DNA under torsional strain undergoes a buckling transition that is the fundamental step in plectoneme nucleation and supercoil dynamics, which are critical for the processing of genomic information. Despite its importance, quantitative models of the buckling transition, in particular to also explain the surprising two-orders-of-magnitude difference between the buckling times for RNA and DNA revealed by single-molecule tweezers experiments, are currently lacking. Additionally, little is known about the configurations of the DNA during the buckling transition because they are not directly observable experimentally. Here, we use a discrete worm-like chain model and Brownian dynamics to simulate the DNA/RNA buckling transition. Our simulations are in good agreement with experimentally determined parameters of the buckling transition. The simulations show that the buckling time strongly and exponentially depends on the bending stiffness, which accounts for more than half the measured difference between DNA and RNA. Analyzing the microscopic conformations of the chain revealed by our simulations, we find clear evidence for a solenoid-shaped transition state and a curl intermediate. The curl intermediate features a single loop and becomes increasingly populated at low forces. Taken together, the simulations suggest that the worm-like chain model can account semiquantitatively for the buckling dynamics of both DNA and RNA.

中文翻译：

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双链 DNA 和 RNA 中屈曲转变的动力学


DNA 在扭转应变下经历屈曲转变，这是皮体成核和超螺旋动力学的基本步骤，这对于基因组信息的处理至关重要。尽管屈曲转变的定量模型很重要，但目前还缺乏对单分子镊子实验揭示的 RNA 和 DNA 屈曲时间之间惊人的两个数量级差异的解释。此外，人们对屈曲转变过程中 DNA 的构型知之甚少，因为它们无法通过实验直接观察到。在这里，我们使用离散蠕虫链模型和布朗动力学来模拟 DNA/RNA 屈曲转变。我们的模拟与实验确定的屈曲转变参数非常一致。模拟表明，屈曲时间强烈且呈指数关系地取决于弯曲刚度，这占 DNA 和 RNA 之间测量差异的一半以上。通过分析模拟揭示的链的微观构象，我们找到了螺线管形过渡态和卷曲中间体的明确证据。卷曲中间部分具有单环，并且在低力下变得越来越多。综上所述，模拟表明蠕虫状链模型可以半定量地解释 DNA 和 RNA 的屈曲动力学。