A Conserved Mechanism within the 5'-Leader RNA Genome among HIV-1 and SIVcpz Strains during Viral Genome Recognition

Abstract

Previous studies in our lab suggested that HIV-1 5′-Leader (5′-L) RNA genome is regulated by a molecular structural switch. The dimer promoting GC-rich loop of the dimer initiation site (DIS) hairpin is sequestered by base pairing with the unique-5’ region (U5) in the monomeric form. The DIS:U5 interaction is then displaced by a stem-loop region containing gag start codon (AUG). The U5:AUG interaction, therefore, occurs and promotes dimerization of the 5′-L.The question raised is whether this structural switch conserved in lentivirus family. Sequence alignment, gel electrophoresis, ITC, and NMR methods are employed in this study to compare RNA constructs from HIV-1, SIVcpz_TAN1, and SIVcpz_US strains. We found both SIVcpz_TAN1 and US strains utilize a similar RNA structural switch to HIV-1 within their 5′-L. This conserved function can be a potential candidate for anti-viral drug development.