Structure of the RNA inside the vesicular stomatitis virus nucleocapsid

The structure of the viral RNA (vRNA) inside intact nucleocapsids of vesicu lar stomatitis virus was studied by chemical probing experiments, Most of t he Watson-Crick positions of the nucleotide bases of vRNA in intact virus a nd in nucleoprotein (N)-RNA template were accessible to the chemical probes and the phosphates were protected. This suggests that the nucleoprotein bi nds to the sugar-phosphate backbone of the RNA and leaves the Watson-Crick positions free for the transcription and replication activities of the vira l RNA-dependent RNA polymerase. The same architecture has been proposed for the influenza virus nucleocapsids. However, about 5% of the nucleotide bas es were found to be relatively nonreactive towards the chemical probes and some bases were hyperreactive. The pattern of reactivities was the same for RNA inside virus and for RNA in N-RNA template that was purified over a Cs Cl gradient and which had more than 94% of the polymerase and phosphoprotei n molecules removed. All reactivities were more or less equal on naked vRNA , This suggests that the variations in reactivity towards the chemical prob es are caused by the presence of the nucleoprotein.