Determining the Structure of the HIV-1 5 Prime Leader Dimeric Conformation

Abstract

The structure of the 5′-Leader (5′-L) of the human immunodeficiency virus (HIV-1) viral RNA genome is under intense study, due to its role in determining the fate of the RNA. Within the host cell, the 5′-L is in equilibrium between a monomeric and dimeric conformation. The monomer is translated into the Gag-polyprotein, while the dimer is packaged as the new genomic material for virions. Although, a three-dimensional structure of a truncated core dimer 5′-L has been solved, the overall conformation of the full-length capped 5′-L has yet to be determined due to the size limitation. Using nuclear magnetic resonance (NMR) spectroscopy, the two-dimensional structure of multiple regions of the dimer have been solved, however there has been difficulty assigning regions near the native cap residue. In order to overcome this obstacle, we use (NMR) spectroscopy techniques including nucleotide-specific deuteration and oligo control overlap. The results for these methods suggests that a novel end-to-end stacking conformation is formed by adjacent two hairpins over forty nucleotides in length each. This interaction sequesters the cap residue needed for translation initiation and thus attenuating functions of the monomer.