Emory University, Department of Physics, Atlanta, Georgia.
Emory University, Department of Physics, Atlanta, Georgia.
Biophys J. 2021 Aug 17;120(16):3242-3252. doi: 10.1016/j.bpj.2021.05.002. Epub 2021 May 8.
Our goal is to review the main theoretical models used to calculate free energy changes associated with common, torsion-induced conformational changes in DNA and provide the resulting equations hoping to facilitate quantitative analysis of both in vitro and in vivo studies. This review begins with a summary of work regarding the energy change of the negative supercoiling-induced B- to L-DNA transition, followed by a discussion of the energetics associated with the transition to Z-form DNA. Finally, it describes the energy changes associated with the formation of DNA curls and plectonemes, which can regulate DNA-protein interactions and promote cross talk between distant DNA elements, respectively. The salient formulas and parameters for each scenario are summarized in table format to facilitate comparison and provide a concise, user-friendly resource.
我们的目标是回顾用于计算与 DNA 中常见的扭转诱导构象变化相关的自由能变化的主要理论模型，并提供所得方程，希望能促进对体外和体内研究的定量分析。本综述首先总结了关于负超螺旋诱导的 B 到 L-DNA 转变的能量变化的工作，然后讨论了与 Z 型 DNA 转变相关的能量。最后，它描述了与 DNA 卷曲和扭结形成相关的能量变化，这些变化可以分别调节 DNA-蛋白质相互作用并促进远距离 DNA 元件之间的串扰。每个场景的突出公式和参数都以表格形式总结，以方便比较，并提供简洁易用的资源。
