Understanding the Structural Elasticity of RNA and DNA: All‐Atom Molecular Dynamics
Understanding the Structural Elasticity of RNA and DNA: All‐Atom Molecular Dynamics
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了解 RNA 和 DNA 的结构弹性：全原子分子动力学
DOI：
10.1002/adts.202200534
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发表时间：
2022-09
影响因子：
3.3
通讯作者：
Xianghong Wang
中科院分区：
文献类型：
--
作者：
Yingtong Zhang;Miao Yan;Tingting Huang;Xianghong Wang
核酸在一些生物过程和纳米技术中起着重要作用。了解它们的结构弹性对生物功能非常重要。本文采用全原子分子动力学方法研究了RNA和DNA双链体结构弹性的差异。使用两种模型双链（ds）B-DNA和A-RNA短序列。针对两种典型的序列，对弯曲持续长度、拉伸模量和扭转模量进行了详细的分析比较。这些结果表明，dsDNA的弯曲持续长度值小于dsRNA，但前者的拉伸模量约为后者的2.6倍，前者的扭转模量小于后者。此外，微观结构参数分析表明，单个碱基对的倾斜角、碱基对中两个碱基之间的二面角以及相邻碱基对之间的滑动影响这两种类型核酸的结构弹性。结果还表明，dsDNA具有正的拉伸-扭转耦合参数，而dsRNA具有负的拉伸-扭转耦合参数。这些结果为研究RNA和DNA的结构弹性提供了全面的比较和理解，为掌握核酸的弹性性质提供了新的视角。
Nucleic acids play essential roles in some biological processes and nanotechnology. Understanding their structural elasticity is very important for biological functions. Differences in structural elasticity of RNA and DNA duplexes are investigated by all-atom molecular dynamics in this work. Two models double-strand (ds) B-DNA and A-RNA short sequences are used. For two typical sequences, bending persistence length, stretch, and twist modulus are analyzed and compared in detail. These results demonstrate that dsDNA has a smaller bending persistence length value than dsRNA, however, the former has about 2.6 times stretch modulus than the latter one and the twist modulus in the former is smaller than the latter. Furthermore, the microstructural parameter analysis indicates that the inclination angle of a single base pair and the dihedral angle between two bases in a base pair, as well as the slide between adjacent base pairs, influences the structural elasticities of these two types of nucleic acids. Results also show that the dsDNA has a positive stretch-twist coupling parameter while the dsRNA has a negative stretch-twist coupling parameter. Results offer research comprehensive comparing and understanding about structural elasticity of RNA and DNA and provide novel perspectives for grasping nucleic acids' elastic properties.
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影响因子：
14.9
作者：
Lavery R;Moakher M;Maddocks JH;Petkeviciute D;Zakrzewska K
通讯作者：
Zakrzewska K
影响因子：
5
作者：
Schipperges A;Hu Y;Moench S;Weigel S;Reith J;Ordoñez-Rueda D;Rabe KS;Niemeyer CM
通讯作者：
Niemeyer CM
DOI：
10.1016/j.ijbiomac.2017.01.068
发表时间：
2017-04
影响因子：
8.2
作者：
K. Ponnuraj;Konda Mani Saravanan
通讯作者：
K. Ponnuraj;Konda Mani Saravanan
DOI：
10.1021/acs.jpcb.8b07687
发表时间：
2018-09
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
C. He;L. Hamlow;Zachary J. Devereaux;Yanlong Zhu;Y.-w. Nei;Lin Fan;Christopher P. McNary;Philippe Maître;Vincent Steinmetz;B. Schindler;Isabelle Compagnon;P. Armentrout;M. Rodgers
通讯作者：
C. He;L. Hamlow;Zachary J. Devereaux;Yanlong Zhu;Y.-w. Nei;Lin Fan;Christopher P. McNary;Philippe Maître;Vincent Steinmetz;B. Schindler;Isabelle Compagnon;P. Armentrout;M. Rodgers
预测单价和二价离子溶液中 RNA 假结的 3D 结构和稳定性
影响因子：
4.3
作者：
Shi YZ;Jin L;Feng CJ;Tan YL;Tan ZJ
通讯作者：
Tan ZJ