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.
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.
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| Alam, Khalid K; Tawiah, Kwaku D; Lichte, Matthew F et al. (2017) A Fluorescent Split Aptamer for Visualizing RNA-RNA Assembly In Vivo. ACS Synth Biol 6:1710-1721 |
| Lange, Margaret J; Nguyen, Phuong D M; Callaway, Mackenzie K et al. (2017) RNA-protein interactions govern antiviral specificity and encapsidation of broad spectrum anti-HIV reverse transcriptase aptamers. Nucleic Acids Res 45:6087-6097 |
| Shebl, Bassem; Menke, Drew E; Pennella, Min et al. (2016) Preparation of ribosomes for smFRET studies: A simplified approach. Arch Biochem Biophys 603:118-30 |
| 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 |
| Chen, Shi-Jie; Burke-Agüero, Donald H (2015) Preface. Methods Enzymol 553:xv-xvii |
| 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 |
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