Bao Lei, Zhang Xi, Shi Ya-Zhou, Wu Yuan-Yan, Tan Zhi-Jie
Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China; Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China.
Biophys J. 2017 Mar 28;112(6):1094-1104. doi: 10.1016/j.bpj.2017.02.022.
The flexibility of double-stranded (ds) RNA and dsDNA is crucial for their biological functions. Recent experiments have shown that the flexibility of dsRNA and dsDNA can be distinctively different in the aspects of stretching and twist-stretch coupling. Although various studies have been performed to understand the flexibility of dsRNA and dsDNA, there is still a lack of deep understanding of the distinctive differences in the flexibility of dsRNA and dsDNA helices as pertains to their stretching and twist-stretch coupling. In this work, we have explored the relative flexibility in stretching and twist-stretch coupling between dsRNA and dsDNA by all-atom molecular dynamics simulations. The calculated stretch modulus and twist-stretch coupling are in good accordance with the existing experiments. Our analyses show that the differences in stretching and twist-stretch coupling between dsRNA and dsDNA helices are mainly attributed to their different (A- and B-form) helical structures. Stronger basepair inclination and slide in dsRNA is responsible for the apparently weaker stretching rigidity versus that of dsDNA, and the opposite twist-stretch coupling for dsRNA and dsDNA is also attributed to the stronger basepair inclination in dsRNA than in dsDNA. Our calculated macroscopic elastic parameters and microscopic analyses are tested and validated by different force fields for both dsRNA and dsDNA.
双链（ds）RNA和dsDNA的柔韧性对其生物学功能至关重要。最近的实验表明，dsRNA和dsDNA的柔韧性在拉伸和扭曲-拉伸耦合方面可能存在显著差异。尽管已经进行了各种研究来了解dsRNA和dsDNA的柔韧性，但对于dsRNA和dsDNA螺旋在拉伸和扭曲-拉伸耦合方面柔韧性的显著差异仍缺乏深入理解。在这项工作中，我们通过全原子分子动力学模拟探索了dsRNA和dsDNA在拉伸和扭曲-拉伸耦合方面的相对柔韧性。计算得到的拉伸模量和扭曲-拉伸耦合与现有实验结果吻合良好。我们的分析表明，dsRNA和dsDNA螺旋在拉伸和扭曲-拉伸耦合方面的差异主要归因于它们不同的（A-型和B-型）螺旋结构。dsRNA中更强的碱基对倾斜和滑动导致其拉伸刚性明显弱于dsDNA，dsRNA和dsDNA相反的扭曲-拉伸耦合也归因于dsRNA中比dsDNA更强的碱基对倾斜。我们计算得到的宏观弹性参数和微观分析通过针对dsRNA和dsDNA的不同力场进行了测试和验证。
