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利用Langevin动力学方法模拟了脱氧核糖核酸(DNA)单链在电场力作用下穿越纳米孔道的动力学过程.研究表明，不同种类的单体对应着不同的居留时间，相邻单体的居留时间随着孔道长度的增大而减小.在简化模型的基础上，可以从居留时间图中一次性地推测出一条DNA链的嘌呤和嘧啶的分布.应用该方法对17条不同序列的DNA链进行了预测，平均准确率为951%.在此方法的基础上做一些改进，可以为DNA链的测序提供一种高效的低成本方法.
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关键词:
- Langevin动力学 /
- 脱氧核糖核酸单链 /
- 序列预测
The dynamics of the translocation of single-stranded desoxyribonucleic acid (DNA) chains through a nanopore under the driving of an applied field is studied by three-dimensional Langevin dynamics simulations. It was found that different monomers correspond to different residence times. With the increase of the length of nanopore, the difference in residence time becomes smaller and smaller. Based on the simplified model, a new method is proposed to discriminate between the poly(dA) and poly(dC) of single-stranded DNA chains by recording the residence time of monomer. The method is utilized to predict the sequence of seventeen different chains, and the average accuracy is about 951%. If the residence time of monomer can be well recorded in the DNA translocation experiment, the sequence of the whole DNA will be predicted once and for all. With the improvement of the method, it will provide a low-cost high-throughput way to predict the sequence of DNA.[1] ［1］Miller R V 1998 Sci. Am. 278 66
[2] ［2］Kasianowicz J J, Brandin E, Branton D, Deamer D W 1996 Proc. Natl. Acad. Sci. USA 93 13770
[3] ［3］Storm A J, Storm C, Chen J, Zandbergen H, Joanny J F, Dekker C 2005 Nano. Lett. 5 1193
[4] ［4］Meller A, Nivon L, Branton D 2001 Phys. Rev. Lett. 85 3435
[5] ［5］Lagerqvist J, Zwolak M, Ventra M D 2006 Nano. Lett. 6 779
[6] ［6］Meller A, Nivon L, Brandin E, Golovchenko J, Branton D 2000 Proc. Natl. Acad. Sci. USA 97 1079
[7] ［7］Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler P F, Mang Y, Tommerup N, Gilchrist M J, Nygrd A B, Cirera S, Jrgensen C B, Fredholm M, Gorodkin J 2009 Comput. Biol. Chem. 33 121
[8] ［8］Luo K F, Nissila T A, Ying S C, Bhattacharya A 2007 Phys. Rev. Lett. 99 148102
[9] ［9］Luo K F, Nissila T A, Ying S C, Bhattacharya A 2008 Phys. Rev. Lett. 100 058101
[10] ］Shen Y, Zhang L X 2008 Chin. Phys. B 17 1480
[11] ］Allen M P, Tildesley D J 1987 Computer Simulation of Liquids (New York: Oxford University Press) p327
[12] ］Smith S B, Cui Y, Bustamante C 1996 Science 271 795
[13] ］Wang Y, Zhang L X 2008 Acta Phys. Sin. 57 3281 (in Chinese) ［王禹、章林溪 2008 57 3281］
[14] ］Liu J T, Duan H M 2009 Acta Phys. Sin. 58 4826 (in Chinese) ［刘建廷、段海明 2009 58 4826］
[15] ］Luo K F, Nissila T A, Ying S C, Bhattacharya A 2007 J. Chem. Phys. 126 145101
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[1] ［1］Miller R V 1998 Sci. Am. 278 66
[2] ［2］Kasianowicz J J, Brandin E, Branton D, Deamer D W 1996 Proc. Natl. Acad. Sci. USA 93 13770
[3] ［3］Storm A J, Storm C, Chen J, Zandbergen H, Joanny J F, Dekker C 2005 Nano. Lett. 5 1193
[4] ［4］Meller A, Nivon L, Branton D 2001 Phys. Rev. Lett. 85 3435
[5] ［5］Lagerqvist J, Zwolak M, Ventra M D 2006 Nano. Lett. 6 779
[6] ［6］Meller A, Nivon L, Brandin E, Golovchenko J, Branton D 2000 Proc. Natl. Acad. Sci. USA 97 1079
[7] ［7］Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler P F, Mang Y, Tommerup N, Gilchrist M J, Nygrd A B, Cirera S, Jrgensen C B, Fredholm M, Gorodkin J 2009 Comput. Biol. Chem. 33 121
[8] ［8］Luo K F, Nissila T A, Ying S C, Bhattacharya A 2007 Phys. Rev. Lett. 99 148102
[9] ［9］Luo K F, Nissila T A, Ying S C, Bhattacharya A 2008 Phys. Rev. Lett. 100 058101
[10] ］Shen Y, Zhang L X 2008 Chin. Phys. B 17 1480
[11] ］Allen M P, Tildesley D J 1987 Computer Simulation of Liquids (New York: Oxford University Press) p327
[12] ］Smith S B, Cui Y, Bustamante C 1996 Science 271 795
[13] ］Wang Y, Zhang L X 2008 Acta Phys. Sin. 57 3281 (in Chinese) ［王禹、章林溪 2008 57 3281］
[14] ］Liu J T, Duan H M 2009 Acta Phys. Sin. 58 4826 (in Chinese) ［刘建廷、段海明 2009 58 4826］
[15] ］Luo K F, Nissila T A, Ying S C, Bhattacharya A 2007 J. Chem. Phys. 126 145101
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