物理化学学报 >> 2011, Vol. 27 >> Issue (11): 2705-2710.doi: 10.3866/PKU.WHXB20111111

生物物理化学 上一篇    下一篇

全伸展DNA链折叠过程中三种非线性作用的布朗动力学模拟

张勇1,2, 肖忠党1   

  1. 1. 东南大学生命科学与医学工程学院, 生物电子学国家重点实验室; 南京 211189;
    2. 东南大学物理系, 南京 211189
  • 收稿日期:2011-05-23 修回日期:2011-07-29 发布日期:2011-10-27
  • 通讯作者: 肖忠党 E-mail:zdxiao@seu.edu.cn
  • 基金资助:

    国家自然科学基金(20875014, 30901285)资助项目

Brownian Dynamics Simulation of Three Nonlinear Interactions on the Folding Process of Single Completely Stretched DNA Chain

ZHANG Yong1,2, XIAO Zhong-Dang1   

  1. 1. State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 211189, P. R. China;
    2. Department of Physics, Southeast University, Nanjing 211189, P. R. China
  • Received:2011-05-23 Revised:2011-07-29 Published:2011-10-27
  • Contact: XIAO Zhong-Dang E-mail:zdxiao@seu.edu.cn
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (20875014, 30901285).

摘要: 脱氧核糖核酸(DNA)单分子链从完全拉伸状态折叠到平衡状态的动力学过程是溶液中DNA单分子力学的重要特征之一. 通过构建全参数化的珠子-弹簧分子链模型, 并运用一种高效平衡的半隐式预测——校验积分算法, 系统研究了体积排斥作用、有限伸长弹性作用和涨落流体动力学作用等三种非线性作用对稀溶液中DNA分子链折叠过程相对回旋半径和驰豫时间的影响程度和变化趋势. 模拟结果发现: 体积排斥作用不影响分子链的折叠驰豫时间, 但能显著减小平衡时的相对回旋半径; 流体动力学作用不影响分子链的相对回旋半径, 但明显缩短折叠过程的驰豫时间; 有限伸长弹性作用能明显减小短链的相对回旋半径, 能显著延长长链的折叠驰豫时间. 模拟数据进一步表明: 完全伸展的DNA分子链在折叠过程中的相对回旋半径随时间平滑变化,且折叠驰豫时间随长度的标度指数对上述三种非线性作用都具有两种不同的长度依赖性.

关键词: DNA单分子链, 珠子-弹簧模型, 非线性作用, 布朗动力学模拟, 折叠过程

Abstract: The folding dynamics of a completely stretched dexoxyribonucleic acid (DNA) molecule chain is an important feature of single DNA mechanics. By constructing a fully parameterized bead-spring chain model and applying a highly efficient second order semi-implicit predictor-corrector algorithm, we studied the influence of three nonlinear interactions including the excluded volume interaction, the finite extensible nonlinear elastic interaction, and the fluctuating hydrodynamic interaction on the folding process. Simulation results show that the excluded volume interaction decreases the relative radius of gyration of the DNA chain obviously but has no influence on the relaxation time. Instead, the hydrodynamic interaction clearly decreases the relaxation time but it does not change the relative radius of gyration. In addition, the finite extensible elastic interaction was found to decrease the relative radius of gyration of the short chain clearly and increase the relaxation time of the long chain obviously. Furthermore, we obtained a smooth change for the relative radius of gyration with time. The scaling exponent of the relaxation time with the length of chain has two different values under all three nonlinear interactions. These results complete our understanding about single DNA molecule chain mechanics in solution.

Key words: Single DNA molecule chain, Bead-spring model, Nonlinear interaction, Brownian dynamics simulation, Folding process

MSC2000: 

  • O645