了解 RNA 和 DNA 的结构弹性：全原子分子动力学,Advanced Theory and Simulations

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了解 RNA 和 DNA 的结构弹性：全原子分子动力学
Advanced Theory and Simulations ( IF 2.9 ) Pub Date : 2022-09-08 , DOI: 10.1002/adts.202200534
Yingtong Zhang ₁ , Miao Yan ₁ , Tingting Huang ₂ , Xianghong Wang _{1,

2}

Affiliation

核酸在某些生物过程和纳米技术中起着至关重要的作用。了解它们的结构弹性对于生物功能非常重要。在这项工作中，通过全原子分子动力学研究了 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。对于两个典型序列，弯曲持久长度、拉伸和扭转模量进行了详细分析和比较。这些结果表明，dsDNA 具有比 dsRNA 更小的弯曲持久长度值，但是，前者的拉伸模量是后者的约 2.6 倍，前者的扭曲模量小于后者。此外，微观结构参数分析表明，单个碱基对的倾斜角和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，影响了这两类核酸的结构弹性。结果还表明，dsDNA 具有正拉伸扭曲耦合参数，而 dsRNA 具有负拉伸扭曲耦合参数。研究结果提供了对 RNA 和 DNA 结构弹性的综合比较和理解，并为掌握核酸的弹性特性提供了新的视角。结果还表明，dsDNA 具有正拉伸扭曲耦合参数，而 dsRNA 具有负拉伸扭曲耦合参数。研究结果提供了对 RNA 和 DNA 结构弹性的综合比较和理解，并为掌握核酸的弹性特性提供了新的视角。结果还表明，dsDNA 具有正拉伸扭曲耦合参数，而 dsRNA 具有负拉伸扭曲耦合参数。研究结果提供了对 RNA 和 DNA 结构弹性的综合比较和理解，并为掌握核酸的弹性特性提供了新的视角。

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Understanding the Structural Elasticity of RNA and DNA: All-Atom Molecular Dynamics

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.

更新日期：2022-09-08

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