Figure 1. Secondary RNA structure of the FMDV IRES. Domains 1, 2, 3, 4, and 5 as well as the positions of the conserved GNRA, RAAA, and C-rich motifs are indicated. Nucleotide accessibility is colored according to SHAPE reactivity obtained using NMIA and 5′-radiolabeled primers.⁷ SHAPE reactivity was calculated as described⁶¹ and represented in a colored scale in which 0 indicates an unreactive nucleotide and the average intensity at highly reactive nucleotides is set to 1.0. RNA structure was viewed with VARNA.⁶⁰