Building a stable RNA U-turn with a protonated cytidine

  • The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5'-UNR-3' (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3' phosphate group of the R residue as well as a hydrogen bond between the 2'-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3' from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone.

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Author:Sina Gottstein-Schmidtke, Elke Duchardt-FernerORCiD, Florian Groher, Julia WeigandORCiDGND, Daniel GottsteinGND, Beatrix SüßGND, Jens WöhnertORCiDGND
URN:urn:nbn:de:hebis:30:3-443526
DOI:https://doi.org/10.1261/rna.043083.113
ISBN:1355-8382
ISSN:1469-9001
Parent Title (German):RNA
Publisher:Laboratory Press
Place of publication:Cold Spring Harbor, NY
Document Type:Article
Language:English
Year of Completion:2017
Date of first Publication:2014/06/20
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2017/11/06
Tag:NMR; RNA structure; U-turn; hydrogen bond; protonated cytidine
Volume:20
Page Number:11
First Page:1163
Last Page:1172
Note:
This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
HeBIS-PPN:425339882
Institutes:Biowissenschaften / Biowissenschaften
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Licence (English):License LogoCreative Commons - Namensnennung-Nicht kommerziell 4.0