Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles.,Physical Review E

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Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles.
Physical Review E ( IF 2.2 ) Pub Date : 2020-01-01 , DOI: 10.1103/physreve.101.012403
François Sicard ₁ , Nicolas Destainville ₂ , Philippe Rousseau ₃ , Catherine Tardin ₄ , Manoel Manghi ₂

Affiliation

We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of nanometer size and controls their lifetime. Mesoscopic modeling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations encountered in such systems, and offer detailed insight into the thermodynamic and dynamical properties associated with the nucleation and closure mechanisms of long-lived thermally assisted denaturation bubbles which do not stem from bending- or torque-driven stress. Suitable tuning of the degree of supercoiling and size of specifically designed microDNA is observed to lead to the control of opening characteristic times in the millisecond range, and closure characteristic times ranging over well distinct timescales, from microseconds to several minutes. We discuss how our results can be seen as a dynamical bandwidth which might enhance selectivity for specific DNA binding proteins.

中文翻译：

动态控制超螺旋DNA小圆中的变性气泡成核。

我们检查了包含200至400个碱基对的超螺旋DNA小圆的行为，也称为microDNA，其中超螺旋有利于纳米尺寸的热辅助DNA变性气泡并控制其寿命。介观建模和加速动力学模拟使我们能够克服此类系统中遇到的原子模拟的局限性，并详细了解与长期存在的热辅助变性气泡的成核和闭合机理相关的热力学和动力学性质。弯曲或扭矩驱动的应力。观察到超螺旋度和专门设计的microDNA大小的适当调整可将打开特征时间控制在毫秒范围内，闭合特性的时间范围从十分微妙的时间段（从微秒到几分钟）不等。我们讨论了如何将我们的结果视为动态带宽，这可能会增强对特定DNA结合蛋白的选择性。

更新日期：2020-01-08

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