Anionic G•U pairs in bacterial ribosomal rRNAs
- 1Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, F-67084 Strasbourg, France
- 2Department of Chemistry, University of California, Berkeley, California 94720, USA
- 3California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA
- 4Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, Ohio 43403, USA
- 5Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- 6Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- 7Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Corresponding author: e.westhof{at}ibmc-cnrs.unistra.fr
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
- Received January 8, 2023.
- Accepted April 5, 2023.
This article, published in RNA, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
