Crystallography, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.
Institute for Chemistry and Biochemistry, Freie University Berlin, 14195 Berlin, Germany.
RNA. 2018 Feb;24(2):209-218. doi: 10.1261/rna.064048.117. Epub 2017 Nov 9.
Wobble base pairs are critical in various physiological functions and have been linked to local structural perturbations in double-helical structures of nucleic acids. We report a 1.38-Å resolution crystal structure of an antiparallel octadecamer RNA double helix in overall A conformation, which includes a unique, central stretch of six consecutive wobble base pairs (W helix) with two G·U and four rare C·A wobble pairs. Four adenines within the W helix are N1-protonated and wobble-base-paired with the opposing cytosine through two regular hydrogen bonds. Combined with the two G·U pairs, the C·A base pairs facilitate formation of a half turn of W-helical RNA flanked by six regular Watson-Crick base pairs in standard A conformation on either side. RNA melting experiments monitored by differential scanning calorimetry, UV and circular dichroism spectroscopy demonstrate that the RNA octadecamer undergoes a pH-induced structural transition which is consistent with the presence of a duplex with C·A base pairs at acidic pH. Our crystal structure provides a first glimpse of an RNA double helix based entirely on wobble base pairs with possible applications in RNA or DNA nanotechnology and pH biosensors.
摆动碱基对在各种生理功能中至关重要，并且与核酸双螺旋结构中的局部结构扰动有关。我们报告了一个 1.38Å分辨率的反平行十八聚体 RNA 双螺旋的晶体结构，该结构具有独特的中央连续六个摆动碱基对（W 螺旋），其中包含两个 G·U 和四个罕见的 C·A 摆动对。W 螺旋中的四个腺嘌呤通过两个常规氢键与对面的胞嘧啶 N1-质子化并进行摆动碱基配对。结合两个 G·U 对，C·A 碱基对有助于形成一个半圈 W 螺旋 RNA，其两侧分别为标准 A 构象的六个常规 Watson-Crick 碱基对。差示扫描量热法、紫外和圆二色光谱监测的 RNA 熔化实验表明，RNA 十八聚体经历了 pH 诱导的结构转变，这与酸性 pH 下存在 C·A 碱基对的双链一致。我们的晶体结构提供了第一个完全基于摆动碱基对的 RNA 双螺旋的 glimpse，这可能在 RNA 或 DNA 纳米技术和 pH 生物传感器中有应用。
