G-CENTER-DOT-U BASE-PAIRING MOTIFS IN RIBOSOMAL-RNA

An increasing number of recognition mechanisms in RNA are found to inv olve G . U base pairs. In order to detect new functional sites of this type, we exhaustively analyzed the sequence alignments and secondary structures of eubacterial and chloroplast 16S and 23S rRNA, seeking po sitions with high levels of G . U pairs. Approximately 120 such sites were identified and classified according to their secondary structure and sequence environment, Overall biases in the distribution of G . U pairs are consistent with previously proposed structural rules: the si de of the wobble pair that is subject to a loss of stacking is prefere ntially exposed to a secondary structure loop, where stacking is not a s essential as in helical regions. However, multiple sites violate the se rules and display highly conserved G . U pairs in orientations that could cause severe stacking problems. In addition, three motifs displ aying a conserved G . U pair in a specific sequence/structure environm ent occur at an unusually high frequency. These motifs, of which two h ad not been reported before, involve sequences (3'GU5'5'UG3') and (3'G U5'5'UG3') as well as G . U pairs flanked by a bulge loop 3' of U, The possible structures and functions of these recurrent motifs are discu ssed.