Figure 5.

Effect of S-1 compound on SHAPE reactivity of nucleotides in the HCV 5′UTR. (A) Varying concentrations of S-1, an ISIS-11 analogue, were incubated with folded HCV RNA. The resultant SHAPE reactivities versus S-1 concentration were examined using Pearson's correlation coefficient (σ). An adjusted Pearson's score (σ⁴sqrt(RANGE)), for each NT position, which emphasizes strong correlations and incorporates the magnitude of the change in SHAPE reactivity versus nucleotide position, is plotted. Five nucleotides in the HCV 5′UTR were identified as affected by the presence of compound S-1. (B) These 5 nt map to the domain IIa bulge of the HCV 5′UTR, where it has previously been shown that analogue compound ISIS-11 binds, distorting the IIa bulge (22).