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Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules
Annual Review of Biophysics ( IF 10.4 ) Pub Date : 2017-05-22 00:00:00 , DOI: 10.1146/annurev-biophys-070816-033920
Li-Zhen Sun 1 , Dong Zhang 1 , Shi-Jie Chen 1
Affiliation  

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.

中文翻译:



RNA 结构及其与金属离子和小分子相互作用的理论和建模



除了RNA结构测定、探测和生物物理研究不断快速进展外,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着进展。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 RNA 功能的机械理解和 RNA 纳米技术的定量设计变得越来越重要。我们专注于基于物理、基于知识和实验数据导向的 RNA 结构建模的新方法,并探索预测金属离子和配体结合位点以及金属离子依赖性 RNA 稳定性的新理论。这些新方法与 RNA 折叠中细胞环境影响的理论(例如分子拥挤和共转录动力学效应)相结合,可能最终会产生一个包罗万象的 RNA 折叠模型。

更新日期:2017-05-22
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