A MAJOR FAMILY OF MOTIFS INVOLVING G-CENTER-DOT-A MISMATCHES IN RIBOSOMAL-RNA

G . A oppositions and their flanking nucleotides in the internal loops of 16 S and 23 S rRNA were analyzed from a comparative structure pers pective, resulting in an unexpectedly high incidence of the sequence m otifs [GRAPHICS] and [GRAPHICS] The first two motifs can form similar three-dimensional structures containing sheared G . A or A . A pair co nformations. Comparative sequence analysis revealed numerous sites in ribosomal RNAs with distinct combinations of nucleotides capable of fo rming this specific structure. In some cases, the sequence variations provide strong evidence for the sheared tandem structure occurring. In terestingly, the sequence changes would maintain a similar exposure of two adenines in the minor groove, suggesting the possibility that the y are serving as a recognition or anchoring unit. These tandem conform ations are related to that of the [GRAPHICS] tandem observed in 5 S an d 28 S rRNA.