Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211; email:
Annu Rev Biophys. 2017 May 22;46:227-246. doi: 10.1146/annurev-biophys-070816-033920. Epub 2017 Mar 15.
In addition to continuous rapid progress in RNA structure determination, probing, and biophysical studies, the past decade has seen remarkable advances in the development of a new generation of RNA folding theories and models. In this article, we review RNA structure prediction models and models for ion-RNA and ligand-RNA interactions. These new models are becoming increasingly important for a mechanistic understanding of RNA function and quantitative design of RNA nanotechnology. We focus on new methods for physics-based, knowledge-based, and experimental data-directed modeling for RNA structures and explore the new theories for the predictions of metal ion and ligand binding sites and metal ion-dependent RNA stabilities. The integration of these new methods with theories about the cellular environment effects in RNA folding, such as molecular crowding and cotranscriptional kinetic effects, may ultimately lead to an all-encompassing RNA folding model.
除了 RNA 结构测定、探测和生物物理研究的持续快速进展外，过去十年在新一代 RNA 折叠理论和模型的发展方面也取得了显著进展。在本文中，我们回顾了 RNA 结构预测模型以及离子-RNA 和配体-RNA 相互作用的模型。这些新模型对于深入了解 RNA 的功能和定量设计 RNA 纳米技术变得越来越重要。我们专注于基于物理、基于知识和基于实验数据的新方法来进行 RNA 结构建模，并探索用于预测金属离子和配体结合位点以及金属离子依赖的 RNA 稳定性的新理论。将这些新方法与关于 RNA 折叠中细胞环境效应的理论（如分子拥挤和共转录动力学效应）相结合，最终可能会产生一个全面的 RNA 折叠模型。
