Building a stable RNA U-turn with a protonated cytidine
Building a stable RNA U-turn with a protonated cytidine
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DOI：
10.1261/rna.043083.113
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发表时间：
2014-08-01
期刊：
影响因子：
4.5
通讯作者：
Woehnert, Jens
中科院分区：
文献类型：
--
作者：
Gottstein-Schmidtke, Sina R.;Duchardt-Ferner, Elke;Woehnert, Jens
U 型转弯是一种经典的三维 RNA 折叠基序，首先在 tRNA 的反密码子和 T 环中发现。它也经常作为许多不同序列和结构背景中其他功能性 RNA 结构的构建模块出现。 U 型转弯会引起 RNA 主链方向的急剧变化，并且通常符合 3-nt 共有序列 5'-UNR-3'（N = 任何核苷酸，R = 嘌呤）。规范的 U 形转弯基序通过 U 残基的 N3 亚氨基和 R 残基的 3' 磷酸基团之间的氢键以及尿苷的 2'-羟基和 R 残基的 N7 氮之间的氢键来稳定。在这里，我们证明质子化胞苷可以在功能上和结构上取代新霉素核糖开关顶端环中规范 U 型转弯基序的第一个位置处的尿苷。使用NMR光谱，我们直接表明质子化胞苷的N3亚氨基与U形转弯的第三个核苷酸的主链磷酸3'形成氢键，类似于规范基序中尿苷的亚氨基。此外，我们将突变型 U 型转弯基序中氢键的稳定性与野生型进行了比较，并描述了 C+-磷酸盐相互作用的 NMR 特征。我们的结果对 RNA 结构基序的预测具有重要意义，并提出了实验鉴定质子化 C-亚氨基和磷酸主链之间氢键的简单方法。
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.