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首页> 外文期刊>Acta biomaterialia >The dependence of DNA supercoiling on solution electrostatics
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The dependence of DNA supercoiling on solution electrostatics

机译：DNA超螺旋对溶液静电的依赖性

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We develop an elastic-isotropic rod model for twisted DNA in the plectonemic regime. We account for DNA elasticity, electrostatic interactions and entropic effects due to thermal fluctuations. We apply our model to single-molecule experiments on a DNA molecule attached to a substrate at one end, while subjected to a tensile force and twisted by a given number of turns at the other end. The free energy of the DNA molecule is minimized subject to the imposed end rotations. We compute values of the torsional stress, radius, helical angle and key features of the rotation-extension curves. We also include in our model the end loop energetic contributions and obtain estimates for the jumps in the external torque and extension of the DNA molecule seen in experiments. We find that, while the general trends seen in experiments are captured simply by rod mechanics, the details can be accounted for only with the proper choice of electrostatic and entropic interactions. We perform calculations with different ionic concentrations and show that our model yields excellent fits to mechanical data from a large number of experiments. Our methods also allow us to consider scenarios where we have multiple plectonemes or a series of loops forming in the DNA instead of plectonemes. For a given choice of electrostatic and entropic interactions, we find there is a range of forces in which the two regimes can coexist due to thermal motion.
机译：我们开发了一种弹性各向同性的杆状模型，用于plectonemic体制中的扭曲DNA。我们考虑了由于热波动而引起的DNA弹性，静电相互作用和熵效应。我们将模型应用于一端附着于底物的DNA分子的单分子实验，同时承受拉力并在另一端扭曲给定的圈数。受到施加的末端旋转的影响，DNA分子的自由能被最小化。我们计算扭转应力，半径，螺旋角和旋转延伸曲线的关键特征的值。我们还在模型中包括了末端环的能量贡献，并获得了对在实验中看到的DNA分子的外部扭矩和延伸的跳跃的估计。我们发现，虽然在实验中看到的总体趋势只是通过杆力学来捕获的，但只有通过适当选择静电和熵相互作用，才能解释细节。我们用不同的离子浓度进行计算，结果表明我们的模型对大量实验的机械数据具有很好的拟合度。我们的方法还使我们能够考虑在DNA中形成多个plectoneme或一系列环而不是plectoneme的情况。对于给定的静电和熵相互作用选择，我们发现由于热运动，两种状态可以共存。

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