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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 (2014)
Building a stable RNA U-turn with a protonated cytidine.
In: RNA (New York, N.Y.), 20 (8)
Artikel, Bibliographie

Kurzbeschreibung (Abstract)

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.

Typ des Eintrags: Artikel
Erschienen: 2014
Autor(en): Gottstein-Schmidtke, Sina R. ; Duchardt-Ferner, Elke ; Groher, Florian ; Weigand, Julia E. ; Gottstein, Daniel ; Suess, Beatrix ; Wöhnert, Jens
Art des Eintrags: Bibliographie
Titel: Building a stable RNA U-turn with a protonated cytidine.
Sprache: Englisch
Publikationsjahr: 2014
Titel der Zeitschrift, Zeitung oder Schriftenreihe: RNA (New York, N.Y.)
Jahrgang/Volume einer Zeitschrift: 20
(Heft-)Nummer: 8
Kurzbeschreibung (Abstract):

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.

Fachbereich(e)/-gebiet(e): 10 Fachbereich Biologie
10 Fachbereich Biologie > Synthetic Genetic Circuits (2020 umbenannt in "Synthetic RNA biology")
10 Fachbereich Biologie > RNA Biochemie
Hinterlegungsdatum: 24 Jun 2014 11:34
Letzte Änderung: 06 Nov 2020 07:12
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