Figure 4.

Secondary structure models of ASBVd (+) based on the SHAPE analysis. (A) and (B) are the two secondary structure models proposed for ASBVd (+). The color of the circle surrounding each nucleotide reveals their relative reactivity to 1M7 in the presence of 10 mM Mg²⁺, as mentioned in the box. High reactivity reflects single-stranded region, while paired nucleotides are not reactive. Nucleotides for which the reactivity could not be determined are shown in grey and correspond to the primer binding site, or to nucleotide right 3' to the primer for which the electrophoresis resolution is not good enough, or to RT stops. The same experiments were carried out without Mg²⁺ and differences in reactivity are represented on the scheme: nucleotides circled in red show enhanced reactivity in the presence of Mg²⁺, and those in blue are less reactive. The models were designed using VaRNA [31].