AA.AG@Helix.Ends: A : A and A : G base-pairs at the ends of 16 S and 23 S rRNA helices

This study reveals that AA and AG oppositions occur frequently at the ends of helices in RNA crystal and NMR structures in the PDB database and in the 16 S and 23 S rRNA comparative structure models, with the G usually 3 ' to the helix for the AG oppositions. In addition, these oppositions are frequ ently base-paired and usually in the sheared conformation, although other c onformations are present in NMR and crystal structures. These A:A and A:G b ase-pairs are present in a variety of structural environments, including GN RA tetraloops, E and E-like loops, interfaced between two helices that are coaxially stacked, tandem G:A base-pairs, U-turns, and adenosine platforms. Finally, given structural studies that reveal conformational rearrangement s occurring in regions of the RNA with AA and AG oppositions at the ends of helices, we suggest that these conformationally unique helix extensions mi ght be associated with functionally important structural rearrangements. (C ) 2001 Academic Press.