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Probing the Elasticity of DNA on Short Length Scales by Modeling Supercoiling under Tension

机译:通过在张力下建模超螺旋来探测短尺度上的DNA弹性

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摘要

The wormlike-chain (WLC) model is widely used to describe the energetics of DNA bending. Motivated by recent experiments, alternative, so-called subelastic chain models were proposed that predict a lower elastic energy of highly bent DNA conformations. Until now, no unambiguous verification of these models has been obtained because probing the elasticity of DNA on short length scales remains challenging. Here we investigate the limits of the WLC model using coarse-grained Monte Carlo simulations to model the supercoiling of linear DNA molecules under tension. At a critical supercoiling density, the DNA extension decreases abruptly due to the sudden formation of a plectonemic structure. This buckling transition is caused by the large energy required to form the tightly bent end-loop of the plectoneme and should therefore provide a sensitive benchmark for model evaluation. Although simulations based on the WLC energetics could quantitatively reproduce the buckling measured in magnetic tweezers experiments, the buckling almost disappears for the tested linear subelastic chain model. Thus, our data support the validity of a harmonic bending potential even for small bending radii down to 3.5 nm.
机译:蠕虫状链(WLC)模型被广泛用于描述DNA弯曲的能量学。根据最近的实验,提出了一种替代的所谓亚弹性链模型,该模型可预测高度弯曲的DNA构象的较低弹性能。迄今为止,尚未获得对这些模型的明确验证,因为在短长度范围内探测DNA的弹性仍然具有挑战性。在这里,我们使用粗糙粒度的蒙特卡洛模拟法研究WLC模型的极限,以模拟线性DNA分子在张力下的超螺旋。在临界的超螺旋密度下,由于plectonemic结构的突然形成,DNA的延伸突然减少。这种屈曲过渡是由形成拨弦器的紧密弯曲的端环所需的大量能量引起的,因此应为模型评估提供敏感的基准。尽管基于WLC高能学的模拟可以定量再现磁镊实验中测得的屈曲,但对于测试的线性亚弹性链模型,屈曲几乎消失了。因此,即使弯曲半径小至3.5 nm,我们的数据也支持谐波弯曲电位的有效性。

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