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Nucleic Acids Research Advance Access originally published online on October 23, 2008
Nucleic Acids Research 2008 36(21):6739-6751; doi:10.1093/nar/gkn775
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Nucleic Acids Research, 2008, Vol. 36, No. 21 6739-6751
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Aptamers that recognize drug-resistant HIV-1 reverse transcriptase

Na Li, Yuxuan Wang, Arti Pothukuchy, Angel Syrett, Naeem Husain, Siddharth Gopalakrisha, Pradeepa Kosaraju and Andrew D. Ellington*

Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA

*To whom correspondence should be addressed. Tel: +1 512 471 6445; Fax: +1 512 471 7014; Email: andy.ellington{at}mail.utexas.edu

Received July 18, 2008. Revised October 7, 2008. Accepted October 8, 2008.

Drug-resistant variants of HIV-1 reverse transcriptase (RT) are also known to be resistant to anti-RT RNA aptamers. In order to be able to develop diagnostics and therapies that can focus on otherwise drug-resistant viruses, we have isolated two aptamers against a well-known, drug-resistant HIV-1 RT, Mutant 3 (M3) from the multidrug-resistant HIV-1 RT panel. One aptamer, M302, bound M3 but showed no significant affinity for wild-type (WT) HIV-1 RT, while another aptamer, 12.01, bound to both M3 and WT HIV-1 RTs. In contrast to all previously selected anti-RT aptamers, neither of these aptamers showed observable inhibition of either polymerase or RNase H activities. Aptamers M302 and 12.01 competed with one another for binding to M3, but they did not compete with a pseudoknot aptamer for binding to the template/primer cleft of WT HIV-1 RT. These results represent the surprising identification of an additional RNA-binding epitope on the surface of HIV-1 RT. M3 and WT HIV-1 RTs could be distinguished using an aptamer-based microarray. By probing protein conformation as a correlate to drug resistance we introduce an additional and useful measure for determining HIV-1 drug resistance.


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