Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation

Reorganization of domain 3 RNA structure in substitution mutants of motifs A and B. (A) Secondary structure probing of the wild-type IRES using DMS and RNase A, T1, T2, and V1. (B) RNase T2 and DMS probing of motif A mutant. (C) RNase T2 and DMS probing of motif B mutant. Substituted residues are highlighted in red. For simplicity, only main changes relative to the wild type are depicted in the structure of mutants in motif A and B.