Structure of the polyadenylation regulatory element of the human U1A pre-mRNA 3'-untranslated region and interaction with the U1A protein.

The N-terminal RNP domain of U1A binds two different RNA substrates with high affinity and specificity: stem-loop II of the U1 snRNA and a complex secondary structure in the 3'-untranslated region (3'-UTR) of the U1A pre-mRNA. Both RNAs contain a single-stranded sequence which is the main site of interaction with the protein, but in completely different structural contexts. Here we describe the solution structure of the free 3'-UTR RNA molecule and the NMR characterization of its complex with the U1A protein N-terminal domain. The structure of the free RNA indicates that the stems are nearly canonical A-form helices and that the single-stranded region contains local stacking interactions in the context of a generally flexible structure. Upon protein binding, the internal loop region folds into an ordered structure containing significant changes in the local stacking interactions. These results demonstrate the role of RNA structure and folding in specific RNA-protein recognition.