Pedersen Jonas Nyvold, Hansen Mikael Sonne, Novotný Tomás, Ambjörnsson Tobias, Metzler Ralf
Department of Mathematical Physics, Lund University, Box 118, 22100 Lund, Sweden.
J Chem Phys. 2009 Apr 28;130(16):164117. doi: 10.1063/1.3117922.
We investigate the coalescence of two DNA bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behavior, while at high temperatures, the bubble corners perform drift diffusion toward coalescence. In the calculations, we map the bubble dynamics on the problem of two vicious walkers in opposite potentials. We also present a discrete master equation approach to the bubble coalescence problem. Numerical evaluation and stochastic simulation of the master equation show excellent agreement with the results from the continuum approach. Given that the coalesced state is thermodynamically stabilized against a state where only one or a few of the base pairs of the barrier region are re-established, it appears likely that this type of setup could be useful for the quantitative investigation of thermodynamic DNA stability data as well as the rate constants involved in the unzipping and zipping dynamics of DNA in single molecule fluorescence experiments.
我们研究了在一种设计的双链DNA结构中，两个最初位于弱区域且被更稳定的屏障区域隔开的DNA气泡的合并情况。采用连续福克 - 普朗克方法，推导了气泡合并的特征时间及其相应分布，以及沿屏障的合并位置分布。在低于解链温度时，我们发现了一种克莱默斯型的穿越势垒行为，而在高温下，气泡角向合并方向进行漂移扩散。在计算中，我们将气泡动力学映射到处于相反势场中的两个恶性行走者的问题上。我们还提出了一种针对气泡合并问题的离散主方程方法。主方程的数值评估和随机模拟结果与连续方法的结果显示出极好的一致性。鉴于合并状态相对于仅重新建立屏障区域的一个或几个碱基对的状态在热力学上是稳定的，这种设置似乎可能有助于对热力学DNA稳定性数据以及单分子荧光实验中DNA解链和复性动力学所涉及的速率常数进行定量研究。
