TY  - JOUR
A1  - Gottstein-Schmidtke, Sina
A1  - Duchardt-Ferner, Elke
A1  - Groher, Florian
A1  - Weigand, Julia
A1  - Gottstein, Daniel
A1  - Süß, Beatrix
A1  - Wöhnert, Jens
T1  - Building a stable RNA U-turn with a protonated cytidine
T2  - RNA
N2  - 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.
KW  - RNA structure
KW  - U-turn
KW  - protonated cytidine
KW  - NMR
KW  - hydrogen bond
Y1  - 2014
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/44352
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-443526
SN  - 1355-8382
SN  - 1469-9001
N1  - 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/.
VL  - 20
SP  - 1163
EP  - 1172
PB  - Laboratory Press
CY  - Cold Spring Harbor, NY
ER  -