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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.
Author: | Sina Gottstein-Schmidtke, Elke Duchardt-FernerORCiD, Florian Groher, Julia WeigandORCiDGND, Daniel GottsteinGND, Beatrix SüßGND, Jens WöhnertORCiDGND |
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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): | Creative Commons - Namensnennung-Nicht kommerziell 4.0 |