Anionic G•U pairs in bacterial ribosomal rRNAs

RNA. 2023 Jul;29(7):1069-1076. doi: 10.1261/rna.079583.123. Epub 2023 Apr 17.

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 anionic cis Watson-Crick G•G pair is also observed and well conserved in the small subunit. These pairs are observed in tightly folded regions.

Keywords: G•U pair; anionic; anticodon; codon; mRNA; rRNA; tRNA.

MeSH terms

  • Anticodon
  • Bacteria / genetics
  • Codon
  • Nucleic Acid Conformation
  • RNA, Ribosomal* / analysis
  • RNA, Ribosomal* / genetics
  • Ribosomes* / chemistry
  • Ribosomes* / genetics

Substances

  • Codon
  • RNA, Ribosomal
  • Anticodon