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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...

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Autores principales: Gottstein-Schmidtke, Sina R., Duchardt-Ferner, Elke, Groher, Florian, Weigand, Julia E., Gottstein, Daniel, Suess, Beatrix, Wöhnert, Jens
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105743/
https://www.ncbi.nlm.nih.gov/pubmed/24951555
http://dx.doi.org/10.1261/rna.043083.113
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author Gottstein-Schmidtke, Sina R.
Duchardt-Ferner, Elke
Groher, Florian
Weigand, Julia E.
Gottstein, Daniel
Suess, Beatrix
Wöhnert, Jens
author_facet Gottstein-Schmidtke, Sina R.
Duchardt-Ferner, Elke
Groher, Florian
Weigand, Julia E.
Gottstein, Daniel
Suess, Beatrix
Wöhnert, Jens
author_sort Gottstein-Schmidtke, Sina R.
collection PubMed
description 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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spelling pubmed-41057432015-08-01 Building a stable RNA U-turn with a protonated cytidine Gottstein-Schmidtke, Sina R. Duchardt-Ferner, Elke Groher, Florian Weigand, Julia E. Gottstein, Daniel Suess, Beatrix Wöhnert, Jens RNA Report 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. Cold Spring Harbor Laboratory Press 2014-08 /pmc/articles/PMC4105743/ /pubmed/24951555 http://dx.doi.org/10.1261/rna.043083.113 Text en © 2014 Gottstein-Schmidtke et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ 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/.
spellingShingle Report
Gottstein-Schmidtke, Sina R.
Duchardt-Ferner, Elke
Groher, Florian
Weigand, Julia E.
Gottstein, Daniel
Suess, Beatrix
Wöhnert, Jens
Building a stable RNA U-turn with a protonated cytidine
title Building a stable RNA U-turn with a protonated cytidine
title_full Building a stable RNA U-turn with a protonated cytidine
title_fullStr Building a stable RNA U-turn with a protonated cytidine
title_full_unstemmed Building a stable RNA U-turn with a protonated cytidine
title_short Building a stable RNA U-turn with a protonated cytidine
title_sort building a stable rna u-turn with a protonated cytidine
topic Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105743/
https://www.ncbi.nlm.nih.gov/pubmed/24951555
http://dx.doi.org/10.1261/rna.043083.113
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