Theoretical study of overstretching DNA-RNA hybrid duplex
Theoretical study of overstretching DNA-RNA hybrid duplex
复制标题
过度拉伸DNA-RNA杂交双链体的理论研究
DOI：
10.1088/1674-1056/28/6/068701
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发表时间：
2019
影响因子：
1.7
通讯作者：
Ma Jie
中科院分区：
文献类型：
--
作者：
Yang Dong Ni;Zhong Zhen Sheng;Liu Wen Zhao;Rujiralai Thitima;Ma Jie
DNA-RNA杂合体（DRH）在许多生物过程中起着重要作用。在这里，我们使用热力学理论分析的自由能和剥离的过度拉伸跃迁的DRH分子的性质，并与双螺旋DNA的结果进行比较。我们报告说，DRH的RNA链是更容易得到unpeeled比DNA链，而在unpeeling的双螺旋DNA的困难在于之间。我们还研究了序列效应，如GC含量和嘌呤含量，对DRH的剥离性能。为了研究温度效应，计算并比较了DRH和DNA的力-温度相图。最后，利用动力学模型，计算了不同拉伸速率和温度下DRH拉伸和弛豫过程中的力-伸长曲线。结果表明，拉伸速率和温度对DRH的拉伸和松弛动力学有重要影响。把所有这些结果放在一起，我们的工作提供了一个全面的观点在DRH过度拉伸的热力学和动力学。（文件）
DNA–RNA hybrid (DRH) plays important roles in many biological processes. Here, we use a thermodynamic theory to analyze the free energy and unpeeling properties of the overstretching transition for the DRH molecule and compare the results with double-helix DNA. We report that the RNA strand of DRH is easier to get unpeeled than the DNA strand while the difficulty in unpeeling the double helix DNA lies in between. We also investigate the sequence effect, such as GC content and purine content, on the properties of unpeeling the DRH. Further, to study the temperature effect, the force-temperature phase diagram of DRH and DNA are calculated and compared. Finally, using a kinetic model, we calculate the force–extension curves in the DRH stretching and relaxation process under different pulling rates and temperatures. Our results show that both pulling rate and temperature have important influences on the stretching and relaxation kinetics of unpeeling the DRH. Putting all these results together, our work provides a comprehensive view of both the thermodynamics and kinetics in DRH overstretching.(paper)