Alignment of PUF-11 repeats and RNA II-1. (A) A model illustrating how each PUF-11 repeat (R1–R8, shaded) could interact with nine bases (A9–U1, unshaded) in the core binding element of RNA II-1. Black lines indicate hydrogen bonds; stacking interactions and van der Waals forces are not shown. Triangles indicate conserved interactions among PUF proteins; asterisks and a gray box indicate mapped interactions between PUF-11 and RNA II-1 based on B and C. (B,C) Binding of Repeats 3 and 2 mutant proteins to RNA II-1. Binding scheme shown on left, with compensatory protein and RNA mutations unshaded. Binding of wild-type and mutant proteins to RNAs using the three-hybrid assay is shown on the right. The new interactions that map the base to the α-helix are indicated by arrows.
