Selection of primer-template sequences that bind human immunodeficiency virus reverse transcriptase with high affinity

Nucleic Acids Research

Volumn 34, Issue 1, 2006, Pages 130-139

  DeStefano, Jeffrey J ^a   Cristofaro, Jason V ^a  

^a Bldg 142   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; RNA DIRECTED DNA POLYMERASE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BINDING AFFINITY; DNA FLANKING REGION; ENZYME BINDING; GENE AMPLIFICATION; GENE SEQUENCE; HUMAN IMMUNODEFICIENCY VIRUS; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; WILD TYPE;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; BINDING SITES; GUANINE; HIV-1 REVERSE TRANSCRIPTASE; RNA; SELEX APTAMER TECHNIQUE; TEMPLATES, GENETIC;

HUMAN IMMUNODEFICIENCY VIRUS;

EID: 31544465220     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkj426     Document Type: Article

References (40)

1. Ellington,A.D. and Szostak,J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
2. Joyce,G.F. (1989) Amplification, mutation and selection of catalytic RNA. Gene, 82, 83-87.
3. Tuerk,C. and Gold,L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
4. Joshi,P. and Prasad,V.R. (2002) Potent inhibition of human immunodeficiency virus type 1 replication by template analog reverse transcriptase inhibitors derived by SELEX (systematic evolution of ligands by exponential enrichment). J. Virol., 76, 6545-6557.
5. Joshi,P.J., North,T.W. and Prasad,V.R. (2005) Aptamers directed to HIV-1 reverse transcriptase display greater efficacy over small hairpin RNAs targeted to viral RNA in blocking HIV-1 replication. Mol. Ther., 11, 677-686.
6. Joshi,P.J., Fisher,T.S. and Prasad,V.R. (2003) Anti-HIV inhibitors based on nucleic acids: Emergence of aptamers as potent antivirals. Curr. Drug Targets Infect Disord., 3, 383-400.
7. Tuerk,C., MacDougal,S. and Gold,L. (1992) RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl Acad. Sci. USA, 89, 6988-6992.
8. Jaeger,J., Restle,T. and Steitz,T.A. (1998) The structure of HIV-1 reverse transcriptase complexed with an RNA pseudoknot inhibitor. EMBO J., 17, 4535-4542.
9. Chen,H. and Gold,L. (1994) Selection of high-affinity RNA ligands to reverse transcriptase: Inhibition of cDNA synthesis and RNase H activity. Biochemistry, 33, 8746-8756.
10. Schneider,D.J., Feigon,J., Hostomsky,Z. and Gold,L. (1995) High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. Biochemistry, 34, 9599-9610.
11. Brody,E.N. and Gold,L. (2000) Aptamers as therapeutic and diagnostic agents. J. Biotechnol., 74, 5-13.
12. Gold,L.(1995) The SELEX process: A surprising source of therapeutic and diagnostic compounds. Harvey Lect., 91, 47-57.
13. Sambrook,J. and Russell,D.W. (2001) Molecular Cloning: A Laboratory Manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
14. Peliska,J.A. and Benkovic,S.J. (1992) Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase. Science, 258, 1112-1118.
15. Hsieh,J.C., Zinnen,S. and Modrich,P. (1993) Kinetic mechanism of the DNA-dependent DNA polymerase activity of human immunodeficiency virus reverse transcriptase. J. Biol. Chem., 268, 24607-24613.
16. Wöhrl,B.M., Tantillo,C., Arnold,E. and Le Grice,S.F. (1995) An expanded model of replicating human immunodeficiency virus reverse transcriptase. Biochemistry, 34, 5343-5356.
17. DeStefano,J.J., Cristofaro,J.V., Derebail,S., Bohlayer,W.P. and Fitzgerald-Heath,M.J. (2001) Physical mapping of HIV reverse transcriptase to the 5′ end of RNA primers. J. Biol. Chem., 276, 32515-32521.
18. Arion,D., Kaushik,N., McCormick,S., Borkow,G. and Parniak,M.A. (1998) Phenotypic mechanism of HIV-1 resistance to 3′-azido-3′-deoxythymidine (AZT): Increased polymerization processivity and enhanced sensitivity to pyrophosphate of the mutant viral reverse transcriptase. Biochemistry, 37, 15908-15917.
19. Arion,D., Borkow,G., Gu,Z., Wainberg,M.A. and Parniak,M.A. (1996) The K65R mutation confers increased DNA polymerase processivity to HIV-1 reverse transcriptase. J. Biol. Chem., 271, 19860-19864.
20. Rausch,J.W. and Le Grice,S.F. (2004) 'Binding, bending and bonding': polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus. Int. J. Biochem. Cell Biol., 36, 1752-1766.
21. Ivanov,V.I., Minchenkova,L.E., Minyat,E.E., Frank-Kamenetskii,M.D. and Schyolkina,A.K. (1974) The B to A transition of DNA in solution. J. Mol. Biol., 87, 817-833.
22. Minchenkova,L.E., Schyolkina,A.K., Chernov,B.K. and Ivanov,V.I. (1986) CC/GG contacts facilitate the B to A transition of DNA in solution. J. Biomol. Struct. Dyn., 4, 463-476.
23. Zavriev,S.K., Minchenkova,L.E., Frank-Kamenetskii,M.D. and Ivanov,V.I. (1978) On the flexibility of the boundaries between the A-form and B-form sections in DNA molecule. Nucleic Acids Res., 5, 2657-2663.
24. Pilet,J., Rottman,F. and Brahms,J. (1973) Structural parameters of single and double stranded helical polyribonucleotides. Biochem. Biophys. Res. Commun., 52, 517-523.
25. Haran,T.E., Shakked,Z., Wang,A.H. and Rich,A. (1987) The crystal structure of d(CCCCGGGG): A new A-form variant with an extended backbone conformation. J. Biomol. Struct. Dyn., 5, 199-217.
26. Wang,A.H., Fujii,S., van Boom,J.H. and Rich,A. (1982) Molecular structure of the octamer d(G-G-C-C-G-G-C-C): Modified A-DNA. Proc. Natl Acad. Sci. USA, 79, 3968-3972.
27. Mooers,B.H., Schroth,G.P., Baxter,W.W. and Ho,P.S. (1995) Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A-DNA. J. Mol. Biol., 249, 772-784.
28. Kunkel,T.A. and Wilson,S.H. (1998) DNA polymerases on the move. Nature Struct. Biol., 5, 95-99.
29. Brautigam,C.A. and Steitz,T.A. (1998) Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr. Opin. Struct. Biol., 8, 54-63.
30. Huang,H., Chopra,R., Verdine,G.L. and Harrison,S.C. (1998) Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance [see comments]. Science, 282, 1669-1675.
31. Jacobo-Molina,A., Ding,J., Nanni,R.G., Clark,A.D.Jr, Lu,X., Tantillo,C., Williams,R.L., Kamer,G., Ferris,A.L., Clark,P. et al. (1993) Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA. Proc. Natl Acad. Sci. USA, 90, 6320-6324.
32. Wöhrl,B.M., Krebs,R., Goody,R.S. and Restle,T. (1999) Refined model for primer/template binding by HIV-1 reverse transcriptase: pre-steady-state kinetic analyses of primer/template binding and nucleotide incorporation events distinguish between different binding modes depending on the nature of the nucleic acid substrate. J. Mol. Biol., 292, 333-344.
33. Cristofaro,J.V., Rausch,J.W., Le Grice,S.F. and DeStefano,J.J. (2002) Mutations in the ribonuclease H active site of HIV-RT reveal a role for this site in stabilizing enzyme-primer-template binding. Biochemistry, 41, 10968-10975.
34. DeStefano,J.J., Bambara,R.A. and Fay,P.J. (1993) Parameters that influence the binding of human immunodeficiency virus reverse transcriptase to nucleic acid structures. Biochemistry, 32, 6908-6915.
35. Yu,H. and Goodman,M.F. (1992) Comparison of HIV-1 and avian myelblastosis virus reverse transcriptase fidelity on RNA and DNA templates. J. Biol. Chem., 267, 10888-10896.
36. Biburger,M., Niederweis,M. and Hillen,W. (1994) Oligo[d(C).(G)] runs exhibit a helical repeat of 11.1 by in solution and cause slight DNA curvature when properly phased. Nucleic Acids Res., 22, 1562-1566.
37. Merling,A., Sagaydakova,N. and Haran,T.E. (2003) A-tract polarity dominate the curvature in flanking sequences. Biochemistry, 42, 4978-4984.
38. DeStefano,J.J., Mallaber,L.M., Fay,P.J. and Bambara,R.A. (1993) Determinants of the RNase H cleavage specificity of human immunodeficiency virus reverse transcriptase. Nucleic Acids Res., 21, 4330-4338.
39. DeStefano,J.J. (1995) The orientation of binding of human immunodeficiency virus reverse transcriptase on nucleic acid hybrids. Nucleic Acids Res., 23, 3901-3908.
40. Fuentes,G.M., Rodriguez-Rodriguez,L., Fay,P.J. and Bambara,R.A. (1995) Use of an oligoribonucleotide containing the polypurine tract sequence as a primer by HIV reverse transcriptase. J. Biol. Chem., 270, 28169-28176.