Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick.
Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick.
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DOI：
10.1021/acs.jpcb.2c08618
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发表时间：
2023-05
期刊：
影响因子：
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通讯作者：
Ye-Peng Qiao;Chun-Lai Ren;Y. Ma
中科院分区：
文献类型：
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作者：
Ye-Peng Qiao;Chun-Lai Ren;Y. Ma
人们普遍认为DNA缺口是释放超螺旋DNA压力的有效方式，它是由单个链绕DNA螺旋轴旋转的扭曲运动引起的。在此，我们使用基于oxDNA模型的MD模拟来研究336bp超螺旋微环DNA在DNA缺口下的弛豫。我们的模拟表明，应力释放以连接数的突然减少为特征，可能由两种依赖于缺口位置的DNA运动引起。除了扭转运动外，还有一种扭曲运动，即双链集体旋转并去除一个微粒素，这种运动可能发生在DNA与环区缺口位置松弛的过程中。此外，扭动运动更容易发生在硬度相对较高的DNA中，如C-G对。我们的模拟结果揭示了DNA刻痕动态过程中结构转变、应力释放和DNA运动之间的关系，表明刻痕位置对超卷曲DNA松弛的影响。
It is generally believed that DNA nick is an effective way to release stress in supercoiled DNA, resulting from the twisting motion that individual strands rotate around the axis of the DNA helix. Here, we use MD simulations based on the oxDNA model to investigate the relaxation of 336 bp supercoiled minicircular DNA under DNA nick. Our simulations show that stress release, characterized by the abrupt decrease in linking number, may be induced by two types of DNA motion depending on the nick position. Except for the twisting motion, there is a writhing motion, that is, double strands collectively rotating with one plectoneme removal, which may occur in the process of DNA relaxation with the nick position in the loop region. Moreover, the writhing motion is more likely to occur in the DNA with relatively high hardness, such as C-G pairs. Our simulation results uncover the relationship between structural transformation, stress release, and DNA motion during the dynamic process under DNA nick, indicating the influence of nick position on the relaxation of the supercoiled DNA.