Self-assembly of 50 bp poly(dA)·poly(dT) DNA on highly oriented pyrolytic graphite via atomic force microscopy observation and molecular dynamics simulation

Journal of Chemical Physics

Volumn 139, Issue 8, 2013, Pages

  Doi, Kentaro ^a   Takeuchi, Hiroshi ^a   Nii, Ryosuke ^a   Akamatsu, Shingo ^a   Kakizaki, Toshiya ^a   Kawano, Satoyuki ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COARSE-GRAINED MOLECULAR DYNAMICS SIMULATIONS; FORMATION PATTERN; FRACTAL DIMENSION ANALYSIS; HIGHLY ORIENTED PYROLYTIC GRAPHITE; MOLECULAR DYNAMICS SIMULATIONS; NEGATIVELY CHARGED; OPTIMIZED CONDITIONS; SOLUTION CONCENTRATION;

ATOMIC FORCE MICROSCOPY; DNA; FRACTAL DIMENSION; GRAPHITE; MOLECULAR DYNAMICS;

SELF ASSEMBLY;

DNA; GRAPHITE; POLY(DEOXYADENYLATE DEOXYTHYMIDYLATE);

ARTICLE; ATOMIC FORCE MICROSCOPY; CHEMISTRY; MOLECULAR DYNAMICS; SYNTHESIS;

DNA; GRAPHITE; MICROSCOPY, ATOMIC FORCE; MOLECULAR DYNAMICS SIMULATION; POLY DA-DT;

EID: 84884179095     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4818595     Document Type: Article

References (50)

1. E. Winfree, F. Liu, L. A. Wenzler, and N. C. Seeman, Nature (London) 394, 539 (1998). 10.1038/28998
2. H. Yan, S. H. Park, G. Finkelstein, J. H. Reif, and T. H. LaBean, Science 301, 1882 (2003). 10.1126/science.1089389
3. F. A. Aldaye, A. L. Palmer, and H. F. Sleiman, Science 321, 1795 (2008). 10.1126/science.1154533
4. S. Chang, S. Huang, J. He, F. Liang, P. Zhang, S. Li, X. Chen, O. Sankey, and S. Lindsay, Nano Lett. 10, 1070 (2010). 10.1021/nl1001185
5. B. M. Venkatesan and R. Bashir, Nat. Nanotechnol. 6, 615 (2011). 10.1038/nnano.2011.129
6. D. Gerster, J. Reichert, H. Bi, J. V. Barth, S. M. Kaniber, A. W. Holleitner, I. Visoly-Fisher, S. Sergani, and I. Carmeli, Nat. Nanotechnol. 7, 673 (2012). 10.1038/nnano.2012.165
7. S. Tanaka, Y. Maeda, L.-T. Cai, H. Tabata, and T. Kawai, Jpn. J. Appl. Phys. 40, 4217 (2001). 10.1143/JJAP.40.4217
8. S. Tanaka, L.-T. Cai, H. Tabata, and T. Kawai, Jpn. J. Appl. Phys. 42, 2818 (2003). 10.1143/JJAP.42.2818
9. Z. L. J. Zheng, A. Wu, and H. Zhou, Biophys. Chem. 104, 37 (2003). 10.1016/S0301-4622(02)00335-6
10. Z. Xiao, M. Xu, K. Sagisaka, and D. Fujita, Thin Solid Films 438-439, 114 (2003). 10.1016/S0040-6090(03)00785-5
11. A. M. O. Brett and A.-M. Chiorcea, Electrochem. Commun. 5, 178 (2003). 10.1016/S1388-2481(03)00014-6
12. A.-M. Chiorcea and A. M. O. Brett, Bioelectrochemistry 63, 229 (2004). 10.1016/j.bioelechem.2003.09.029
13. A. M. O. Brett and A.-M. C. Paquim, Bioelectrochemistry 66, 117 (2005). 10.1016/j.bioelechem.2004.05.009
14. X. Jiang and X. Lin, Electrochem. Commun. 6, 873 (2004). 10.1016/j.elecom.2004.06.014
15. H. Tanaka, T. Nakagawa, and T. Kawai, Surf. Sci. 364, L575 (1996). 10.1016/0039-6028(96)00792-3
16. H. Tanaka and T. Kawai, Nat. Nanotechnol. 4, 518 (2009). 10.1038/nnano.2009.155
17. C. Jianrong, M. Yuqing, H. Nongyue, W. Xiaohua, and L. Sijiao, Biotechnol. Adv. 22, 505 (2004). 10.1016/j.biotechadv.2004.03.004
18. A.-M. C. Paquim, T. S. Oretskaya, and A. M. O. Brett, Biophys. Chem. 121, 131 (2006). 10.1016/j.bpc.2005.12.017
19. R. G. Endres, D. L. Cox, and R. Singh, Rev. Mod. Phys. 76, 195 (2004). 10.1103/RevModPhys.76.195
20. M. Taniguchi and T. Kawai, Physica E 33, 1 (2006). 10.1016/j.physe.2006. 01.005
21. L. Wu, J. Zhou, J. Luo, and Z. Lin, Electrochim. Acta 45, 2923 (2000). 10.1016/S0013-4686(00)00369-8
22. N. Severin, J. Barner, A. A. Kalachev, and J. P. Rabe, Nano Lett. 4, 577 (2004). 10.1021/nl035147d
23. X. Tu, S. Manohar, A. Jagota, and M. Zheng, Nature (London) 460, 250 (2009). 10.1038/nature08116
24. S. Uehara, H. Shintaku, and S. Kawano, J. Fluids Eng. 133, 121203 (2011). 10.1115/1.4005343
25. S. Kawano, JSME Int. J., Ser. B 48, 191 (2005). 10.1299/jsmeb.48.191
26. I. Hanasaki, H. Shintaku, S. Matsunami, and S. Kawano, Comput. Model. Eng. Sci. 46, 191 (2009). 10.3970/cmes.2009.046.191
27. K. Doi, Y. Toyokita, S. Akamatsu, and S. Kawano, Comput. Methods Biomech. Biomed. Eng. iFirst, 1 (2012). 10.1080/10255842.2012.723701
28. S. Kawano, Phys. Rev. E 58, 4468 (1998). 10.1103/PhysRevE.58.4468
29. S. Nagahiro, S. Kawano, and H. Kotera, Phys. Rev. E 75, 011902 (2007). 10.1103/PhysRevE.75.011902
30. K. Doi, T. Haga, H. Shintaku, and S. Kawano, Phil. Trans. R. Soc. London, Ser. A 368, 2615 (2010). 10.1098/rsta.2010.0068
31. D. K. Schwartz, S. Steinberg, J. Israelackvili, and J. A. N. Zasadzinski, Phys. Rev. Lett. 69, 3354 (1992). 10.1103/PhysRevLett.69.3354
32. E. Ercolini, F. Valle, J. Adamcik, G. Witz, R. Metzler, P. D. L. Rios, J. Roca, and G. Dietler, Phys. Rev. Lett. 98, 058102 (2007). 10.1103/PhysRevLett. 98.058102
33. See supplementary material at http://dx.doi.org/10.1063/1.4818595 E-JCPSA6-139-052332 for the other experimental data and details of the fractal dimension analysis.
34. I. Hanasaki, H. Takahashi, G. Sazaki, K. Nakajima, and S. Kawano, J. Phys. D: Appl. Phys. 41, 095301 (2008). 10.1088/0022-3727/41/9/095301
35. K. Doi, T. Uemura, and S. Kawano, J. Mol. Model. 17, 1457 (2011). 10.1007/s00894-010-0840-3
36. A. K. Rappé, C. J. Casewit, K. S. Colwell, W. A. Goddard III, and W. M. Skid, J. Am. Chem. Soc. 114, 10024 (1992). 10.1021/ja00051a040
37. H.-S. Kim, J. Mol. Struct.: THEOCHEM 541, 59 (2001). 10.1016/S0166- 1280(00)00746-6
38. H. L. Tepper and G. A. Voth, J. Chem. Phys. 122, 124906 (2005). 10.1063/1.1869417
39. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, Clarendon, Oxford, 1989), p. 21.
40. S. S. Sorlie and R. Pecora, Macromolecules 23, 487 (1990). 10.1021/ma00204a022
41. G. L. Lukacs, P. Haggie, O. Seksek, D. Lechardeur, N. Freedman, and A. S. Verkman, J. Biol. Chem. 275, 1625 (2000). 10.1074/jbc.275.3.1625
42. H. Jian, A. V. Vologodskii, and T. Schlick, J. Comput. Phys. 136, 168 (1997). 10.1006/jcph.1997.5765
43. M. J. Booth, D.-M. Duh, and A. D. J. Haymet, J. Chem. Phys. 101, 7925 (1994). 10.1063/1.468219
44. G. W. C. Kaye and T. H. Laby, Tables of Physical and Chemical Constants, 14th ed. (Longman, London, 1973), p. 150.
45. B. T. Kelly, Physics of Graphite (Applied Science Publishers, London, 1981), p. 29.
46. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in Fortran 77, 2nd ed. (Cambridge University Press, 1992), pp. 279-280.
47. M. Tuckerman, B. J. Berne, and A. Rossi, J. Chem. Phys. 94, 1465 (1991). 10.1063/1.460004
48. K. Falconer, Fractal Geometry (John Wiley Sons, Chichester, 2003), Chap..
49. L. A. Chrisey, G. U. Lee, and C. E. O'Ferrall, Nucleic Acids Res. 24, 3031 (1996). 10.1093/nar/24.15.3031
50. M. J. O'Donnell, K. Tang, H. Köster, C. L. Smith, and C. R. Cantor, Anal. Chem. 69, 2438 (1997). 10.1021/ac961007v