搜索

x

留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

非均匀外力对粗粒化DNA穿孔行为影响的模拟研究

马姗 马军 杨光参

引用本文:
Citation:

非均匀外力对粗粒化DNA穿孔行为影响的模拟研究

马姗, 马军, 杨光参

Simulation of translocating pore of DNA in non-uniform force by coarse-grained model

Ma Shan, Ma Jun, Yang Guang-Can
PDF
导出引用
  • 通过建立DNA高分子的粗粒化模型, 采用分子动力学方法模拟其穿孔行为, 研究了不同的孔内非均匀外力对DNA高分子穿孔的影响. 外力及高分子链内部势能在分子水平下对单体的综合作用很复杂, 某些条件穿孔过程会产生后面粒子超过前面粒子而使高分子链堵塞在孔内的情况. 研究还发现, 穿孔行为是否成功与孔口力的大小有关, 在成功穿孔的情况下, 非均匀外力相比于恒力情况穿孔时间至少减少了1/2. 这些结果对理解DNA复杂的穿孔机理提供了新的视角.
    Translocating pore of biomacromolecules is a common phenomenon in many biological processes, such as DNA transcription, cell infection of virus and transmembrane of proteins. The understanding of translocating pore of DNA is important for studying the DNA sequencing, gene therapy and virus infection. According to the coarse-grained model, we use molecular dynamics simulations to investigate the process of translocating pore of DNA under the actions of different non-uniform forces. In the present study, we consider five kinds of non-uniform forces, i.e., linearly increasing, linearly decreasing, V-type, inverted V-shaped, and periodic type. In the simulations of coarse-grained DNA, we find that the force on the pore opening palys a key role in the process of translocation of polymer. When the force is small, the probability of successful translocation of DNA is low accordingly. In the case of inverted V-shaped potential, the difference between the maximum and minimum force should be in a limited range to a probable translocation of DNA. Out of the range it might lead to clogged pores in the polymer chain. In the action of a non-uniform force, the translocating pore of DNA shows a series of complicated behaviors. For example, the end of a polymer can move faster than its head, resulting in the hole clogging and accumulation of polymers. A reversion can occasionally occur after a successful translocation of polymer. Therefore, non-uniform force leads to various scenarios of translocating pore of polymers.In summary, due to the complicated interactions between external forces and internal potential of polymer chains, particles can be clogged in the pore since the following particles overtake the leading ones in the chain. It is also found that the success of pore translation of DNA is significantly dependent on the acting force on the pore. Among all the cases of translating the pore successfully, the translation time in the case of non-uniform force is about half that in the case of uniform force. These results might provide an insight into the understanding of the complicated pore translating mechanism of DNA.
      通信作者: 杨光参, yanggc@wzu.edu.cn
    • 基金项目: 国家自然科学基金(批准号:11274245,11574243)和国家自然科学基金青年科学基金(批准号:11304232)资助的课题.
      Corresponding author: Yang Guang-Can, yanggc@wzu.edu.cn
    • Funds: Project supported by the National Natural Science Foundation of China (Grant Nos. 11274245, 11574243) and the Young Scientists Fund of the National Natural Science Foundation of China (Grant No. 11304232).
    [1]

    Kasianowich J J, Brandin E, Branton D, Deamer D W 1996 Proc. Natl. Acad. Sci. USA 93 13770

    [2]

    Meller A, Nivon L, Brandin E, Golovchenko J, Branton D 2000 Proc. Natl. Acad. Sci. USA 97 1079

    [3]

    Gu L Q, Braha O, Conlan S, Cheley S, Bayley H 1999 Nature 398 686

    [4]

    Sung W, Park P J 1996 Phys. Rev. Lett. 77 783

    [5]

    Luo K F, Ollila S T T, Huopaniemi I, Ala-Nissila T, Pomorski P, Karttunen M, Ying S C, Bhattacharya A 2008 Phys. Rev. E 78 050901

    [6]

    Luo K F, Ala-Nissila T, Ying S C, Bhattacharya A 2008 Phys. Rev. E 78 061911

    [7]

    Chen Z, Jiang Y B, Dunphy D R, Adams D P, Hodges C, Liu N G, Zhang N, Xomeritakis G, Jin X Z, Aluru N R, Gaik S J, Hillhouse H W, Brinker C J 2010 Nat. Mater. 9 667

    [8]

    Storm A J, Storm C, Chen J, Zandbergen H, Joanny J F, Dekker C 2005 Nano Lett. 5 1193

    [9]

    Venkatesan B M, Dorvel B, Yemenicioglu S, Watkins N, Petrov I, Bashir R 2009 Adv. Mater. 21 2771

    [10]

    Stoddart D, Heron A J, Mikhailova E, Maglia G, Bayley H 2009 Proc. Natl. Acad. Sci. USA 106 7702

    [11]

    Chen Z L, Xu W R, Tang L D 2007 Molecular Simulation Theory and Practice (Vol. 1) (Beijing: Chemical Industry Press) p67 (in Chinese) [陈正隆, 徐为人, 汤立达 2007 分子模拟的理论与实践 (第1卷) (北京: 化学工业出版社) 第67页]

    [12]

    Li Y L, Luo C L 2002 Acta. Phys. Sin. 51 2589 (in Chinese) [李延龄, 罗成林 2002 物理学报 51 2589]

    [13]

    Knotts IV T A, Rathore N, Schwartz D C, de Pablo J J 2007 J. Chem. Phys. 126 084901

    [14]

    Forrey C, Muthukumar M 2007 J. Chem. Phys. 127 015102

    [15]

    Kenward M, Slater G W 2004 Eur. Phys. J. E 14 55

    [16]

    Maglia G, Restrepo M R, Mikhailova E, Bayley H 2008 P. Natl. Acad. Sci. 105 19720

  • [1]

    Kasianowich J J, Brandin E, Branton D, Deamer D W 1996 Proc. Natl. Acad. Sci. USA 93 13770

    [2]

    Meller A, Nivon L, Brandin E, Golovchenko J, Branton D 2000 Proc. Natl. Acad. Sci. USA 97 1079

    [3]

    Gu L Q, Braha O, Conlan S, Cheley S, Bayley H 1999 Nature 398 686

    [4]

    Sung W, Park P J 1996 Phys. Rev. Lett. 77 783

    [5]

    Luo K F, Ollila S T T, Huopaniemi I, Ala-Nissila T, Pomorski P, Karttunen M, Ying S C, Bhattacharya A 2008 Phys. Rev. E 78 050901

    [6]

    Luo K F, Ala-Nissila T, Ying S C, Bhattacharya A 2008 Phys. Rev. E 78 061911

    [7]

    Chen Z, Jiang Y B, Dunphy D R, Adams D P, Hodges C, Liu N G, Zhang N, Xomeritakis G, Jin X Z, Aluru N R, Gaik S J, Hillhouse H W, Brinker C J 2010 Nat. Mater. 9 667

    [8]

    Storm A J, Storm C, Chen J, Zandbergen H, Joanny J F, Dekker C 2005 Nano Lett. 5 1193

    [9]

    Venkatesan B M, Dorvel B, Yemenicioglu S, Watkins N, Petrov I, Bashir R 2009 Adv. Mater. 21 2771

    [10]

    Stoddart D, Heron A J, Mikhailova E, Maglia G, Bayley H 2009 Proc. Natl. Acad. Sci. USA 106 7702

    [11]

    Chen Z L, Xu W R, Tang L D 2007 Molecular Simulation Theory and Practice (Vol. 1) (Beijing: Chemical Industry Press) p67 (in Chinese) [陈正隆, 徐为人, 汤立达 2007 分子模拟的理论与实践 (第1卷) (北京: 化学工业出版社) 第67页]

    [12]

    Li Y L, Luo C L 2002 Acta. Phys. Sin. 51 2589 (in Chinese) [李延龄, 罗成林 2002 物理学报 51 2589]

    [13]

    Knotts IV T A, Rathore N, Schwartz D C, de Pablo J J 2007 J. Chem. Phys. 126 084901

    [14]

    Forrey C, Muthukumar M 2007 J. Chem. Phys. 127 015102

    [15]

    Kenward M, Slater G W 2004 Eur. Phys. J. E 14 55

    [16]

    Maglia G, Restrepo M R, Mikhailova E, Bayley H 2008 P. Natl. Acad. Sci. 105 19720

计量
  • 文章访问数:  1838
  • PDF下载量:  244
  • 被引次数: 0
出版历程
  • 收稿日期:  2016-03-08
  • 修回日期:  2016-04-07
  • 刊出日期:  2016-07-05

非均匀外力对粗粒化DNA穿孔行为影响的模拟研究

  • 1. 温州大学物理与电子信息学院, 温州 325035
  • 通信作者: 杨光参, yanggc@wzu.edu.cn
    基金项目: 

    国家自然科学基金(批准号:11274245,11574243)和国家自然科学基金青年科学基金(批准号:11304232)资助的课题.

摘要: 通过建立DNA高分子的粗粒化模型, 采用分子动力学方法模拟其穿孔行为, 研究了不同的孔内非均匀外力对DNA高分子穿孔的影响. 外力及高分子链内部势能在分子水平下对单体的综合作用很复杂, 某些条件穿孔过程会产生后面粒子超过前面粒子而使高分子链堵塞在孔内的情况. 研究还发现, 穿孔行为是否成功与孔口力的大小有关, 在成功穿孔的情况下, 非均匀外力相比于恒力情况穿孔时间至少减少了1/2. 这些结果对理解DNA复杂的穿孔机理提供了新的视角.

English Abstract

参考文献 (16)

目录

    /

    返回文章
    返回