Jeon Jae-Hyung, Park Pyeong Jun, Sung Wokyung
Department of Physics, Pohang University of Science and Technology, Pohang 790-784, South Korea.
J Chem Phys. 2006 Oct 28;125(16):164901. doi: 10.1063/1.2359724.
DNA exists stably in the double-stranded structure at physiological temperatures, but base pairs are observed to unbind locally, giving way to bubbles (i.e., locally denatured states) due to thermal fluctuation. In this study, we consider the effect of sequence on the bubble statistics. On the basis of the Edwards equation description [W. Sung and J.-H. Jeons, Phys. Rev. E 69, 031902 (2004) ], we develop a stochastic model incorporating the sequence randomness as a dichotomic noise, where the bubble and its size are identified as a returning random walk and its first passage time, respectively. By simulating the model Langevin equation, we obtain the bubble size distribution and show how it is affected by the sequence correlation. We find that the bubble size distribution of DNA with finite sequence correlation deviates from the Poland-Scheraga-type distribution. In particular, the formation of large bubbles is dramatically enhanced as sequence correlation length gets longer.
在生理温度下，DNA以双链结构稳定存在，但由于热涨落，碱基对会局部解链，形成气泡（即局部变性状态）。在本研究中，我们考虑序列对气泡统计的影响。基于爱德华兹方程描述[W. Sung和J.-H. Jeons，《物理评论E》69，031902（2004）]，我们开发了一个将序列随机性作为二分噪声纳入的随机模型，其中气泡及其大小分别被识别为返回随机游走及其首次通过时间。通过模拟模型朗之万方程，我们得到了气泡大小分布，并展示了它如何受到序列相关性的影响。我们发现，具有有限序列相关性的DNA的气泡大小分布偏离了波兰-谢拉加型分布。特别是，随着序列相关长度变长，大气泡的形成显著增强。
