Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109, USA.
Nucleic Acids Res. 2012 Feb;40(3):1345-55. doi: 10.1093/nar/gkr833. Epub 2011 Oct 18.
Single-stranded RNAs (ssRNAs) are ubiquitous RNA elements that serve diverse functional roles. Much of our understanding of ssRNA conformational behavior is limited to structures in which ssRNA directly engages in tertiary interactions or is recognized by proteins. Little is known about the structural and dynamic behavior of free ssRNAs at atomic resolution. Here, we report the collaborative application of nuclear magnetic resonance (NMR) and replica exchange molecular dynamics (REMD) simulations to characterize the 12 nt ssRNA tail derived from the prequeuosine riboswitch. NMR carbon spin relaxation data and residual dipolar coupling measurements reveal a flexible yet stacked core adopting an A-form-like conformation, with the level of order decreasing toward the terminal ends. An A-to-C mutation within the polyadenine tract alters the observed dynamics consistent with the introduction of a dynamic kink. Pre-ordering of the tail may increase the efficacy of ligand binding above that achieved by a random-coil ssRNA. The REMD simulations recapitulate important trends in the NMR data, but suggest more internal motions than inferred from the NMR analysis. Our study unmasks a previously unappreciated level of complexity in ssRNA, which we believe will also serve as an excellent model system for testing and developing computational force fields.
单链 RNA（ssRNA）是普遍存在的 RNA 元件，具有多种功能作用。我们对 ssRNA 构象行为的理解很大程度上仅限于 ssRNA 直接参与三级相互作用或被蛋白质识别的结构。对于游离 ssRNA 的原子分辨率结构和动态行为知之甚少。在这里，我们报告了核磁共振（NMR）和复制交换分子动力学（REMD）模拟的协同应用，以表征来自预 Queuosine 核糖开关的 12 个核苷酸 ssRNA 尾巴。NMR 碳自旋弛豫数据和残余偶极耦合测量结果表明，该 ssRNA 尾巴具有灵活但堆叠的核心，采用 A 型样构象，有序性向末端降低。多聚腺苷酸链内的 A 到 C 突变改变了观察到的动力学，与引入动态拐点一致。尾巴的预排序可能会提高配体结合的效率，超过随机卷曲 ssRNA 所达到的效率。REMD 模拟再现了 NMR 数据中的重要趋势，但与 NMR 分析推断的相比，模拟表明存在更多的内部运动。我们的研究揭示了 ssRNA 中以前未被重视的复杂程度，我们相信它也将成为测试和开发计算力场的优秀模型系统。
