Fig. 3.

Domain II-like RNAs in viral IRES elements. (A) Consensus secondary structure of domain II analogs from viral IRES elements. The internal loop of subdomain IIa consists of an unpaired stretch of nucleotides in either the 5′ or 3′ proximal strand of the lower stem. (B) Mg²⁺-induced folding of viral subdomain IIa motifs. FRET signal from terminally Cy3/Cy5 labeled RNA constructs was monitored while increasing Mg²⁺ concentration. See SI Appendix, Fig. S1 for RNA construct structures. Fitting of dose–response curves resulted in EC₅₀ values for Mg²⁺-induced folding at 598 ± 25 μM (HCV, ■) (23), 196 ± 21 μM (CSFV, ○), 219 ± 19 μM (BVDV, ▼), 131 ± 21 μM (AEV, Δ), and 579 ± 86 μM (SVV, ●). Error bars represent ±1 SD calculated from triplicate experiments.