论文标题
DNA plectonemes的平衡波动
Equilibrium Fluctuations of DNA Plectonemes
论文作者
论文摘要
plectonemes是旋转的螺旋环域，当DNA分子被超螺旋时，即过度或下孔时形成。它们在细胞DNA中无处不在，其物理特性引起了实验和建模方面的重大兴趣。在这项工作中，我们研究了受外部拉伸力的超螺旋线性DNA分子的端点距离z的波动。我们的分析基于一个两相模型，该模型描述了由拉伸和斑块阶段组成的超涂的DNA。发现几种不同的机制导致延伸波动，其特征是扩展方差。我们发现对方差的主要贡献是源自相位交换的波动，plectonemes的瞬时收缩和膨胀，伴随着两个相之间的分子长度的交换。我们对可扭曲的虫状链进行蒙特卡洛模拟，并分析各种数量的波动，发现这些波动与两相模型的预测一致。此外，我们表明，只要一个阶段模型超越了二次近似值，就可以很好地捕获高力的扩展及其在高力下的差异。
Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e. over- or under-wounded. They are ubiquitous in cellular DNA and their physical properties have attracted significant interest both from the experimental and modeling side. In this work, we investigate fluctuations of the end-point distance z of supercoiled linear DNA molecules subject to external stretching forces. Our analysis is based on a two-phase model, which describes the supercoiled DNA as composed of a stretched and of a plectonemic phase. Several different mechanisms are found to contribute to extension fluctuations, characterized by the extension variance. We find the dominant contribution to the variance to originate from phase-exchange fluctuations, the transient shrinking and expansion of plectonemes, which is accompanied by an exchange of molecular length between the two phases. We perform Monte Carlo simulations of the Twistable Wormlike Chain and analyze the fluctuation of various quantities, which are found to agree with the two-phase model predictions. Furthermore, we show that the extension and its variance at high forces are very well captured by the two-phase model, provided that one goes beyond quadratic approximations.
