Structure of the RNA inside influenza virus RNPs

Abstract

Influenza virus nucleoprotein binds to the phosphate sugar backbone of the viral RNA and exposes the nucleotide bases to the solvent. In viral RNP, all nucleotide bases are exposed apart from those at the conserved 3′ and 5′ ends of the vRNA whose Watson–Crick (W–C) positions are protected against modification by chemical reagents. However, when the polymerase is removed from the RNP, the bases in the conserved ends become available for chemical attack. So the presence of the polymerase is correlated with protection of the vRNA ends, either by direct contact between the nucleotide bases and the polymerase or by inducing base pairing between the ends. We also present our latest results on the footprint of the polymerase on the vRNA ends in the intact RNPs, in particular the protection of the N7 positions of the guanine and adenine residues in this region. Our results on the structure of the ends of the RNA and the footprint of the polymerase on these ends are compared with other models from the literature.