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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.
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Keywords:
- non-uniform force field /
- molecular dynamics simulation /
- DNA coarse-grained /
- clogged pores
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[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 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
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[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 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
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