DNA十字形臂通过相关但非同步的合作机制成核
DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism
摘要：
DNA中的反向重复序列（IR）可以形成非经典的十字形结构来缓解扭转应力。我们使用蒙特卡罗模拟最近开发的粗粒度模型的DNA证明，一个十字形的成核可以通过一个合作机制进行。首先，扭曲诱导的变性气泡必须扩散，使得其中点靠近IR序列的对称中心。其次，泡沫的波动必须足够大，以允许其中一个臂形成少量的发夹键。一旦第一臂部分地形成，第二臂可以快速地生长到类似的尺寸。由于气泡可以自行扭转，因此它们需要比最终十字形状态少得多的基础来解决扭转应力。因此，最初稳定的十字形继续生长，这通常是同步进行的，让人想起十字形形成的S型机制。通过使用伞采样技术，我们计算，对于不同的温度和超螺旋密度，自由能作为一个函数的键的数量在每个十字形沿相关的，但非同步的成核途径，我们观察到在直接模拟。
英文摘要：
Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. Firstly, a twist-induced denaturation bubble must diffuse so that its midpoint is near the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must be large enough to allow one of the arms to form a small number of hairpin bonds. Once the first arm is partially formed, the second arm can rapidly grow to a similar size. Because bubbles can twist back on themselves, they need considerably fewer bases to resolve torsional stress than the final cruciform state does. The initially stabilised cruciform therefore continues to grow, which typically proceeds synchronously, reminiscent of the S-type mechanism of cruciform formation. By using umbrella sampling techniques we calculate, for different temperatures and superhelical densities, the free energy as a function of the number of bonds in each cruciform along the correlated but non-synchronous nucleation pathways we observed in direct simulations.
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