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Nucleic Acids Res
v.39(18); 2011 Oct
PMC3185408
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Nucleic Acids Res. 2011 Oct; 39(18): 8237–8247.
Published online 2011 Jul 1. doi: 10.1093/nar/gkr381
Find articles by Nikolozi Shkriabai
1 Molecular Microbiology and Immunology, University of Missouri, 2 Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India, 3 Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, 4 Department of Biochemistry, University of Missouri, and 5 Bond Life Sciences Center, University of Missouri, Columbia, MO 65211
*To whom correspondence should be addressed. Tel: +1 573 884 1316; Fax: +1 573 884 9676; Email: ude.iruossim@hdekrub
Received 2011 Mar 10; Revised 2011 Apr 27; Accepted 2011 Apr 29.
Copyright © The Author(s) 2011. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0 ), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
GUID: A10AF1B2-93D4-44C8-8B00-AB450864D4DB
GUID: B6C7EA52-5363-4E23-A5D0-F99B85ED58DD
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2. Ng EW, Shima DT, Calias P, Cunningham ET, Jr, Guyer DR, Adamis AP. Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nat. Rev. Drug Discov. 2006; 5 :123–132. [ PubMed ] [ Google Scholar ]
3. Dyke CK, Steinhubl SR, Kleiman NS, Cannon RO, Aberle LG, Lin M, Myles SK, Melloni C, Harrington RA, Alexander JH, et al. First-in-human experience of an antidote-controlled anticoagulant using RNA aptamer technology: a phase 1a pharmacodynamic evaluation of a drug-antidote pair for the controlled regulation of factor IXa activity. Circulation. 2006; 114 :2490–2497. [ PubMed ] [ Google Scholar ]
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8. Li N, Wang Y, Pothukuchy A, Syrett A, Husain N, Gopalakrisha S, Kosaraju P, Ellington AD. Aptamers that recognize drug-resistant HIV-1 reverse transcriptase. Nucleic Acids Res. 2008; 36 :6739–6751. [ PMC free article ] [ PubMed ] [ Google Scholar ]
9. Michalowski D, Chitima-Matsiga R, Held DM, Burke DH. Novel bimodular DNA aptamers with guanosine quadruplexes inhibit phylogenetically diverse HIV-1 reverse transcriptases. Nucleic Acids Res. 2008; 36 :7124–7135. [ PMC free article ] [ PubMed ] [ Google Scholar ]
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21. Bellecave P, Cazenave C, Rumi J, Staedel C, Cosnefroy O, Andreola ML, Ventura M, Tarrago-Litvak L, Astier-Gin T. Inhibition of hepatitis C virus (HCV) RNA polymerase by DNA aptamers: mechanism of inhibition of in vitro RNA synthesis and effect on HCV-infected cells. Antimicrob. Agents Chemother. 2008; 52 :2097–2110. [ PMC free article ] [ PubMed ] [ Google Scholar ]
22. Pan Q, Zhang XL, Wu HY, He PW, Wang F, Zhang MS, Hu JM, Xia B, Wu J. Aptamers that preferentially bind type IVB pili and inhibit human monocytic-cell invasion by Salmonella enterica serovar typhi. Antimicrob. Agents Chemother. 2005; 49 :4052–4060. [ PMC free article ] [ PubMed ] [ Google Scholar ]
23. Kissel JD, Held DM, Hardy RW, Burke DH. Single-stranded DNA aptamer RT1t49 inhibits RT polymerase and RNase H functions of HIV type 1, HIV type 2, and SIVCPZ RTs. AIDS Res. Hum. Retroviruses. 2007; 23 :699–708. [ PubMed ] [ Google Scholar ]
24. Fisher TS, Joshi P, Prasad VR. HIV-1 reverse transcriptase mutations that confer decreased in vitro susceptibility to anti-RT DNA aptamer RT1t49 confer cross resistance to other anti-RT aptamers but not to standard RT inhibitors. AIDS Res. Ther. 2005; 2 :8. [ PMC free article ] [ PubMed ] [ Google Scholar ]
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Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press
1. Jellinek D, Green LS, Bell C, Janjic N. Inhibition of receptor binding by high-affinity RNA ligands to vascular endothelial growth factor. Biochemistry. 1994; 33 :10450–10456. [ PubMed ] [ Google Scholar ] [ Ref list ]
2. Ng EW, Shima DT, Calias P, Cunningham ET, Jr, Guyer DR, Adamis AP. Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nat. Rev. Drug Discov. 2006; 5 :123–132. [ PubMed ] [ Google Scholar ] [ Ref list ]
3. Dyke CK, Steinhubl SR, Kleiman NS, Cannon RO, Aberle LG, Lin M, Myles SK, Melloni C, Harrington RA, Alexander JH, et al. First-in-human experience of an antidote-controlled anticoagulant using RNA aptamer technology: a phase 1a pharmacodynamic evaluation of a drug-antidote pair for the controlled regulation of factor IXa activity. Circulation. 2006; 114 :2490–2497. [ PubMed ] [ Google Scholar ] [ Ref list ]
6. Tuerk C, MacDougal S, Gold L. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl Acad. Sci. USA. 1992; 89 :6988–6992. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
15. Boomer RM, Lewis SD, Healy JM, Kurz M, Wilson C, McCauley TG. Conjugation to polyethylene glycol polymer promotes aptamer biodistribution to healthy and inflamed tissues. Oligonucleotides. 2005; 15 :183–195. [ PubMed ] [ Google Scholar ] [ Ref list ]
16. Wilson C, Keefe AD. Building oligonucleotide therapeutics using non-natural chemistries. Curr. Opin. Chem. Biol. 2006; 10 :607–614. [ PubMed ] [ Google Scholar ] [ Ref list ]
17. McNamara JO, II, Andrechek ER, Wang Y, Viles KD, Rempel RE, Gilboa E, Sullenger BA, Giangrande PH. Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras. Nat. Biotechnol. 2006; 24 :1005–1015. [ PubMed ] [ Google Scholar ] [ Ref list ]
18. Zhou J, Li H, Li S, Zaia J, Rossi JJ. Novel dual inhibitory function aptamer-siRNA delivery system for HIV-1 therapy. Mol. Ther. 2008; 16 :1481–1489. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
19. Joshi P, Prasad VR. 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. 2002; 76 :6545–6557. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
20. Chen F, Hu Y, Li D, Chen H, Zhang XL. CS-SELEX generates high-affinity ssDNA aptamers as molecular probes for hepatitis C virus envelope glycoprotein E2. PLoS One. 2009; 4 :e8142. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
21. Bellecave P, Cazenave C, Rumi J, Staedel C, Cosnefroy O, Andreola ML, Ventura M, Tarrago-Litvak L, Astier-Gin T. Inhibition of hepatitis C virus (HCV) RNA polymerase by DNA aptamers: mechanism of inhibition of in vitro RNA synthesis and effect on HCV-infected cells. Antimicrob. Agents Chemother. 2008; 52 :2097–2110. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
22. Pan Q, Zhang XL, Wu HY, He PW, Wang F, Zhang MS, Hu JM, Xia B, Wu J. Aptamers that preferentially bind type IVB pili and inhibit human monocytic-cell invasion by Salmonella enterica serovar typhi. Antimicrob. Agents Chemother. 2005; 49 :4052–4060. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
7. Schneider DJ, Feigon J, Hostomsky Z, Gold L. High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. Biochemistry. 1995; 34 :9599–9610. [ PubMed ] [ Google Scholar ] [ Ref list ]
9. Michalowski D, Chitima-Matsiga R, Held DM, Burke DH. Novel bimodular DNA aptamers with guanosine quadruplexes inhibit phylogenetically diverse HIV-1 reverse transcriptases. Nucleic Acids Res. 2008; 36 :7124–7135. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
23. Kissel JD, Held DM, Hardy RW, Burke DH. Single-stranded DNA aptamer RT1t49 inhibits RT polymerase and RNase H functions of HIV type 1, HIV type 2, and SIVCPZ RTs. AIDS Res. Hum. Retroviruses. 2007; 23 :699–708. [ PubMed ] [ Google Scholar ] [ Ref list ]
24. Fisher TS, Joshi P, Prasad VR. HIV-1 reverse transcriptase mutations that confer decreased in vitro susceptibility to anti-RT DNA aptamer RT1t49 confer cross resistance to other anti-RT aptamers but not to standard RT inhibitors. AIDS Res. Ther. 2005; 2 :8. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
8. Li N, Wang Y, Pothukuchy A, Syrett A, Husain N, Gopalakrisha S, Kosaraju P, Ellington AD. Aptamers that recognize drug-resistant HIV-1 reverse transcriptase. Nucleic Acids Res. 2008; 36 :6739–6751. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
13. Burke DH, Scates L, Andrews K, Gold L. Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase. J. Mol. Biol. 1996; 264 :650–666. [ PubMed ] [ Google Scholar ] [ Ref list ]
25. Held DM, Kissel JD, Thacker SJ, Michalowski D, Saran D, Ji J, Hardy RW, Rossi JJ, Burke DH. Cross-clade inhibition of recombinant human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus SIVcpz reverse transcriptases by RNA pseudoknot aptamers. J. Virol. 2007; 81 :5375–5384. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
26. Kissel JD, Held DM, Hardy RW, Burke DH. Active site binding and sequence requirements for inhibition of HIV-1 reverse transcriptase by the RT1 family of single-stranded DNA aptamers. Nucleic Acids Res. 2007; 35 :5039–5050. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
27. Michailidis E, Marchand B, Kodama EN, Singh K, Matsuoka M, Kirby KA, Ryan EM, Sawani AM, Nagy E, Ashida N, et al. Mechanism of inhibition of HIV-1 reverse transcriptase by 4'-Ethynyl-2-fluoro-2'-deoxyadenosine triphosphate, a translocation-defective reverse transcriptase inhibitor. J. Biol. Chem. 2009; 284 :35681–35691. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
11. Mosing RK, Mendonsa SD, Bowser MT. Capillary electrophoresis-SELEX selection of aptamers with affinity for HIV-1 reverse transcriptase. Anal. Chem. 2005; 77 :6107–6112. [ PubMed ] [ Google Scholar ] [ Ref list ]
28. Gotte M, Maier G, Gross HJ, Heumann H. Localization of the active site of HIV-1 reverse transcriptase-associated RNase H domain on a DNA template using site-specific generated hydroxyl radicals. J. Biol. Chem. 1998; 273 :10139–10146. [ PubMed ] [ Google Scholar ] [ Ref list ]
29. Metzger W, Hermann T, Schatz O, Le Grice SF, Heumann H. Hydroxyl radical footprint analysis of human immunodeficiency virus reverse transcriptase-template.primer complexes. Proc. Natl Acad. Sc
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