New therapeutic strategies are needed to circumvent the rapid selection of drug resistant virus and the toxicity of current anti-HIV drugs. RNA aptamers targeted to the reverse transcriptase (RT) inhibit viral replication when expressed inside cells, and they offer great potential in future therapies against HIV/AIDS. There is little known about how the virus might evolve in the face of continual selection pressure, or about how the aptamers can be improved to circumvent potential resistance. The long-term goal of this project is to develop RNA aptamers as gene therapy agents that provide long-term antiviral protection against a rapidly-evolving virus. Our emphasis is on defining the influence of RT amino acid sequence variations on inhibition by aptamers, and on identifying new aptamer sequences and structures with improved inhibition, both in vitro and in cells.
Aim 1 will determine the biophysical and structural basis for aptamer recognition and for differential inhibition by aptamers across phylogenetically diverse lentiviral RT's.
Aim 2 will identify new aptamers with broad recognition and improved potency, and delineate the secondary structures associated with cross-clade enzymatic inhibition.
Aim 3 examines inhibition of pseudotyped and replication-competent HIV-1 by intracellularly expressed aptamers, moving from optimization of the design elements that control expression, localization and inhibition to high throughput screens of aptamer and RT libraries.
Aim 4 evaluates the de novo evolution of aptamer resistance with emphasis on establishing genetic threshold, resistance loci, and the molecular basis of resistance.

Public Health Relevance

This project will evaluate the potential for, and the nature of, HIV-1 resistance to nucleic acid aptamers-a promising class of molecules for eventual use in gene therapy strategies to combat HIV-1-and it will generate new aptamers that are less subject to escape mutations.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
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Special Emphasis Panel (ZRG1-AARR-D (09))
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Gupta, Kailash C
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University of Missouri-Columbia
Schools of Medicine
United States
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Salamango, Daniel J; Alam, Khalid K; Burke, Donald H et al. (2016) In Vivo Analysis of Infectivity, Fusogenicity, and Incorporation of a Mutagenic Viral Glycoprotein Library Reveals Determinants for Virus Incorporation. J Virol 90:6502-14
Alam, Khalid K; Chang, Jonathan L; Burke, Donald H (2015) FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections. Mol Ther Nucleic Acids 4:e230
Lange, Margaret J; Burke, Donald H (2014) Screening inhibitory potential of anti-HIV RT RNA aptamers. Methods Mol Biol 1103:11-29
Michailidis, Eleftherios; Ryan, Emily M; Hachiya, Atsuko et al. (2013) Hypersusceptibility mechanism of Tenofovir-resistant HIV to EFdA. Retrovirology 10:65
Whatley, Angela S; Ditzler, Mark A; Lange, Margaret J et al. (2013) Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, ""UCAA-motif"" RNA Aptamers. Mol Ther Nucleic Acids 2:e71
Ditzler, Mark A; Lange, Margaret J; Bose, Debojit et al. (2013) High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase. Nucleic Acids Res 41:1873-84
Shimane, Kazuki; Kawaji, Kumi; Miyamoto, Fusako et al. (2013) HIV-1 resistance mechanism to an electrostatically constrained peptide fusion inhibitor that is active against T-20-resistant strains. Antimicrob Agents Chemother 57:4035-8
Hachiya, Atsuko; Reeve, Aaron B; Marchand, Bruno et al. (2013) Evaluation of combinations of 4'-ethynyl-2-fluoro-2'-deoxyadenosine with clinically used antiretroviral drugs. Antimicrob Agents Chemother :
Michailidis, E; Singh, K; Ryan, E M et al. (2012) Effect of translocation defective reverse transcriptase inhibitors on the activity of N348I, a connection subdomain drug resistant HIV-1 reverse transcriptase mutant. Cell Mol Biol (Noisy-le-grand) 58:187-95
Sohl, Christal D; Singh, Kamlendra; Kasiviswanathan, Rajesh et al. (2012) Mechanism of interaction of human mitochondrial DNA polymerase γ with the novel nucleoside reverse transcriptase inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine indicates a low potential for host toxicity. Antimicrob Agents Chemother 56:1630-4

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