Figure 8. Nucleocapsid Increases SHAPE Reactivity and, by Inference, RNA Flexibility at Multiple Sites 5′ to the tRNA(lys3) Primer Binding Site.

(A) Absolute SHAPE reactivities for the ex virio (red), in virio (green) and AT-2 treated (blue) states.

(B) Difference plot reporting the effect of AT-2 treatment on the in virio state. Position of bound 3′ end of the tRNA primer is shown with a black arrow; large gray arrow and downward-pointing arrowheads indicate sites of structure destabilization by nucleocapsid.