School of Life Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, 100084, Beijing, China.
Nat Commun. 2022 Mar 21;13(1):1523. doi: 10.1038/s41467-022-29194-8.
RNA excited states represent a class of high-energy-level and thus low-populated conformational states of RNAs that are sequestered within the free energy landscape until being activated by cellular cues. In recent years, there has been growing interest in structural and functional studies of these transient states, but the rational design of excited states remains unexplored. Here we developed a method to design small hairpin RNAs with predefined excited states that exchange with ground states through base pair reshuffling, and verified these transient states by combining NMR relaxation dispersion technique and imino chemical shift prediction. Using van't Hoff analysis and accelerated molecular dynamics simulations, a mechanism of multi-step sequential transition has been revealed. The efforts made in this study will expand the scope of RNA rational design, and also contribute towards improved predictions of RNA secondary structure.
RNA 激发态代表了一类高能级且因此低占据构象状态的 RNA，这些状态被隔离在自由能景观中，直到被细胞信号激活。近年来，人们对这些瞬态状态的结构和功能研究越来越感兴趣，但激发态的合理设计仍未得到探索。在这里，我们开发了一种设计具有预定义激发态的小发夹 RNA 的方法，这些激发态通过碱基对重排与基态交换，并通过结合 NMR 弛豫分散技术和亚氨基化学位移预测来验证这些瞬态状态。通过范特霍夫分析和加速分子动力学模拟，揭示了多步顺序跃迁的机制。本研究中的努力将扩展 RNA 合理设计的范围，并有助于改进 RNA 二级结构的预测。
