Thermodynamics of Writhe in DNA Minicircles from Molecular Dynamics Simulations
Thermodynamics of Writhe in DNA Minicircles from Molecular Dynamics Simulations
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DOI：
10.1103/physrevlett.110.148105
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发表时间：
2013-04-05
影响因子：
8.6
通讯作者：
Harris, Sarah A.
中科院分区：
文献类型：
--
作者：
Mitchell, Jonathan S.;Harris, Sarah A.
DNA超螺旋通过施加扭转应力在遗传控制中起作用。这可能会导致扭曲，从而改变DNA的整体形状。我们已经使用原子分子动力学模拟分区的自由能变化驱动的扭曲和unwirthing过渡超螺旋微环DNA。计算结果表明，在能量驱动下，由于环状态的构型熵比缀位体的高，所以会发生非扭曲跃迁。扭曲改善了堆叠的碱基之间的货车范德华相互作用，但在静电屏蔽差的低盐条件下，可以通过带负电荷的主链链内的静电排斥来抑制。环状DNA和plectonemic DNA之间的自由能差异是由相反的热力学项的微妙平衡决定的，环境中的任何扰动，如盐浓度的变化，都足以在这两种状态之间转换。这种可转换的行为为超螺旋DNA提供了一种机制，以物理和化学方式存储和交流生物信息。DOI：10.1103/PhysRevLett.110.148105
DNA supercoiling plays a role in genetic control by imposing torsional stress. This can induce writhe, which changes the global shape of the DNA. We have used atomistic molecular dynamics simulations to partition the free energy changes driving the writhing and unwrithing transitions in supercoiled minicircle DNA. The calculations show that while writhing is energetically driven, the unwrithing transition occurs because the circular state has a higher configurational entropy than the plectoneme. Writhing improves the van der Waals interactions between stacked bases, but can be suppressed by electrostatic repulsion within the negatively charged backbone strands in low salt conditions where electrostatic screening is poor. The free energy difference between circular and plectonemic DNA is determined by such a delicate balance of opposing thermodynamic terms that any perturbation in the environment, such as a change in salt concentration, can be sufficient to convert between these two states. This switchable behavior provides a mechanism for supercoiled DNA to store and communicate biological information physically as well as chemically. DOI: 10.1103/PhysRevLett.110.148105