Nakano Shu-Ichi
Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan.
Subcell Biochem. 2025;109:155-185. doi: 10.1007/978-3-032-03370-3_7.
Dynamic and thermodynamic properties of RNA molecules vary across different cellular locations through multiple environmental factors, such as excluded volume interactions of cellular substances, alteration of the physical properties of the surrounding medium, and binding interactions with cellular substances. These environmental factors modulate the energy landscape of RNA transitions, thereby consideration of the effects of the intracellular environment on molecular interactions contributing to RNA folding and RNA-protein complexation is important for understanding RNA structures and their interactions in living cells. This chapter describes the dynamics and interactions of several RNA structures, including functional RNAs such as aptamers and ribozymes, in the environment of molecular crowding, revealed by in-cell, in silico, and in vitro studies. Specifically, in vitro model studies that have used cell-mimicking solutions comprising cellular substances or artificial molecular crowding agents have enhanced our understanding of RNA interactions and their molecular functions under molecular crowding conditions and increased our ability to predict RNA structures in cells. This chapter also provides an overview of the comparison between RNA and DNA interactions because the effects of the environmental factors on DNA are similar to those on RNA.
RNA分子的动力学和热力学性质会通过多种环境因素在不同的细胞位置发生变化，这些因素包括细胞物质的排阻体积相互作用、周围介质物理性质的改变以及与细胞物质的结合相互作用。这些环境因素调节RNA转变的能量景观，因此考虑细胞内环境对促成RNA折叠和RNA-蛋白质复合的分子相互作用的影响，对于理解活细胞中的RNA结构及其相互作用很重要。本章描述了几种RNA结构在分子拥挤环境中的动力学和相互作用，包括适体和核酶等功能性RNA，这些是通过细胞内、计算机模拟和体外研究揭示的。具体而言，使用包含细胞物质或人工分子拥挤剂的细胞模拟溶液进行的体外模型研究，增强了我们对分子拥挤条件下RNA相互作用及其分子功能的理解，并提高了我们预测细胞中RNA结构的能力。本章还概述了RNA和DNA相互作用的比较，因为环境因素对DNA的影响与对RNA的影响相似。
