HIV frameshift site RNA structure and ligand binding

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DESCRIPTION (provided by applicant): The expression of HIV Pol genes is entirely dependent upon a programmed -1 translational frameshift. Frameshifting is mediated by an RNA element that includes a slippery site and a highly conserved, downstream structure. The downstream RNA structure stimulates frameshifting through an unknown mechansim. The objective is to develop an atomic-level understanding of the structure and function of the frameshift site RNA. Dr. Butcher will determine the NMR structures of the frameshift site RNAs from HIV-1 group M, as well as from HIV-2 and SIV-SMM. These structures are broadly recognized to be attractive targets for the development of new therapeutics. Therefore, as a step towards the rational development of second generation RNA binding ligands with enhanced specificity, the structure of the HIV-1 frameshift site RNA bound to a novel small molecule with anti-HIV activity, guanidino neomycin B will be determined. Finally, in order to more broadly understand the structure and function of the frameshift site RNA, photoreactive RNA modifications will be used to probe its interactions with the translational machinery by laser-induced cross-linking. The resulting data will be mapped to the ribosomal and frameshift site RNA structures to produce the first view of the frameshifting interaction. The specific aims are: 1. Determine the NMR structure of the entire HIV-1 frameshift site (FS) RNA. 2. Investigate the structural and thermodynamic effects of guanidino glycoside binding. 3. Determine the structure of the HIV-2 and SIV-SMM FS RNAs. 4. Identify sites of interaction between the HIV FS RNA and translational machinery.