The 5′ Leader (5′-L) of the human immunodeficiency virus-1 (HIV-1) RNA genome is highly conserved and constantly in an equilibrium between the monomer and dimer conformations. In the monomer conformation, the RNA is preferentially translated into proteins necessary for reproduction, while in the dimer conformation, the RNA is packaged as the genome for a new virion. The exact start site of the RNA has not been listed consistently in the literature in the past years. It was found that <i>in vivo</i>, there exists a mixed population of capped viral RNA with start sites that begin with one, two, or three guanosines (Cap1G, Cap2G, and Cap3G, respectively). This discrepancy had a profound effect on the folding patterns of the RNA, as it was observed using native gel electrophoresis Cap1G 5′-L favored the dimer conformation, whereas the Cap2G and Cap3G preferred the monomer conformation. This difference in start sites therefore influences the structure and function of the RNA. We use nuclear magnetic resonance spectroscopy to determine the exact structural mechanism by which start site differences direct this change. Using specific nucleotide- and site- specific labeling schemes, we were able to identify a sensitive signal that is unique to the Cap2G construct only. Assigning signals in the full 5′-L is difficult due to the numerous signal overlap. To overcome this problem and assign the residue that the sensitive signal belongs to, we constructed smaller oligo controls of the full 5′-L. Our future works include making oligo control constructs of the TAR hairpin with different start sites to compare the signals.<br/>

5′ Start site heterogeneity of the HIV-1 RNA and its effect on structure and function

253rd National Meeting (2017)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.