domain are single Ts and the linker domain connecting the G-quadruplex domain and the double helical domain is HEG, (increasing final concentrations of inhibitor in reactions as follows: 0.3, 1, 3, 10, 30, 100 and 300 nM; N - the control reaction, without RT protein; K- the control reaction, without any inhibitor).

[0023] Figure 7 shows the inhibition of HIV-I (HXB2) RT polymerization using ssDNA molecules. S4 - a nucleic acid molecule in which the intervening bases in the quadruplex domain are single Ts, and the helical domain includes a shortened hairpin loop relative to RlT. The sequence of the helical domain is otherwise identical to RlT (increasing final concentrations of inhibitor in reactions are following: 0.3, 1, 3, 10, 30, 100 and 300 nM); S5 - a nucleic acid molecule in which the intervening bases in the quadruplex domain are single Ts, and the helical domain sequence is modified relative to RlT (increasing final concentrations of inhibitor in reactions as follows: 0.3, 1, 3, 10, 30, 100 and 300 nM; N - the control reaction, without RT protein; K- the control reaction, without any inhibitor).

[0024] Figure 8 shows the inhibition of HIV-I (HXB2) RT polymerization using ssDNA molecules. RlT - the nucleic acid molecule in which the intervening bases in the quadruplex domain are single Ts (increasing final concentrations of inhibitor in reactions are following: 10, 30 and 100 nM); DyIl - a topologically variant nucleic acid molecule in which the intervening bases in the quadruplex domain remain single Ts (increasing final concentrations of inhibitor in reactions are following: 10, 30 and 100 nM); Dyl2 - another topologically variant nucleic acid molecule in which the intervening bases in the quadruplex domain remain single Ts (increasing final concentrations of inhibitor in reactions are following: 10, 30 and 100 nM); Dyl3 - another topologically variant nucleic acid molecule in which the intervening bases in the quadruplex domain remain single Ts (increasing final concentrations of inhibitor in reactions as follows: 10, 30 and 100 nM; N - the control reaction, without RT protein; K- the control reaction, without any inhibitor).

[0025] Figure 9 shows the inhibition of HIV-I (HXB2) RT polymerization using ssDNA molecules. TQKl - a nucleic acid molecule in which one G in the quadruplex domain is replaced with A (increasing final concentrations of inhibitor in reactions are following: 0.3, 1, 3, 10, 30, 100 and 300 nM); TQK2 - another nucleic acid molecule in which another G in the quadruplex domain is replaced with A (increasing final concentrations of inhibitor in reactions as follows: 0.3, 1, 3, 10, 30, 100 and 300 nM; N - the control reaction, without RT protein; K- the control reaction, without any inhibitor).

[0026] Figure 10 shows the inhibition of HIV-I (HXB2) RT polymerization using ssDNA molecules. ML4 - a nucleic acid molecule having contains four G4 sequences in the quadruplex domain (increasing final concentrations of inhibitor in reactions as follows: 0.3, 1, 3, 10, 30, 100 and 300 nM; N - the control reaction, without RT protein; K- the control reaction, without any inhibitor).

[0027] Figure 11 shows the inhibition of HIV-I (HXB2) RT polymerization using ssDNA molecules. RlT - the nucleic acid molecule in which the intervening bases in the quadruplex domain are single Ts; Acut - a nucleic acid molecule in which terminal ends are positioned within the quadruplex domain in which the intervening bases remain single Ts; Bcut - another nucleic acid molecule in which terminal ends are positioned within the quadruplex domain in which the intervening bases remain single Ts (increasing final concentrations of inhibitor in

reactions as follows: 10, 30 and 100 nM for RlT and for Acut, and 0.3, 1, 3, 10, 30, 100 and 300 nM for Bcut; N - the control reaction, without RT protein; K- the control reaction, without any inhibitor).

[0028] Figure 12 Quadruplex model for RT6 family of aptamers to HIV-I RT. (A) Sequences of aptamers RT5, RT6 and RT47 from Schneider et al. et al. as described elsewhere herein. Primer-binding sites for library amplification are in lower case, 35N originally random nucleotides are in upper case, guanosine clusters are underlined. Note that all aptamers analyzed in this work are given in Table 1. (B) Generalized secondary structure of most aptamers studied in this work. Stem and connector sequences shown are those of RlT, SN and several other aptamers. Intra-quadruplex loops are shown as curved lines. (C) Inhibition of HIV-I RT DDDP activity by aptamer RlT. Aptamer concentrations (nM) are indicated above the lanes. RT and primer/template concentrations used in these assays are 3 nM and 30 nM, respectively. Open and filled arrows on the left indicate positions of unextended primer and full-length product bands, respectively.

[0029] Figure 13 Sequence plasticity of stems and loops. Inhibition of RT DDDP activity by aptamer variants. Aptamer concentrations (nM) are indicated above the lanes. (A) Aptamer TKQ4 retains inhibition even though it carries a G-to-A mutation in the fourth of the 12 G' s that comprise the quadruplex. _A nother G-to-A variants were inactive for inhibition (data not shown). (B) Full concentration range of aptamers from 0.3 nM to 30OnM was used in establishing IC50 values for RlT variants in which quadruplex loops are replaced with multiple thymidines or multiple adenosines. Similar titrations were carried out in triplicate for _a u aptamers for which IC50 values are reported. Aptamer RlT was included in subsequent panels to provide a consistent reference baseline of inhibition. (C) RT inhibition by aptamer SN, in which quadruplex loops are replaced with hexaethylene glycol. (D)and (E), RT inhibition by aptamers carrying mutations in helical stem domain, as detailed in text.

[0030] Figure 14 Loop sequences modulate ionic sensitivity. RT inhibition by aptamers RT6- B, RlT and SN was carried out in normal buffer (potassium as the primary monovalent cation), or in buffers in which potassium was replaced with sodium. Note that in sodium, RlT effected the most potent inhibition.

[0031] Figure 15 CD analysis of aptamer structure. Aptamers RT6-B and RlT were analyzed at either 2 ILM or 4 ILM, as indicated on the figure. Black traces indicate normal buffer containing potassium. Red traces indicate buffer in which potassium was replaced with sodium.

[0032] Figure 16 Topological requirements. (A) Schematic diagrams of topological variants described in the text, assuming three-layer, parallel quadruplex stacks. (B) RT inhibition assays utilizing separated subdomains of RlT ('Stem' and 'Q16'). Inhibition is essentially eliminated when the two domains are not physically connected. 'Mix' refers to a 1 : 1 mixture of stem and Q 16 oligos, each at the indicated concentrations. 'Ctrl' is an irrelevant control DNA: 5' d(GCGGGACAATGGAGAGAGGG). (C) RT inhibition assays in which the connector domain is replaced with HEG. (D) RT inhibition assays in which inter-module connection is via two strands, with 5' and 3' termini in the stem module (Dyl5) or between the second and third guanosine triplets (Acut).

DETAILED DESCRIPTION

[0033] The present disclosure relates to novel nucleic acid molecules that are characterized by a novel set of structural features and which are strong inhibitors of retroviral Reverse Transcriptase (RT) activity. The nucleic acids of the present disclosure have been found to demonstrate potent inhibition of phylogenetically diverse primate lentiviral reverse transcriptases (RT), including HIV-I reverse transcriptases. These nucleic acid molecules are characterized in particular by a double helical domain and a guanosine-rich, G-quadruplex domain, wherein these two elements are physically coupled by a linker domain that may be nucleosidic or may be a non-nucleosidic molecule. Surprisingly, the exact nucleotide sequence of the double helical domain and the G-quadruplex domain matters less to the anti-RT activity of the molecule than whether the resulting nucleic acid molecule exhibits the above-specified structural features and other characteristics as further set forth herein below. The present disclosure further provides methods of using the nucleic acid molecules, including in the preparation of nucleic acid molecules that inhibit the activity of primate lentiviral reverse transcriptases.

A. Definitions

[0034] Section headings as used in this section and the entire disclosure herein are not intended to be limiting.

[0035] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety.

[0036] As used herein, the singular forms "a," "an" and "the" include plural referents unless the context clearly dictates otherwise. For the recitation of numeric ranges herein, each intervening number there between with the same degree of precision is explicitly contemplated. For example, for the range 6-9, the numbers 7 and 8 are contemplated in addition to 6 and 9, and for the range 6.0-7.0, the numbers 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9 and 7.0 are explicitly contemplated.

[0037] As used herein, the term "polynucleotide" means any macromolecule that is a polymer of monomeric nucleotides, which is at least 10 bases, or paired bases in length. The nucleotiode bases may be either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide, including those that display increased thermal stabilities when hybridized to complementary DNAs or RNAs as compared to unmodified DNA:DNA and DNA:RNA pairs. Such modified nucleotides include morpholino and locked nucleic acids (LNAs), peptide nucleic acids (PNAs), 1 ', 5'- anhydrohexitol nucleic acids (HNAs), glycol nucleic acids (GNAs) and threose nucleic acids (TNAs), all of which are characterized by changes to the backbone of the molecule and are capable of folding to form quadruplex structures. The term "polynucleotide" also is meant to encompass single and double stranded forms of nucleotides. As used herein and in the art, the term "polynucleotide" is interchangeable with "oligonucleotide". Polynucleotides that comprise a nucleotide sequence as disclosed herein also encompass those polynucleotides wherein thymidine (T) may be replaced in the sequence by uracil (U), such as when uracil (U) in an RNA sequence replaces thymidine (T) in a corresponding DNA sequence, inasmuch as one of the four major bases in RNA is uracil (U) rather than thymidine (T) as in DNA. [0038] The term "nucleic acid" refers to a macromolecule composed of chains of monomeric nucleotides, which forms a structure that demonstrates a biological function and may also carry genetic information. As is the case with polynucleotides, nucleic acids encompass DNA and RNA in double- and single-stranded forms, and also encompass nucleic acids wherein the bases are a modified form of either type of nucleotide, including LNAs, PNAs, HNAs, GNAs and TNAs. It will be understood that nucleic acids that comprise a nucleotide sequence as disclosed

herein also encompass those nucleic acids wherein thymidine (T) may be replaced in the sequence by uracil (U), such as when uracil (U) in an RNA sequence replaces thymidine (T) in a corresponding DNA sequence.

[0039] As used herein, the term "polypeptide" means a polymer of at least about 4 to about

10 amino acids. Throughout the specification, standard three letter or single letter designations for amino acids are used. As used herein and in the art, this term is often used interchangeably with "peptide" or "protein".

[0040] As used herein, the term "isolated" refers to a molecule that has been identified and separated out from components of the environment in which the molecule is produced, particularly those components of the environment that may interfere with uses for the nucleic acids of the present disclosure. Such components include for example polypeptides, proteins, other polynucleotides, and non-proteinaceous solutes.

[0041] As used herein the term "lentiviral reverse transcriptase" encompasses any of a number of known, phylogenetically diverse enzymes all characterized by reverse transcriptase activity, examples of which are provided herein, and including their homodimeric precursors, heterodimeric forms, and any subunit thereof, i.e. either the p66 subunit or the p51 subunit, including any such peptide having at least about 60% sequence identity with SEQ ID NO.: 1

(BHlO). The term encompasses for example each of the peptides of SEQ ID NOS. 1-9.

[0042] As used herein the term "vector" encompasses any nucleic acid that can drive the expression of a gene incorporated therein, in a cell containing the vector. As used herein the term encompasses for example a circular DNA (plasmid), linear or circular DNA in a package

(e.g. in a virus-like adenovirus or AAV), or RNA in a package (e.g. a retrovirus).

[0043] As used herein the term "in vitro" refers to activities conducted in cells in a controlled environment. As used herein and in the art, this term is often used interchangeably with "in culture", which may refer to cells in a cell culture or cells in an organ culture.

[0044] As used herein the term "in vivo" refers to activities conducted in a whole organism, particularly an animal, for example a mouse, a rat, a cat, a dog, a pig, a sheep, a horse or a human.

[0045] As used herein the term "aptamer sequence" refers to the one-dimensional order of a series of monomeric nucleotides, which are covalently linked to from a nucleic acid molecule,

wherein the order defines a primary structure of the nucleic acid that includes a double helical domain and a G-quadruplex domain coupled by a linker domain.

[0046] As used herein the term "double helical domain" encompasses any polynucleotide having a sequence defining two antiparallel base-paired strands capable of forming helices intertwined about a common axis, without further limitation as to nucleotide sequence, length of the sequence, or localization of terminal ends, including any conformational and structural variants thereof. A double helical domain as used herein encompasses a polynucleotide that forms a hairpin or terminal loop such that a single polynucleotide strand doubles back on itself and forms base parings to form a double helix.

[0047] As used herein the term "G-quadruplex domain" refers to any guanosine-rich polynucleotide sequence capable of forming G-tetrads, each of which is a square arrangement of guanines stabilized by Hoogsteen hydrogen bonding, and which may be further stabilized by the presence of a monovalent cation (especially potassium) in the center of the tetrads, without further limitation as to sequence. A G-quadruplex structure may include 2, 3, 4, 5 or more tetrads. A G-quadruplex structure may be formed of DNA, RNA or a modified nucleic acid such as an LNA or a PNA. Resources including algorithms for identifying and predicting sequences which have the capacity to form G-quadruplexes are readily available, for example online and in Qu ADRUPLEX NUCLEIC ACIDS, Neidle & Balasubramanian (Eds.) 2006.

[0048] As used herein the term "linker domain" refers to any nucleosidic or non-nucleosidic molecule that can provide a physical connection between the double helical domain and the G- quadruplex domain, without further limitation as to precise sequence (in the case of a nucleosidic molecule). The linker domain may couple one end of the double helical domain to one end of the G-quadruple domain, or may couple both ends the G-quadruplex domain and both ends of the G-quadruplex domain.

B. Lenitviral reverse transcriptases

[0049] Lentiviral reverse transcriptases (RT 's) include several phylogenetically diverse enzymes, or subunits thereof, that were used in functional assays of the nucleic acid molecules described herein. All such RT 's have at least about 60% sequence identity with RT from HIV-I strain BHlO(SEQ ID NO: 1) as listed herein below. Typically, testing a nucleic acid molecule of the present disclosure for RT inhibition includes testing the nucleic acid molecule for inhibition of the RT from HIV-I strain HXB2 (SEQ ID NO: 2) as provided below. However, several

different RT 's were and can be used in evaluating RT inhibition by nucleic acid molecules according to the present disclosure. All of these demonstrate at least 60% sequence identity with that of the RT from HIV-I strain BHlO. The RT 's used and their sequence identity to that from

HIVl strain BHlO are as follows (% sequence identity in complete RT sequences in comparison with HIV-I strain BHlO):

[0050] HXB2 98.9

[0051] 94CY pol 90.4

[0052] 92UG021 92.9

[0053] 93TH253.3 90.5

[0054] 98CN009 92.9

[0055] MVP5180 78.2

[0056] HIV-2 EHO-287 60.5

[0057] SIVcpzTANl 72.7

[0058] The amino acid sequence of the RT from strain BHlO is:

[0059] PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPEN

PYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDV G

DAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILE PFKK

QNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWM G

YELHPDKWTVQPIVLPEKDSWTVNDIQKL VGKLNWASQIYPGIKVRQLCKLLRGTKALT

EVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFK NLK

TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQ

ATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQ K

VVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQII EQLI

KKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKIL (SEQ ID NO: 1).

[0060] The amino acid sequence of the RT from strain HXB2 is:

[0061 ] PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPEN

PYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDV G

DAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILE PFRK

QNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWM G

YELHPDKWTVQPIVLPEKDSWTVNDIQKL VGKLNWASQIYPGIKVRQLCKLLRGTKALT

EVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFK NLK

TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQ

ATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQ K

VVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQII EQLI

KKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVL (SEQ ID NO: 2).

[0062] The amino acid sequence of the RT from strain 94CY pol is:

[0063] PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALTEICKEMEKEGKISKIGPEN

PYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKAVTVLDV G

DAYFSVPLHEDFRKYTAFTIPSTNNETPGVRYQYNVLPQGWKGSPAIFQSSMTKILE PFR

SKNTELIIYQYMDDLYVGSDLEISQHRVKIEELRAHLLKWGFYTPDKKHQKEPPFLW MG

YELHPDKWTVQPIKLPEKDSWTWDIQKLVGKLNWASQIYAGIKVKQLCKLLRGAKAL

TDIVTLTKEAELELEENREILKTPVHGVYYDPSKDLIAEIQKQGQDQWTYQIYQEPF KNL

KTGKYAKRRSTHTNDIKQLTEAVQKITMESIVIWGKTPKFKLPIQKETWETWWAEYW Q

ATWIPEWEFVNTPPLVKLWYQLEKEPIAGAETFYVDGAANRETKLGKAGYVTDRGRQ K

IVSLTETTNQKTELHAIYLALQDSGLEVNIVTDSQYALGIIQAQPERSESEIVNQII EKLIEK

ERVYLSWVPAHKGIGGNEQVDKLVSSGIRKVL. (SEQ ID NO:3).

[0064] The amino acid sequence of the RT from strain 92UG021 is:

[0065] PISPIDTVPVKLKPGMDGPKVKQWPLTEEKIKALTEICTEMEKEGKISRIGPEN

PYNTPIFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDV GD

AYFSVPLCEDFRKYT AFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILDPFRKQ

NPEMVIYQYMDDLYVGSDLEIGQHRTKIEELREHLLKWGFTTPDKKHQKEPPFLWMG Y

ELHPDKWTVQPIMLPEKESWTVNDIQKL VGKLNWASQIYPGIRVKQLCKCLRGAKALT

EVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQDPWTYQIYQEQYK NLK

TGKYAKTRGTHTNDVKQLTEAVQKIAQECIVIWGKTPKFRLPIQKETWETWWTEYWQ A

TWVPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTDKGRQK

VVSMTDITNQKAELQAINLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQII EQLIK

KEKVYLSWVPAHKGIGGNEQVDKLVSNGIRKIL (SEQ ID NO:4).

[0066] The amino acid sequence of the RT from strain 93TH253.3 is:

[0067] PISPIDTVPVKLKPGMDGPKVKQWPLTEEKIKALTEICKEMEEEGKISKIGPEN

PYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDV G

DAYFSVPLDESFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILE PFRIK

NPEMVIYQYMDDLYVGSDLEIGQHRTKIEELRAHLLSWGFTTPDKKHQKEPPFLWMG Y

ELHPDRWTVQPIELPEKDSWTVNDIQKL VGKLNWASQIYAGIKVKQLCKLLRGTKALT

DIVPLTEEAELELEENREILRIPVHGVYYDPSKDLVAEVQKQGQDQWTYQIYQEPFK NLK

TGKYSRKRSAHTNDVRQLTEVVQKIATESIVIWGKTPKFRLPIQRETWETWWMEYWQ A

TWIPEWEFVNTPPLVKLWYQLEKDPIVGAETFYVDGAASRETKLGKAGYVTDRGRQK V

ISLTETTNQKTELHAIHLALQDSGSEVNIVTDSQYALGIIQAQPDRSESEVVSQIIE ELIKKE

KVYLSWVPAHKGIGGNEQVDKLVISGIRKVL (SEQ ID NO:5).

[0068] The amino acid sequence of the RT from strain 98CN009 pol is:

[0069] PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALTAICDEMEKEGKITKIGPEN

PYNTPIFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKRKKSVTVLDV GD

AYFSVPLYEDFRKYTAFTIPSTNNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEP FRKQ

NPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMG YE

LHPDKWTVQPIQLPEKDSWTVNDIQKL VGKLNWASQIYPGIKVRQLCKLLRGAKALTDI

VPLTEEAELELAENREILKEPVHGIYYDPSKDLIAEIQKQGQDQWTYQIYQEPFKNL KTG

KYAKMRTAHTNDVKQLTEAVQKIAMESIVIWGKTPKFRLPIQKETWEIWWTDYWQAT

WIPEWEFVNTPPLVKLWYQLEKDPIVGVETFYVDGAANRETKIGKAGYVTDRGRKKV V

SLTETTNQKTELHAICIALQDSGSEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQ LIKKE

RVYLSWVPAHKGIGGNEQVDKLVSSGIRKVL (SEQ ID NO:6).

[0070] The amino acid sequence of the RT from strain HIV -2 EHO-287 pol is:

[0071 ] PVARIEPVKVQLKPEKDGPKIRQWPLSKEKILALKEICEKMEKEGQLEEAPPT

NPYNSPTFAIKKKDKNKWRMLIDFRELNKVTQEFTEVQLGIPHPAGLASKKRITVLD VG

DAYFSVPLDPDFRQYTAFTLPAVNNAEPGKRYLYKVLPQGWKGSPAIFQYTMAKVLD P

FRKANNDVTIIQYMDDILVASDRSDLEHDRVVSQLKELLNNMGFSTPEEKFQKDPPF KW

MGYELWPKKWKLQKIQLPEKEVWTVNDIQKLVGVLNWAAQLFPGIKTRHICKLIRGK M

TLTEEVQWTELAEAEFQENKIILEQEQEGSYYKEGVPLEATVQKNLANQWTYKIHQG D

KILKVGKYAKVKNTHTNGVRLLAHVVQKIGKEALVIWGEIPMFHLPVERETWDQWWT

DYWQVTWIPEWDFVSTPPLIRLAYNLVKDPLEGVETYYTDGSCNKASKEGKAGYVTD R

GKDKVKPLEQTTNQQAELEAFALALQDSGPQVNIIVDSQYVMGIVAAQPTETESPIV REII

EEMIKKEKIYVGWVPAHKGLGGNQEVDHLVSQGIRQIL. (SEQ ID NO:7).

[0072] The amino acid sequence of the RT from strain MVP5180 is:

[0073] PISPIAPVPVKLKPGMDGPKVKQWPLSREKIEALTAICQEMEQEGKISRIGPEN

PYNTPIFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPGGLKQRQSVTVLDV GD

AYFSCPLDPDFRKYT AFTIPSVNNETPGVRYQYNVLPQGWKGSPAIFQSSMTKILDPFRK

SNPEVEIYQYIDDLYVGSDLPLAEHRKRVELLREHLYQWGFTTPDKKHQKEPPFLWM G

YELHPDKWTVQPIQLPDKEVWTVNDIQKLVGKLNWASQIYQGIRVKELCKLIRGTKS LT

EVVPLSKEAELELEENREKLKEPVHGVYYQPDKDLWVSIQKHGEGQWTYQVYQDEHK

NLKTGKYARQKASHTNDIRQLAEVVQKVSQEAIVIWGKLPKFRLPVTRETWETWWAE Y

WQATWIPEWEFVSTPPLIKLWYQLETEPIVGAETFYVDGAANRNTKLGKAGYVTEQG K

QNIIKLEETTNQKAELMAVLIALQDSKEQVNIVTDSQYVLGIISSQPTQSDSPIVQQ IIEELT

KKERVYLTWVPAHKGIGGNEKIDKLVSKDIRRVL. (SEQ ID NO: 8).

[0074] The amino acid sequence of the RT from strain SIVcpzTANl is:

[0075] PISPIEVVKVQLKEGMDGPKVKQWPLSKEKIEALTEICKTLEKEGKISAVGPEN

PYNTPIFAIKKKDTSKWRKLVDFRELNKRTQDFWELQLGIPHPAGLRKRNMVTVLDV G

DAYFSIPLDPDFRKYTAFTIPSLNNNTPGKRFQYNVLPQGWKGSPAIFQSSMTKILD PFRK

EHPDVDIYQYMDDLYIGSDLNEEEHRKLIKKLRQHLLTWGLETPDKKYQEKPPFMWM G

YELHPNKWTVQNITLPEPEQWTVNHIQKL VGKLNWASQIYHGIKTKELCKLIRGVKGLT

EPVEMTREAELELEENKQILKEKVQGAYYDPKLPLQAAIQKQGQGQWTYQIYQEEGK N

LKTGKYAKSPGTHTNEIRQLAGLIQKIGNESIIIWGIVPKFLLPVSKETWSQWWTDY WQV

TWVPEWEFINTPPLIRLWYNLLSDPIPEAETFYVDGAANRDSKKGRAGYVTNRGRYR SK

DLENTTNQQAELWAVDLALKDSGAQVNIVTDSQYVMGVLQGLPDQSDSPIVEQIIQK LT

QKTAIYLAWVPAHKGIGGNEEVDKLVSKNIRKIL. (SEQ ID NO:9).

[0076] RT' s can be expressed in E. coli and purified as well known in the art and described for example in Held, D., et al, (2006) J. Biol. Chem., 281, 25712-25722.

C. Aptamers

[0077] The present disclosure describes aptamers having a bimodular structure comprising quadruplex and helical domains. Both domains are required for the observed RT inhibition, and they must be physically connected by a linker domain. (See Michalowski, D. et al., (2008) Nucleic Acids Research 36, 7124-7135, which is herein incorporated by reference in its entirety). Relatively few sequence constraints exist within either of the two main domains or in the linkage between them. Moreover, the chemical nature of the linkages between the two major structural elements and within the G-quadruplex plays no significant role in determining inhibition of RT. Importantly, the bimodular aptamer exhibits potent inhibition of RT derived from phylogentically diverse HIV and SIV strains. These novel nucleic acid molecules are useful for

variety of applications, including methods for investigating the mechanism of HIV RT inhibition with structured DNA inhibitors, methods for developing targeted small molecules for therapeutic applications in treating HIV and SIV, and in therapeutic compositions.

[0078] The aptamers described herein can be generated based on a set of 81 nt ssDNA aptamers selected to bind HIV-I RT as described in Schneider,D.J. et al., (1995) Biochem. 34,

9599-9610. Sequences of starting "full-length" aptamers are listed below:

[0079] "RT5":TCCGCCTGATTAGCGATACTCAGGCGCC gggGgggTgggAATACAGTGATCAGCGACTTGA GCAAAATCACCTGCAgggg (SEQ ID

NO:10).

[0080] "RT47":ATCCGCCTGATTAGCGATACTCAGGCCTT gggCgggCCgggACAATGGAGAGATTTACTTGA GCAAAATCACCTGCAgggg (SEQ ID

NO:11).

[0081] "RT6": ATCCGCCTGATTAGCGATACTC AGGCGTT

AgggAAgggCGTCGAAAGCAgggTgggACTTGA GCAAAATCACCTGCAgggg (SEQ ID

NO:12).

[0082] "RT6-A": ATCCGCCTGATTAGCGATACTCAGGCGTTA gggAAgggTAGCGATACAgggTggg (SEQ ID NO:13).

[0083] "RT6-B" ("Vor"):CGCCTGATTAGCGATACTCAGGCGTTA gggAAgggCGTCGAAAGCAgggTggg (SEQ ID NO: 14).

[0084] Aptamers such as the nucleic acid molecules described herein can be and are derived from the combinatorial method of in vitro selection, or SELEX (for Selective Evolution of

Ligands by Exponential enrichment; Tuerk C. & Gold L., SCIENCE (1990), 249 (4968): 505-

510). Aptamers having sequences generated according to the teachings of the present disclosure can be commercially synthesized and purified by any of a number of contract laboratories, such as for example, Operon Biotechnologies, Inc., (Huntsville, AL), or Integrated DNA

Technologies, Inc.

[0085] The nucleic acids molecules of the present disclosure have a bi-modular structure consisting of the double helical domain coupled to a guanosine-rich domain forming a G- quadruplex. These two domains are physically coupled by a short, for example (but not limited to) a 2, 3, or 4 nt single stranded fragment, or by another chemical compound(s), such as for example, Sp-C 18 (hexaethylene glycol, HEG). In one embodiment, as shown in Figure IA, the

double helical domain (HF) forms a hairpin, terminal loop and the 3 'end of the double helical domain is coupled to a single-stranded linker domain, and the linker domain is coupled to the 5'- end of the G-quadruplex domain. In another embodiment, as shown in Figure IB, the 3' end of the double helical domain is coupled to a linker domain first strand, which is coupled to the 5 ' end of the G-quadruplex domain, and the 5' end of the double helical domain is coupled to a second linker domain strand, which is coupled to the 3' end of the G-quadruplex domain, leaving two free terminal ends of the double helical domain. Nucleic acids having the configuration shown in Figure IB appear to be especially structurally plastic and well-suited to various modifications as described herein, such as in drug delivery as carriers, or as therapeutic agents coupled to a carrier or cell-penetrating peptide. Representative nucleic acid molecules having the structure shown in Figure IB include those identified as DyIl (SEQ ID NO:49), DyB (SEQ ID NO:51), and Dyl5 (SEQ ID NO:52).

[0086] Surprisingly, the nucleotide sequence of the nucleic acid molecules is not a primary determining factor for inhibitory activity of these molecules with respect to RT. Provided that the sequence includes a double helical domain and the G-quadruplex domain coupled by a linker domain, such that the sequence is capable of forming these structures, many different and varied sequences are shown to provide the observed inhibitory activity against RT. This holds true for the complete apatmer sequence as well as for the individual domains, particularly the linker domain and the G-quadruplex domain. That is, neither the exact sequence nor the chemical composition of the nucleic acid used is necessarily limiting of the inhibitory activity of the resulting nucleic acid molecule. For example, within the provisions stated herein, various changes can be made to any of the domain sequences without eliminating inhibition by the molecule of RT. The nucleic acid molecules of the present disclosure also encompass different structural variants of double helical fragments, G-quadruplex structures and different single stranded connectors/linkers/bridges using different 3' and 5' ends in any possible combinations. Double helical domain

[0087] The double helical domain encompasses any polynucleotide forming a double helical structure, i.e. a "stem", regardless of length or localization of the 3' and 5' terminal ends. The sequence of the double helical domain is not critical provided only that the sequence allows for the folding needed to from a duplex structure. Preferably the sequence is any sequence that provides at least the thermodynamical stability equivalent of four (4) continuous Watson-Crick

base pairs. Exemplary nucleic acids demonstrating a range of sequences suitable for the double helical domain are provided in Tables 2 and 4 below and identified as Sl, S2, S4, S5, DyIl, Dyl2, DyB, Dyl5, Acut, and Bcut.

[0088] Preferably the double helical domain has a sequence of about 4 to about 20 base pairs in length. However, helical domains of much longer length are also contemplated. In one exemplary embodiment the double helical domain is a sequence of 7, 8, 9 or 10 base pairs in length. In another embodiment the double helical domain is a sequence of 15 base pairs in length. An exemplary double helical domain sequence is CGCCTGA paired with TCAGGCG. The double helical element may include a hairpin, terminal loop. The loop may include a sequence having a length of 1 to 15 bases, in addition to the base-paired portion. In an exemplary embodiment a double helical element includes a hairpin loop having 10 bases. In an exemplary embodiment a double helical element includes a hairpin loop having 7 bases. In an exemplary embodiment a double helical element includes a hairpin loop having 3 bases. The exact sequence of the loop if present is not critical.

[0089] The double helical domain may be a DNA, and RNA, or a modified nucleic acid such as a LNA, PNA, GNA, HNA and the like. The double helical domain may also include chemical modifications, different conformations of the helices, and/or additional structural motifs (e.g. a bulge, internal loops, mismatches, etc.). The double helical may be intramolecular, but also may be extended to form an intermolecular duplex, or a hybrid duplex or triplex.

G-quadruplex domain

[0090] The G-quadruplex domain has a sequence capable of forming at least two layers of G- tetrads that will form a G-quadruplex. In various embodiments the G-quadruplex domain can comprise a sequence capable of forming 2, 3, 4, 5, 6 or more G-tetrad layers, preferably two or three G-tetrad layers. The G-quadruplex domain sequence is guanosine-rich, such as but not limited to a sequence including about 8 to about 24 guanosines as four pairs (gg), triplets (ggg), or quadruplets (gggg), wherein the pairs, triplets or quadruplets are separated by at least one intervening base, which may be any nucleotide base. Alternatively the pairs, triplets or quadruplets may be separated by another intervening molecule, such as HEG. [0091] In an exemplary embodiment the sequence includes 12 guanosines as four triplets. The intervening base is for example any of adenine (A), cytosine (C), or thymidine (T), and may be multiples or combinations thereof. The intervening base(s) may form a loop. In certain

embodiments the intervening base is thymidine (T), and the intervening base can be two or more thymidines. In certain embodiments the intervening base is cytosine (C), and the intervening base can be two or more cytosines. In certain embodiments the intervening base is adenine (A), and the intervening base can be two or more adenines. In an exemplary embodiment the G- quadruplex domain has the sequence: gggTgggTgggTggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggTTgggTTgggTTggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggTTTgggTTTgggTTTggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggTTTTgggTTTTgggTTTTggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggTTTTTgggTTTTTgggTTTTTggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggTTTTTTgggTTTTTTgggTTTTTTggg. . In another exemplary embodiment the G-quadruplex domain has the sequence: gggTTTTTTTgggTTTTTTTgggTTTTTTTggg. In another exemplary embodiment the G- quadruplex domain has the sequence: gggTTTTTTTTgggTTTTTTTTgggTTTTTTTTggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggAgggAgggAggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggAAgggAAgggAAggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggAAAgggAAAgggAAAggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggAAAAgggAAAAgggAAAAggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggAAAAgggAAAAgggAAAAggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggCgggCgggCggg. In another exemplary embodiment the G- quadruplex domain has the sequence: gggCCgggCCgggCCggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggCCCgggCCCgggCCCggg. In another exemplary embodiment the G-quadruplex domain has the sequence: gggCCCCgggCCCCgggCCCCggg. However, it is not a requirement that the intervening sequences all include the same bases, or same number of bases, and different intervening sequences may include combinations of bases. For example, in another exemplary embodiment the G-quadruplex domain has the sequence: gggAAgggCGTCGAAAGCAgggTggg. In yet another exemplary embodiment in which the G-pairs, triplets or quadruplets are separated by a non-nucleosidic molecule, the G-quadruplex domain has the sequence:

ggg(HEG)ggg(HEG)ggg(HEG)ggg, where HEG indicates hexaethylene glycol. An exemplary formula for the G-quadruplex domain sequence is:

[0092] G _n L _n G _n L _n G _n L _n G _n , where n is >=1 and L is a nucleotide, deoxynucleotide, LNA nucleotide or any chemical compound (propanediol, octanediol, hexaethylene glycol, etc). In one embodiment, the following rule can be used to generate a sequence capable of forming a G- qaudruplex structure:

[0093] G ₃₊ LI-VG ₃₊ LI-VG ₃₊ LI-VG ₃₊ .

Thus it will be understood that a variety of G-rich sequences are capable of providing the G- quadruplex domain. The G-quadruplex domain may also take the form of any one of several recognized structural variants, such as a "chair"-like type, or a "basket"-like type. Other sequences that have the capacity to form G-quadruplexes can be readily identified using any of a number of other G-quadruplex predicting algorithms. As explained above, L may also include any combination of two or more different bases. Further guidance on identifying sequences that form G-quadruplex structures can be found for example in QUADRUPLEX NUCLEIC ACIDS, Neidle

& Balasubramanian (Eds.) 2006.

Linker domain

[0094] The linker domain coupling the double helical domain and the G-quadruplex domain can be any nucleosidic or non-nucleosidic molecule having appropriate moities for coupling at least one end of the double helical domain to at least one end of the G-quadruplex domain. The linker domain may be single or double-stranded. For example, the linker domain can be a single- stranded nucleotide sequence of any one of adenine (A), cytosine (C), guanine (G) or thymidine (T), or multiples thereof or a combination thereof. Preferably the linker is no more than about 16 nucleotides or base pairs in length, or if non-nucleosidic, its length equivalent. For example in one embodiment, the linker domain sequence is 1-16 thymidines (T 's) in series. In another embodiment the linker domain is 1-16 adenines (A's) in series. In another embodiment the linker domain is 1-16 cytosines (Cs) in series. In an exemplary embodiment the linker domain sequence is TT. Alternatively the linker domain may be a non-nucleosidic molecule such as but not limited to SP-C 18 (HEG). Linker domains including octanediol, propanediol, and the like are also contemplated.

[0095] The linker domain may connect the double helical domain and the G-quadruplex domain to one another using the terminal ends of each domain in any possible combination.

Figure 1 shows two possible configurations that are exemplary of the nucleic acids of the present disclosure. However, other configurations are contemplated provided only that the linker domain provides a physical connection between at least one terminal end of the double helical domain and at least one terminal end of the G-quadruplex domain. A surprising finding is that a nucleic acid according to the present disclosure exhibits strong inhibition of RT regardless of whether the double helical domain or G-quadruplex fragment independently show any such inhibitory activity, whether alone or combined in a mixture but lacking a physical linkage. [0096] The discovery of the basic structural elements of the nucleic acid molecules according to the present disclosure was surprising because the structural elements identified herein were not previously predicted or expected by the starting full-length aptamer sequences. Surprisingly, the novel nucleic acid molecules according to the present disclosure all demonstrated, on a nanomolar scale, strong inhibition of primate lentiviral reverse transcriptase function in vitro. Moreover, RT proteins isolated from different clades and subtypes of HIV-I, HIV -2 and SIV (Held D.M., et. al, J Virol. (2007), 81(10):5375-5384) were tested, and the inhibitory effects were observed across a phylogenetically diverse group of RT's tested. [0097] Representative DNA aptamers which are nucleic acid molecules according to the present disclosure include all those listed in Tables 1-5 below, except that the apatmers identified as 93del and Stem 93del (SEQ ID NOS: 57 and 58) were used as controls.

D. Compositions Including Detectable Labels and Other Molecules

[0098] The nucleic acid molecules according to the present disclosure may be coupled with other molecules for use in a variety of applications. For example, the nucleic acid molecules may be labeled with a detectable label. Alternatively, the nucleic acid molecules may be coupled to a peptide, such as a carrier peptide or a cell-penetrating polypeptide. As is well known, nucleic acids are especially well-suited to chemical modifications of many kinds. [0099] Detectable labels suitable for such use include any compound or composition having a moiety that is detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical, or chemical means, and can be coupled directly or indirectly to the nucleic acid molecule. Such labels include, for example, a radiolabel, a fluorescent probe, an enzyme, oligonucleotide, a nanoparticle, or chemiluminophore. As is well known, in detection methods employing an optical signal, the optical signal can be measured as a concentration dependent change in chemiluminescence, fluorescence, phosphorescence, electrochemiluminescence, ultraviolet absorption, visible absorption, infrared absorption, refraction, and the like. Similarly, in detection methods employing an an electrical signal, the electrical signal is measured as a concentration dependent change in current, resistance, potential, mass to charge ratio, or ion count.

[0100] Useful labels according to the present disclosure include for example fluorescent dyes (e.g., fluorescein, Texas Red, rhodamine, green fluorescent protein) and the like (see, e.g., Molecular Probes, Eugene, Oreg., USA), and radiolabels (e.g., 3H, 1251, 35S, 14C, or 32P), and catalysts such as enzymes (e.g., horse radish peroxidase, alkaline phosphatase, beta-galactosidase and others).

[0101] Alternatively, the nucleic acid can be coupled or conjugated to another molecule or molecules with other useful functions. For example, the nucleic acid may be advantageously

coupled to a polypeptide, such as a carrier peptide or a cell-penetrating polypeptide. Such peptides can be useful in delivering the nucleic acids to cells to provide inhibition of RT. [0102] Peptide carriers are increasingly well known and have been described for use in the delivery of anti-tumoral, anti-viral or antibiotic drugs, which otherwise cannot cross the cell membrane. Peptide carriers, particularly in the present context, are useful because they are readily synthesized and modified and therefore readily adapted for attaching cargo consisting of small molecules. The ability of a wide variety of short peptides to act as carriers for the delivery of oligonucleotides into a cell has been demonstrated. Examples include human calcitonin (hCT), fragments of transduction proteins domains such as VP22, Tat (HIV transactivator of transcription), Antennapedia (Antp), MPG peptide (N-methylpurine DNA glycosylase, or 3- methyladenine; "3MeA"), Pepl, arginine-rich peptides, β-peptides, peptoids and loligomers (branched peptides rich in Lys). All these cell penetrating peptides have proven to be valuable in the delivery of biologically active cargoes to the cytoplasm and nucleus. [0103] Typically a complex of a nucleic acid molecule with a cell-penetrating peptide is formed through covalent bonding. Such complexes have been synthesized using either stable or cleavable linkages. A common method is to form cleavable disulfide linkages through total stepwise solid-phase synthesis or solution-phase or solid-phase fragment coupling. Other linking strategies include forming stable amide, thiazolidine, oxime and hydrazine linkages. Newer, non-covalent linking strategies using either electrostatic or hydrophobic interactions can avoid the need for chemical modification. This approach may be preferred to maintain full biological activity.

E. Pharmaceutical Compositions

[0104] A nucleic acid molecule of the present disclosure can be contained within a pharmaceutical composition, for example together with a pharmaceutical carrier, excipient or stabilizer. The present disclosure also relates to drug-carrier complexes and to the use of the nucleic acids in drug-carrier complexes used as pharmaceutical compositions to deliver specific drugs in cells, tissues and organisms. In particular such compositions can be useful in antiviral therapies directed against a primate lentivirus such as HIVl, HIV-2 and SIV. Methods for systemic delivery of such compositions include typical routes of administration, as well as intracellular production of ssDNA and RNA. Methods for local delivery include delivery into cells by lipid-DNA complexes and the like, as further described in the art (see e.g., Chen Y., et

al, Antisense & Nucleic Acid Drug Development (2000), 10:415-420; and Jing N., et al, Biochemistry (2002), 41 :5397-5403).

[0105] The present disclosure provides methods for modulating RT activity in mammalian cells, wherein the method includes exposing the cells to an amount of the anti-RT aptamer sufficient to inhibit RT activity in the cells. Preferably, the amount of anti-RT aptamer employed will be an amount effective to reduce or eliminate the activity of RT so to achieve a therapeutic effect. This can be accomplished in vivo or ex vivo in accordance, for instance, with the methods described below. Exemplary conditions or disorders to be treated with anti-RT aptamers include infection with HIV-I, HIV -2 or SIV. In particular, the molecules described herein are useful in treating various pathological conditions associated with HIV-I, HIV-2 or SIV infection. Such conditions can be treated by modulating a selected activity associated with RT activity in a mammal through, for example, administration of one or more anti-RT aptamers as described herein.

[0106] The anti-RT aptamers can be administered by known routes of administration including intravenous administration, intramuscular, intraperitoneal, intracerebrospinal, subcutaneous, intra-articular, intrasynovial, intrathecal, oral, topical, or inhalation routes. Effective dosages and schedules for administering antagonists or agonists are determined empirically according to guidelines generally recognized by those of skill in the art. Single or multiple dosages may be employed.

[0107] As noted above, the anti-RT aptamers useful in the methods of the present disclosure can be incorporated into pharmaceutical compositions suitable for administration into an animal such as a mammal. Methods for formulating such compositions are generally well known. Guidance is available for example from Remington: THE SCIENCE AND PRACTICE OF PHARMACY, 19th Edition, Gennaro (ed.) 1995, Mack Publishing Company, Easton, Pa. Such compositions typically comprise at least one anti-RT aptamer and a pharmaceutically acceptable carrier. The term "pharmaceutically acceptable carrier" refers to any and all coatings, excipients, solvents, dispersion media, absorption delaying agents, and the like, compatible with pharmaceutical administration. Such carriers also include for example sodium chloride, colloidal silica, talc, various polymeric carriers including polyvinyl pyrrolidone, cellulose-based compounds such as carboxymethylcellulose or methylcellulose, polyvinylpyrrolidone, polyacrylates, and polyethylene glycol.

[0108] Dosage forms include, for example, oral or sublingual tablets, pellets, micro- and nano-capsules, liposomes, inhalation forms, nasal sprays, and sustained-release preparations. [0109] Pharmaceutical compositions of the present disclosure, comprising anti-RT aptamers, are administered in therapeutically effective amounts. As used herein, the term "therapeutically effective amount" refers to a nontoxic dosage level sufficient to induce a targeted biological effect (e.g. a diminution of the severity of the symptoms associated with a pathological condition such as breast or ovarian cancer). Amounts for administration may vary depending on the current condition of the animal being treated, the selected dosage form and route of administration, and other patient-specific factors such as age, gender and cooperativeness. A therapeutically effective amount may be provided in a broad range of amounts. Such amounts can be selected according to in vitro and/or in vivo assays.

[0110] Solutions or suspensions used for administering anti-RT aptamers can include one or more of 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 EDTA; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. In one embodiment, a pharmaceutical composition can be delivered via slow release formulation or matrix comprising anti-RT aptamers or DNA constructs suitable for expression of anti-RT aptamers in or around a site within the body.

[0111] In another aspect the present disclosure provides novel compositions for antiviral therapy. For example, the nucleic acids of the present disclosure can serve as a carrier for other known or novel antiviral or other drugs. For example these nucleic acids can be used in a pharmaceutical composition targeting biological targets in cells, tissues, organisms, etc. Given the suitability of nucleic acid molecules to modification, a drug-carrier complex can be formed by chemical modifications to any one or more of the domains described herein. In particular any free end of the helical domain, and portions of the linker domain, can be coupled to or conjugated with other molecules to accomplish delivery and inhibition of targeted proteins. In particular, other drug molecules can be covalent bound or reversibly associated with any domain of the nucleic acid molecules described herein, but particularly the linker domain and the double helical domain. Moreover, each domain may be separately introduced to another known drug

molecule to from a modified domain that may then be incorporated into a nucleic acid molecule as described herein. For example, the double helical domain or G-quadruplex domain can be separately introduced to another known drug then incorporated into a nucleic acid molecule as described herein, to provide a carrier for the drug.

F. Vectors

[0112] Other embodiments of the present disclosure include a vector comprising the nucleic acid molecules of the present disclosure. Generally a vector can be any nucleic acid that in a cell or cells directs expression of a sequence, gene or genes of interest that is incorporated in the vector sequence. Such vectors are useful for propagating the nucleic acid molecules or for expression as well as other applications. Such vectors, methods of producing them, and methods for cloning the nucleic acids molecules into said vectors are generally well known in the art. [0113] The vector may particularly be a plasmid, a cosmid, a virus, recombinant virus or a bacteriophage such as any of those used conventionally in genetic engineering. The vector may be for example a DNA vector wherein thymidine (T) replaces uridine (U). Also encompassed by the present disclosure is a host cell or cells comprising such vectors. Vectors may also include marker genes, such as, e.g., luciferase and green fluorescent protein genes. Sequences, inserts, clones, vectors and the like can be isolated from natural sources, obtained from such known sources such as ATCC or GenBank libraries or from commercial sources, or prepared by synthetic or recombinant methods.

[0114] Expression vectors can be derived for example from viruses, especially retroviruses, vaccinia virus, adeno-associated virus, herpes viruses, or bovine papilloma virus. Those of skill in the art are well-acquainted with methods for constructing recombinant viral vectors. Further guidance can be obtained for example from Sambrook, Molecular Cloning A Laboratory Manual, Cold Spring Harbor Laboratory (1989) N. Y. and Ausubel, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N. Y. (1989). [0115] The vectors containing the nucleic acid molecules of the present disclosure can be transferred into the host cell by well-known methods. Such methods may vary depending on the cellular host (prokaryotic or eukaryotic cells). In particular, eukaryotic cells can be trans fected with a variety of known transfection agents, such as calcium phosphate treatment or electroporation techniques. For transfection of prokaryotic cells, calcium chloride for example can be used.

[0116] The vectors may further include genes such as marker genes. Marker genes can be used to select the vector in a suitable host cell and under suitable conditions. In an exemplary embodiment, a nucleic acid molecule of the present disclosure is operatively linked to expression control sequences allowing expression in prokaryotic or eukaryotic cells. By "expression " is meant transcription of the polynucleotide into a translatable mRNA. In some embodiments, regulatory elements such as are well known to those of skill in the art can be used to promote expression in eukaryotic cells, especially expression in mammalian cells. Regulatory elements may comprise for example regulatory sequences ensuring initiation of transcription. PoIy-A signals (SV40-poly-A site or the tk-poly-A site) may also be used downstream of the nucleic acid molecule to ensure termination of transcription and to stabilize the transcript. Other regulatory elements are known and include for example transcriptional and translational enhancers, and promoter regions. Examples relating to expression in prokaryotic host cells include the PL, lac, trp or tac promoter in E. coli. Examples relating to expression in eukaryotic host cells include the AOXl or GALl promoter in yeast, the CMV-, SV40-, RSV-promoters (Rous sarcoma virus), CMV-enhancer, SV40-enhancer and the globin intron in mammalian and other animal cells.

[0117] Additionally, the invention relates to a host or host cells transformed with the vector of the invention. Appropriate hosts include transgenic animals, cells such as bacteria, yeast and animal, preferably mammalian cells, fungal cells and insect cells. Transformation protocols including transfection, microinjection, electroporation, etc., are also well known in the art. [0118] Alternatively, the nucleic acid molecules and vectors of the invention can be reconstituted into liposomes for delivery to cells.

G. Methods

[0119] In another aspect the present disclosure provides a method of binding a nucleic acid molecule to a primate lentiviral reverse transcriptase polypeptide. The method includes combining a nucleic acid molecule as described herein and the lentiviral reverse transcriptase polypeptide for a time and under conditions effective to allow the nucleic acid molecule to bind to the lentiviral reverse transcriptase polypeptide such that the binding occurs. The combination may take place in vitro or in vivo. In an exemplary embodiment the lentiviral reverse transcriptase polypeptide has at least 60% sequence identity with SEQ ID. NO: 1. The method

can include combining the lentiviral reverse transcriptase polypeptide as expressed by a bacterial cell, and the further step of examining inhibition of the lentiviral reverse transcriptase polypeptide activity. For example, a functional assay showing inhibition of DNA-dependent DNA polymerization following combining the nucleic acid molecule as described herein and the lentiviral reverse transcriptase polypeptide, provides evidence of binding. Alternatively, evidence of binding may be obtained from a polymerase-independent RNase H activity assay. The method may further include examining the affinity of the nucleic acid molecule for the lentiviral reverse transcriptase polypeptide. The method may also include examining the number of binding sites for the nucleic acid molecule present on the lentiviral reverse transcriptase polypeptide. The method may also involve examining or measuring binding of the nucleic acid to the lentiviral reverse transcriptase polypeptide by labeling the nucleic acid molecule with a detectable marker, and then using a signal generated by the detectable marker to detect or measure binding according to method generally well known in the art.

[0120] In another aspect the present disclosure provides a method of preparing an isolated nucleic acid molecule that binds a primate lentiviral reverse transcriptase polypeptide, the method including identifying a first nucleotide sequence that provides the double-helical domain, identifying a second nucleotide sequence that provides the G-quadruplex domain, identifying a linker domain which may be nucleosidic or non-nucleosidic (such as HEG), and identifying an aptamer sequence for the isolated nucleic acid molecule that comprises the double helical domain coupled to the G-quadruplex domain by the linker domain. The aptamer sequence is for example a sequence of 30 to 80 nt. The method may further include providing the isolated nucleic acid molecule having the aptamer sequence, for example by providing the identified sequence to a contact laboratory for synthesis, and once having obtained the synthesized molecule having the aptamer sequence, combining the nucleic acid molecule and the lentiviral reverse transcriptase polypeptide expressed by a bacterial cell, for a time and under conditions effective to allow the nucleic acid molecule to bind to the lentiviral reverse transcriptase polypeptide such that binding occurs. The combining may take pale in vitro or in vivo. The method may further include examining inhibition of the lentiviral reverse transcriptase polypeptide activity, for example using any one of a number of RT functional assays such as those described in Held et al (2006). For example, such functional assays include an assay examining inhibition of DNA-dependent DNA polymerization, as described herein elsewhere

and in Held et al. (2006). Alternatively the assay may be a polymerase-independent RNase H Activity Assay as described as also described herein elsewhere and in Held et al. (2006). [0121] The method may further include examining the affinity of the nucleic acid molecule for the lentiviral reverse transcriptase polypeptide. The method may further include examining the number of binding sites for the nucleic acid molecule present on the lentiviral reverse transcriptase polypeptide. In some embodiments of the method, the nucleic acid molecule is labeled with a detectable marker which can be used to generate a signal corresponding to the occurrence or amount of binding. Alternatively, methods using the nucleic acid molecule can include conjugating the nucleic acid molecule to a polypeptide, such as a carrier peptide or a cell-penetrating polypeptide.

H. Kits

[0122] In another aspect the present disclosure relates to kits including at least one nucleic acid molecule according to the present disclosure, which is used for inhibiting a primate lentiviral reverse transcriptase. Kits according to the present disclosure can include one or more additional reagents useful for inhibiting, or measuring inhibition of a primate lentiviral RT according to the present disclosure. A kit generally includes a package with one or more containers holding the reagents, as one or more separate compositions or, optionally, as admixture where the compatibility of the reagents will allow. The kit can also include other material(s), which may be desirable from a user standpoint, such as a buffer(s), a diluent(s), a standard(s), and/or any other material useful in sample processing, washing, or conducting any other step of the assay. For example, a kit according to the present disclosure may contain a labeled DNA primer and a DNA template corresponding to a portion of a nucleotide sequence encoding the lentiviral reverse transcriptase polypeptide.

[0123] Test kits according to the present disclosure preferably include instructions for carrying out one or more assays of inhibition for measuring inhibition of a primate lentiviral RT by nucleic acid molecules according to the present disclosure. Instructions included in kits of the present disclosure can be affixed to packaging material or can be included as a package insert. While the instructions are typically written or printed materials they are not limited to such. Any medium capable of storing such instructions and communicating them to an end user is contemplated by this disclosure. Such media include, but are not limited to, electronic storage

media (e.g., magnetic discs, tapes, cartridges, chips), optical media (e.g., CD ROM), and the like. As used herein, the term "instructions" can include the address of an internet site that provides the instructions.

[0124] By way of example and not of limitation, examples of the present disclosures shall now be given.

I. Examples

Experimental Materials and methods

[0125] For all examples, RT 's were expressed in Escherichia coli and purified as previously described in Held, D., et al, (2006) J. Biol. Chem., 281, 25712-25722, which is herein incorporated by reference in its entirety. Except where noted, all assays utilized RT from HIV-I strain HXB2 (group M, subtype B). Aptamer RT6 was synthesized and purified by Operon Biotechnologies, Inc., (Huntsville, AL, USA; www. operon.com). All other aptamer oligonucleotides and primer/template substrates were synthesized and purified by Integrated DNA Technologies, Inc. (www. idtdna.com). The original full-length aptamers were 81 nt in length and previously described in Schneider,D.J., et al. (1995) Biochem. 34, 9599-9610. The "full-length" aptamers studied here were synthesized as 80-nt molecules by removing the 3'- terminal dG residue. This change was without functional consequence, as observed IC50 values were similar to those measured previously as described in Schneider,D.J., et al. (1995). Computational predictions of DNA secondary structures with mfold 3.1 (www.rpi.edu/ -zukerm/; as described in Mathews, D. et al.(1999) J. MoI. Biol, 288, 911-940; and Zuker, M. (2003) Nucleic Acids Res. 31, 3406-3415) utilized only the nonquadruplex portions of each molecule. All peptides and oligonucleotides used in the examples are listed herein above, provided in Tables 1-5, or set forth below in the following section describing RT functional assays.

Inhibition of RT enzymatic activities

[0126] Aptamer DNA was denatured by heating to 95°C for 5 min, followed by slow cooling at a rate of 2° per minute to room temperature and stored in frozen condition.

Subsequent dilutions were made from this refolded stock without additional refolding.

Measurements of DNA- dependent DNA polymerization (DDDP) were carried out essentially as described in Held, D., et al., (2006).

[0127] For DDDP assays, an 18- nt Cy3-labeled DNA primer (Cy3-

GTCCCTGTTCGGGCGCCA, SEQ ID NO. 64), was annealed to a 103-nt synthetic DNA

template corresponding to the primer-binding sequence and U5 segments of HIV-I strain HXB2

(103 Template sequence:

AAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCT

TTT; SEQ ID NO: 65).

[0128] Reactions were assembled in reaction buffer (50 mM Tris-HCl pH 8.3, 75 mM KCl,

5 mM MgC12, 10 mM DTT) with 30 nM primer, 45 nM template and 0.2 mM dNTPs. After annealing primer and template strands, DNA aptamers were added. Reactions were initiated by adding RT to a final concentration of 3 nM active site. For IC50 measurements, final aptamer concentrations were 0 nM, 0.3 nM, 1.0 nM, 3.0 nM, 10 nM, 30 nM, 100 nM and 300 nM.

Additional reactions included 1 μM and 3 μM where indicated. After 10 min at 37°C, reactions were quenched by addition of 2 volumes (20 μl) of gel-loading buffer (95% formamide with

0.01% bromophenol blue). For reactions assessing monovalent ion dependence, 75 mM KCl was replaced with 75 mM NaCl where indicated.

[0129] Reaction products were separated using denaturing (8M urea) 10% PAGE and scanned for fluorescence using a Fujifilm FLA5000 imaging system. RT activity data were collected using Fujifilm Multi Gauge V2.3 image analysis software. Competitive inhibition by aptamers is due to a decrease in the concentration of available enzyme, and is described by the two-state model for RT-aptamer binding [Equation (I)] :

[0130] Y = 100[aptamer]=(IC50 + [aptamer] 1 where Y is the measured percent activity at a given inhibitor concentration. This equation can be rearranged to a convenient form [Equation (2)] for curve-fitting with GraphPad Prism software to obtain IC50 values for aptamer inhibition:

[0131] Y= 100/[l + 10(logIC50~Xi] 2 where X is the log of the inhibitor concentration. Error terms for reported IC50 values are the standard deviations among triplicate assays.

[0132] For the polymerase independent RNase H Activity Assay, a 43-nt, fluorescently labeled RNA oligonucleotide corresponding to the 5 '-end of the HXB2 RNA genome (5'-Cy3-

GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGG-S') (SEQ ID NO:

66) was subjected to RNase H cleavage by RT when annealed to a DNA oligonucleotide complementary to the 5' 53 nt of the HXB2 genomic RNA (5'-

CCCTAGTTAGCCAGAGAGCTCCCAGGCTCAGATCTGGTCTAACCAGAGAGACC-S')

(SEQ ID NO: 66). Reactions were assembled by mixing 30 nM RNA and 60 nM DNA complement in reaction buffer, and individual reaction aliquots (including aptamer) were prepared as described above. Reactions were initiated by the addition of 4μl of RT, incubated at 37 ⁰ C for 3 min, and quenched and analyzed as described for the above assays.

Circular dichroism spectroscopy

[0133] DNA aptamer samples (SN, RIT and RT6-B) were prepared essentially as for inhibition assays, by heating to 90 ⁰ C and renaturing at 25 ⁰ C for 20 min. The concentrations 4 μM or 2 μM were adjusted in the corresponding buffers (K-buffer = 50 mM Tris-HCl pH 8.3, 75 mM KCl, 5 mM MgC12, 10 mM DTT; Na-buffer = 50 mM Tris-HCl pH 8.3, 75 mM NaCl, 5 mM MgC12, 10 mM DTT). Near- UV circular dichroism (CD) spectra were acquired at 25°C using an Aviv 62DS spectrometer (Lakewood, NJ) at 1.0 nm intervals between 350 nm and 210 nm in a 1.0 mm quartz cuvette, averaging each data point for 10 s.

Example 1: Nucleic acid molecules with extended quadruplex loops

[0134] Figure 1 shows two alternative configurations for exemplary aptamers according to the present disclosure. The upper drawing shows a hairpin loop structure in which a 3' end of the double helical domain is coupled to the linker domain, and the linker domain is coupled to a 5' end of the G-quadruplex domain. The lower drawing shows an alternative structure involving a terminal loop, a 3' end of the double helical domain coupled to the linker domain, and a 5' end of the double helical domain coupled to the linker domain.

[0135] Nucleic acid molecules having one of the two forms were prepared and tested as set forth elsewhere herein. As shown in Figures 2-3, RlT, RlA and RlC (Table 1) demonstrated strong inhibitory effects on RT, particularly in comparison to a helical domain alone, and control sequences. These aptamers are characterized by extended mononucleotide loops of varying length. As shown in Figure 5, R4T and R8T showed a relatively high level of RT inhibition. Also, SN, which is characterized by extended loops created by replacing nucleotides with HEG, demonstrated a relatively high level of RT inhibition as shown in Figure 4A-B.

Example 2: Nucleic acid molecules with linker domains of varying length and composition

[0136] The effect of changing the length and composition of the linker domain in the aptamers was examined by changing the linker domain sequence, varying its length from one

through sixteen nucleotides, or substituting N7 (2 '-hydroxy ethyl) guanine for the nucleotide sequence, and then testing each variant for inhibition of RT.

[0137] Figures 6-11 show various gel-blot results obtained for each aptamer tested, as indicated near the top of each figure. The results show that increasing the length of the linker domain does not significantly affect the level of RT inhibition by the aptamer. For example, the

RlN type aptamers are highly tolerant of a linker of increased length. For example, the results obtained with sequence LlO, in which the length of linker domain is sixteen (all T's), were not significantly different from those obtained with Ll in which the linker domain consisted of a single T .

[0138] Sequences tested included the following:

[0139] Ll : CGCCTGATTAGCGATACTcaggcgTgggTgggTgggTggg

[0140] L3 : CGCCTGATT AGCGATACTcaggcgTTTTgggTgggTgggTggg

[0141] L4: CGCCTGATTAGCGATACTcaggcgTTTTTTTTgggTgggTgggTggg

[0142] L5 : CGCCTGATT AGCGATACTcaggcgAgggTgggTgggTggg

[0143] L6: CGCCTGATTAGCGATACTcaggcgAAgggTgggTgggTggg

[0144] L7: CGCCTGATTAGCGATACTcaggcgAAAAgggTgggTgggTggg

[0145] L8: CGCCTGATTAGCGATACTcaggcgAAAAAAAAgggTgggTgggTggg

[0146] L9: CGCCTGATT AGCGAT ACTcaggcgTTTTTTTTTTTTgggTgggTgggTggg

[0147] LlO: CGCCTGATTAGCGATACTcaggcgTTTTTTTTTTTTTTTTgggTgggTgggTggg

[0148] HEG (alt. RlT-HEG): CGCCTGATTAGCGATACTcaggcg(HEG)gggTgggTgggTggg

Additional results from the functional assay of sequence HEG (alt. RlT-HEG) as shown in Figure 6, also showed that substituting HEG for the linker domain did not significantly reduce RT inhibition by the aptamer.

Example 3: Nucleic acid molecules with varying sequences, sequence length and configuration

[0149] Nucleic acid molecules having the following sequences were prepared and then assayed for RT inhibition. The results for S4 and S 5 are shown in Figure 7. No significant differences in RT inhibition among these variants was observed.

[0150] Sl : CGTGATTAGCGATACTcacgTTgggTgggTgggTggg

[0151] S2: CGGATTAGCGATACTccgTTgggTgggTgggTggg

[0152] S4: CGCCTGA ccct TcaggcgTTgggTgggTgggTggg

[0153] S5: ATCCGCCTGA TT AGCGAT ACTcagaaggat TTgggTgggTgggTggg

Example 4: Nucleic acid molecules with varying topology

[0154] Nucleic acid molecules having the following sequences and thus varying topology were prepared and then assayed for RT inhibition, and compared to the results obtained with RlT. The results for DyI 1, Dyl2 and DyI 3are shown in Figure 8. Dyl5 was also tested.

[0155] DyIl : cgcGCtacTcaggcgTTgggTgggTgggTgggTTCGCCTGAttaGCgcg

[0156] Dyl2: CGCGCGCGCTACTCAGGCGTTGGGTGGGTGGGTGGGTTCG

CCTGATTAGCGCGCGCG

[0157] DyB: CGCGGCGCGCGCTACTCAGGCGTTGGGTGGGTGGGTGGGTTCGCC

TGATTAGCGCGCGCCGCG

[0158] Acut: GGGTGGGTTCGCCTGATTAGCGATACTcaggcgTTGGGtGGG

[0159] Bcut: GGGTTCGCCTGATTAGCGATACTcaggcgTTGGGtGGGtGGG

Example 5: Nucleic acid molecules with varying G-quadruplex domains

[0160] Nucleic acid molecules having the following sequences were prepared and then assayed for RT inhibition. The results for TQKl and TQK2 are shown in Figure 9. The results showed that the number of guanosines in each G-quadruplex domain plays an important role in the level of RT inhibition by the nucleic acid molecule.

[0161] TQKl CGCCTGATTAGCGATACTcaggcgTTAggTgggTgggTggg

[0162] TQK2 CGCCTGATTAGCGATACTcaggcgTTgAgTgggTgggTggg

[0163] TQK3 CGCCTGATT AGCGAT ACTcaggcgTTggATgggTgggTggg

[0164] TQK4 CGCCTGATT AGCGAT ACTcaggcgTTgggTAggTgggTggg

[0165] TQK5 CGCCTGATTAGCGATACTcaggcgTTgggTgAgTgggTggg

[0166] TQK6 CGCCTGATT AGCGATACTcaggcgTTgggTggATgggTggg

[0167] TQK7 CGCCTGATTAGCGATACTcaggcgTTgggTgggTAggTggg

[0168] TQK8 CGCCTGATTAGCGATACTcaggcgTTgggTgggTgAgTggg

[0169] TQK9 CGCCTGATT AGCGAT ACTcaggcgTTgggTgggTggATggg

[0170] TQKlO CGCCTGATT AGCGAT ACTcaggcgTTgggTgggTgggTAgg

[0171] TQKI l CGCCTGATT AGCGAT ACTcaggcgTTgggTgggTgggTgAg

[0172] TQKl 2 CGCCTGATT AGCGAT ACTcaggcgTTgggTgggTgggTggA

Example 6: Nucleic acid molecules with varying G-quadruplex domains

[0173] The importance of triplet of guanosines in G-tracts was tested by changing G3 for G2 and G4. The results for ML4 are shown in Figure 10. The results indicated that nucleic acid molecules having four G3 -tracts provide the highest level of RT Inhibition. However other G- quadruplex structures maintain some level of RT inhibition. [0174] QK (alt. ML2): CGCCTGATT AGCGATACTcaggcgTTggTggTggTgg

[0175] aMu(alt.ML4): CGCCTGATTAGCGATACTcaggcgTTggggTggggTggggTgggg

Example 7:Identifϊcation of a novel inhibitory DNA structure within ssDNA aptamers RT6, RT5 and RT47

[0176] Aptamers RT5, RT6 and RT47 form a subgroup of closely related sequences within Family VI of the ssDNA aptamers identified by Schneider et al.. Results disclosed herein show show strong inhibition of DNA polymerization by RT from a subtype B strain of HIV-I by 80-nt modified versions of each of these three aptamers. The concentration required for half-maximal inhibition (IC50) by RT6 was 36 f 3 nM and was similar for the other two (data not shown). All three aptamers share the same sequence in the first 5-6 nt of

the initial 35N random segment (Figure 12A), and this shared segment is complementary to nucleotides within the 5 '-primer-binding constant region. The remainder of each molecule includes four or more stretches of guanosine tri-nucleotide repeats. Five such repeats are evident in RT6. Aptamer RT6-A was generated by removing the 25 nt on the 3'-side of the fourth repeat of RT6 and modifying 5 nt between the third and fourth repeat. Aptamer RT6-A was more than 2-fold more potent for RT inhibition relative to the original RT6 aptamer (IC50 =16 f 3 nM). Similar 3' deletions from RT5 and RT47 inactivated these aptamers for RT inhibition unless three guanosines were appended onto the 3'-ends of the truncated species to restore their original termini (data not shown). Removing both the 3'- terminal 25 nt and the 5 '-terminal three unpaired nucleotides (ACG) of RT6 generated a 53-nt species designated RT6-B that retained potent RT inhibition (IC50 = 5.7 f 0.8 nM). Finally, the 41-nt aptamer variant R IT (IC50 =14 f 2 nM, Figure 12C) was generated in which the intra-quadruplex loop sequences connecting the guanosine triplets in RT6-B were replaced with single thymidine nucleotides. These data suggest a structural model in which each of these aptamers forms a 5 '-helical domain connected to a 3'-guanosine quadruplex domain (Figure 12B).

Example 8: Mutational support for quadruplex formation

[0177] To establish the quadruplex positions at which guanosine is required, each of the nucleotides that are proposed to define the G-quadruplex structures within RT6-A was individually changed to adenosine. All 12 G-to-A substitutions abolished RT inhibition (data not shown). These data provide strong evidence that RT inhibition by RT6-A (and by the original RT6) requires a three-tiered quadruplex. When similar mutations were generated in RlT, 11 of the 12 G-to-A mutations were similarly disruptive. However, deleting the first guanosine of the second triplet or changing it to A, C or T only reduced RT inhibition by two- to threefold (TQK4, Figure 13 A, and data not shown). These data suggest that only two tiers of the quadruplex may be absolutely required within RlT. However, inserting or removing one guanosine from each (TGGG) repeat in the original RlT quadruplex to yield (TGGGG)4 in ML4 and (TGG)4 in ML2 prevents aptamer-mediated RT inhibition (data not shown).

Example 9: Sequence plasticity of quadruplex loops and stem

[0178] To define further the sequence requirements within intraquadruplex loops, the single Ts in each loop of RlT were changed to other sizes and sequences. Replacement with single adenosines (RlA, IC50 =18 f 7 nM, Figure 13B) or cytidines (RlC, IC50 = 26 f 9 nM) was well tolerated, while replacement with single guanosines was not (RlG, IC50»250 nM). Expanding the loops with runs of two (R2T, i _C50 =13 f 2 nM), four (R4T, IC50 ~ 35 nM) or eight (R8T, IC50 = 20 f 3 nM) thymidines was also well-tolerated. In contrast, expansion of the loops to two (R2A), four (R4A) or eight (R8A) adenosines or with two (R2C) or four (R4C) cytidines yielded aptamers with greatly reduced capacity for inhibiting RT (Figure 13B). To eliminate the possibility that RT-loop nucleotide contacts are essential for aptamer recognition, the intra-quadruplex loops were replaced with the relatively inert, nonnucleosidic hexaethylene glycol (HEG) to yield the SN aptamer. Interestingly, inhibition by the SN aptamer is more than 10 times more potent (IC50 = 3.5 f 0.1 nM, Figure 13C) than the original RT6, and more than fourfold more potent than RlT. The results show that specific loop nucleotides within the quadruplex region are not required for inhibition or for stability, and that the loops are only minimally constrained as to sequence.

[0179] Additional variants of RlT were generated to identify sequence constraints within the 7-bp stem comprising the 5'-structural domain. Deletion of 2 bp (S l , IC50=59f 2 nM) or 3 bp (S2, IC50 =1 10 f 5 nM) from the stem progressively compromised RT inhibition (data not shown), while lengthening the stem to 22 bp slightly improved inhibition (ZAM 1 , IC 50 =10.0 f 1.5 nM). Reversing the sequence orientation within this domain (Srevstem, IC50 = 26 f 7 nM) had minimal impact on IC50 (Figure 13D) . Replacing the 10 nt at the end o f the R l T stem with a C C CT tetraloop (S 4 , IC50 = 32 f 1 nM, Figure 13E) had only a twofold effect on RT inhibition. These results establish that the 5 '-domain requires a generic double-helical fragment stabilized by seven or more base pairs of essentially any sequence.

Example 10:Loop sequences affect sensitivity to ionic environment

[0180] Potassium ions strongly favor quadruplex formation, while sodium ions are usually less stabilizing and lithium ions are destabilizing. We observed equivalent DNA polymerization activity by HIV-I RT in buffers containing either K ⁺ or Na ⁺ . RT inhibition by aptamers SN, RlT and RT6-B was therefore monitored in the original buffer containing K ⁺ and also in a buffer in which K ⁺ was replaced with Na ⁺ . The same RT was nearly inactive in buffers containing Li ⁺ , preventing analysis of inhibition in the presence Of Li ⁺ . All three aptamers strongly inhibited RT in the presence of K ⁺ . Aptamers SN and RlT were also strongly inhibitory in the Na ⁺ -containing buffer, while aptamer RT6-B lost all inhibition under these conditions (Figure 14). Because these three aptamers differ only in the loop sequences connecting the individual guanosine triplets of the quadruplex, it is concluded that the loop sequences in RT6-B render that aptamer sensitive to ionic destabilization, while the simplified structures of Rl T and SN stabilize those aptamers to ionic substitution.

[0181] Circular dichroism (CD) spectroscopy is a powerful analytical tool for identifying quadruplexes DNA structures. For quadruplexes in which all four strands are in the same orientation (parallel), CD minima and maxima are typically near 240 nm and 264 nm, respectively. For quadruplexes in which strands orientation alternates (antiparallel), the corresponding values are typically near 265 nm and 295 nm, respectively. The CD spectra for RT6-B and RlT both show maxima at 262 nm and minima at 242 nm at room temperature in the presence of K ⁺ (Figure 15). In Na ⁺ buffer the ellipticity is strongly flattened for RT6-B, especially at low DNA concentration, indicting destabilization of the quadruplex structure. Slight flattening is also evident in RlT, although to a lesser extent. Quadruplexes containing HEG loops, such as the one in aptamer SN, have previously been shown to be more stable than quadruplexes with single T loops in both K ⁺ and Na ⁺ buffers; thus, SN is also expected to retain its quadruplex in the Na ⁺ buffer. These data provide independent confirmation of guanosine quadruplex formation within the RT6 family of aptamers, and they establish that the structural integrity of the simple quadruplex within RlT is less sensitive to ionic conditions, consistent with the inhibition data above.

Example 11: A generic, physical connection is required between the duplex and quadruplex modules

[0182] RT inhibition was measured for several variants of RlT to determine the importance of the physical connection between the two structural modules (Figure 16A). No inhibition was observed for a 28-nt oligo containing only the 5' stem — loop motif (stem), nor for a 16-nt oligo containing the (TGGG) ₄ quadruplex motif (Q 16). Similarly, no inhibition was observed when both oligos were added simultaneously at a ratio of 1 : 1 , even when their individual concentrations were increased to 3000 nM (Figure 16B). A physical (covalent) connection between the DNA duplex and G-quadruplex is therefore required to effect inhibition.

[0183] The stem — loop and G-quadruplex elements within aptamers RT6, RT5 and RT47 are joined by single-stranded segments with the sequences TTA, CTT and CC, respectively, while in RlT the connector is TT. To determine the effect of varying this connector sequence, RT inhibition was measured for variants of RlT in which the connector was changed to several other sequences. Changing those two thymidines to two adenosines (A ₂ connector in L6), or expanding it to four (T ₄ in L3) or eight (T ₈ in L4) thymidines had minimal effect on IC ₅₀ values (13 ± 1, 13 ±2 and 28 ± 2 nM, respectively) (data not shown). To determine whether the negative charges or other nucleic acid-related features of these connector sequences are required for RT inhibition, the duplex and quadruplex modules were joined via HEG (Figure 16C). The IC ₅₀ value of the HEGlinked molecule (29 ± 3 nM, HEG) is similar to that of the T ₈ - linked molecule. Thus, the primary role of the connector is to provide a physical connection between the two domains, rather than to provide a specific structural or functional role. However, there is an optimal range of lengths for the connector, as increasing it to T16 significantly weakened inhibition (LlO, IC50 = 120 ± 6 nM).

Example 12: Topological malleability of the connectivity between the structural elements

[0184] In all of the aptamer variants above, the two structural elements are connected via one flexible linker between the 3 '-end of the helical element and the 5 '-end of the quadruplex element. The 5'- and 3 '-ends of the molecule are located, respectively, at the termini of the helical and quadruplex elements. Several variants of RlT were evaluated to determine whether alternative topologies are allowed. To accommodate relocating the 5' and 3' termini to other positions, the helical fragment was joined to the quadruplex by separate thymidine

dinucleotides at each end of the quadruplex (Figure 16A). For variants DyIl , Dyl2, Dyl3 and Dy 15, the 5' and 3' termini lie within the original loop at the distal end of the helical element. The helical portions of these molecules contain a total of 15 bp, 19 bp, 22 by or 35 bp, including an internal mismatch derived from the original stem in RT6. All four variants strongly inhibit HIV-I RT (e.g. IC ₅₀ = 21.0 ± 3.5 nM for Dyl5) (Figure 16D). The 5' and 3' termini were next relocated to internal positions within the quadruplex (Figure 16A). Placing the 3'-end after the second guano sine triplet (Acut, IC50 = 22 ± 4 nM, Figure 16D) yielded inhibition within a factor of two of the potency of RlT. Reversing the sequence within the central loop at the distal end of the helical element (Acutrev, IC50 = 33 f 2 nM) had only a slight effect on IC50. Inhibitory potency was further reduced when the 3'-end was placed after the first guanosine triplet (Bcut, IC50 = 48 f 1 nM) or after the third guanosine triplet (Ecut, IC50 = 99 f 2 nM), likely reflecting a destabilization of the quadruplex module. Potent inhibitors based on RlT can therefore be generated by joining the helical fragment and quadruplex by either a single or a double linker between the helical and quadruplex elements.

Example 13:Cross-clade inhibition of divergent primate lentiviral RT's

[0185] The ssDNA aptamers studied here were originally selected to bind RT from HIV-I strain BHlO (group M, subtype B). The inhibition studies presented above all utilize RT from the closely related HIV-I strain HXB2 (six amino acid differences in 560 positions, preserving 98.9% identity). To define the phylogenetic breadth of inhibition by these bimodular ssDNA aptamers, DNA- dependent DNA polymerization was monitored for a panel of five RT variants from diverse primate lentiviral strains from within HIV-I group M (average 92% identity with RT from BHlO) and three from outside this group (see Held, D., et al. (2007) J. Virol, 81, 5375- 5384). Aptamer SN was chosen for this analysis, as it was the most potent inhibitor among those studied here. All eight lentiviral RT's were inhibited. With the exception of the HIV-2 isolate, all IC50 values were (within error) within a factor of two of being identical to IC50 for inhibition of the subtype B enzyme . The SN aptamer (and related forms) are therefore highly promising reagents for developing broad-spectrum anti-HIV agents.

[0186] One skilled in the art would readily appreciate that the nucleic acids and methods described in the present disclosure are well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. The molecules and the methods, procedures, treatments, molecules, specific compounds described herein are presently

representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the present disclosure. It will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the present disclosure disclosed herein without departing from the scope and spirit of the present disclosure.

[0187] All patents and publications mentioned in the specification are indicative of the levels of those skilled in the art to which the present disclosure pertains. All patents and publications are herein incorporated by reference to the same extent as if each individual publication was specifically and individually indicated to be incorporated by reference.

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