Anionic G•U pairs in bacterial ribosomal rRNAs

Abstract

Wobble GU pairs (or G•U) occur frequently within double-stranded RNA helices interspersed between standard G=C and A-U Watson–Crick pairs. Another type of G•U pair interacting via their Watson–Crick edges has been observed in the A site of ribosome structures between a modified U34 in the tRNA anticodon triplet and G + 3 in the mRNA. In such pairs, the electronic structure of the U is changed with a negative charge on N3(U), resulting in two H-bonds between N1(G)…O4(U) and N2(G)…N3(U). Here, we report that such pairs occur in other highly conserved positions in ribosomal RNAs of bacteria in the absence of U modification. An anioniccisWatson–Crick G•G pair is also observed and well conserved in the small subunit. These pairs are observed in tightly folded regions.