STRUCTURE OF THE POLYADENYLATION REGULATORY ELEMENT OF THE HUMAN U1A PRE-MESSENGER-RNA 3'-UNTRANSLATED REGION AND INTERACTION WITH THE U1A PROTEIN

The N-terminal RNP domain of U1A binds two different RNA substrates wi th high affinity and specificity: stem-loop II of the U1 snRNA and a c omplex secondary structure in the 3'-untranslated region (3'-UTR) of t he U1A pre-mRNA. Both RNAs contain a single-stranded sequence which is the main site of interaction with the protein, but in completely diff erent structural contexts. Here we describe the solution structure of the free 3'-UTR RNA molecule and the NMR characterization of its compl ex with the U1A protein N-terminal domain. The structure of the free R NA indicates that the stems are nearly canonical A-form helices and th at the single-stranded region contains local stacking interactions in the context of a generally flexible structure. Upon protein binding, t he internal loop region folds into an ordered structure containing sig nificant changes in the local stacking interactions. These results dem onstrate the role of RNA structure and folding in specific RNA-protein recognition.