A major family of motifs involving G.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 perspective, resulting in an unexpectedly high incidence of the sequence motifs [formula: see text], [formula: see text] and [formula: see text]. The first two motifs can form similar three-dimensional structures containing sheared G.A or A.A pair conformations. Comparative sequence analysis revealed numerous sites in ribosomal RNAs with distinct combinations of nucleotides capable of forming this specific structure. In some cases, the sequence variations provide strong evidence for the sheared tandem structure occurring. Interestingly, the sequence changes would maintain a similar exposure of two adenines in the minor groove, suggesting the possibility that they are serving as a recognition or anchoring unit. These tandem conformations are related to that of the [formula: see text] tandem observed in 5 S and 28 S rRNA.