Building a stable RNA U-turn with a protonated cytidine

作者：Gottstein Schmidtke Sina R; Duchardt Ferner Elke^*; Groher Florian; Weigand Julia E; Gottstein Daniel; Suess Beatrix; Woehnert Jens

来源：RNA-A Publication of the RNA Society, 2014, 20(8): 1163-1172.

DOI：10.1261/rna.043083.113

• RNA structure
• U-turn
• protonated cytidine
• NMR
• hydrogen bond

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%26apos;-UNR-3%26apos; (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%26apos; phosphate group of the R residue as well as a hydrogen bond between the 2%26apos;-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%26apos; 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.

• 出版日期2014-8