| CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY |
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Local Compression Properties of Double-Stranded DNA Based on a Dynamic Simulation |
| LEI Xiao-Ling**, QI Wen-Peng, FANG Hai-Ping |
Division of Interfacial Water, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800-204, Shanghai 201800
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| Cite this article: |
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LEI Xiao-Ling, QI Wen-Peng, FANG Hai-Ping 2013 Chin. Phys. Lett. 30 128701 |
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Abstract Using a simple sphere-tip compression system, the local radial mechanical properties of DNA are systematically studied by changing the tip size. When the tip size decreases, the radial compression elastic properties under external loads become sensitive to the tip size and the local DNA conformation. A sudden force break appears in the compression-force curve when the tip size is less than or equal to 12 nm in diameter. The analysis of the hydrogen bonds and the base stacking interaction shows that a local unwinding process occurs. During the compression process, firstly the hydrogen bonds between complement base pairs are broken. With the compression accumulating, the local backbones in the compression center are unwound from the double helix conformation to a kind of parallel conformation. This local unwinding behavior deduced by external loads is helpful to understand the biological process and is important to DNA-based nanomechanical devices.
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Received: 18 September 2013
Published: 13 December 2013
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[1] Bryant Z et al 2003 Nature 424 338
[2] Giresi P G, GuptaM and Lieb J D 2006 Curr. Opin. Genet. Dev. 16 171
[3] Werner M H, Gronenborn A M and Clore G M 1996 Science 271 778
[4] Seeman N C 2003 Nature 421 427
[5] Song B, Cuniberti G, Sanvito S and Fang H P 2012 Appl. Phys. Lett. 100 063101
[6] Mosconi F, Allemand J F, Bensimon D and Croquette V 2009 Phys. Rev. Lett. 102 078301
[7] Wiggins P A et al 2006 Nat. Nanotechnol. 1 137
[8] Changhong K, Michael H, Hanna S G and Piotr E M 2007 Phys. Rev. Lett. 99 018302
[9] Yan J and Marko J F 2004 Phys. Rev. Lett. 93 108108
[10] Chen H and Yan J 2008 Phys. Rev. E 77 041907
[11] Chen H, Fu H, Zhou Z and Yan J 2010 Int. J. Mod. Phys. B 24 5475
[12] Mastroianni A J, Sivak D A, Geissler P L and Alivisatos A P 2009 Biophys. J. 97 1408
[13] Danilowicz C et al 2009 Proc. Natl. Acad. Sci. USA 106 19824
[14] Wang H B et al 2010 Langmuir 26 7523
[15] Zhou X F et al 2005 Phys. Rev. E 71 062901
[16] Cloutie T E and Widom J 2005 Proc. Natl. Acad. Sci. USA 102 3645
[17] Yuan C L, Chen H M, Lou X W and Archer L A 2008 Phys. Rev. Lett. 100 018102
[18] Witz G, Rechendorff K, Adamcik J and Dietler G 2008 Phys. Rev. Lett. 101 148103
[19] Lei X L, Hu J and Fang H P 2010 Europhys. Lett. 89 48003
[20] Zhou H J, Zhang Y and Ou-Yang Z C 1999 Phys. Rev. Lett. 82 4560
[21] Smith S B, Cui Y and Bustamante C 1996 Science 271 795
[22] Lei X L, Wang X F, Hu J and Fang H P 2005 Chin. Phys. Lett. 22 1540
[23] Dessinges M N et al 2002 Phys. Rev. Lett. 89 248102
[24] Cocco S, Monasson R and Marko J F 2001 Proc. Natl. Acad. Sci. USA 98 8608
[25] Cluzel P et al 1996 Science 271 792
[26] Luo K, Ala Nissila T, Ying S C and Bhattacharya A 2008 Phys. Rev. Lett. 100 058101
[27] Zuo G, Hu J and Fang H P 2009 Phys. Rev. E 79 031925
[28] Frenkel D and Smit B 2001 Understanding Molecular Simulation: From Algorithms to Applications (San Diego: Academic) p 1
[29] Aldaye F A, Palmer A L and Sleiman H F 2008 Science 321 1795
[30] Thanthiriwatte K S, Hohenstein E G, Burns L A and Sherrill C D 2011 J. Chem. Theory Comput. 7 88
[31] Dragan A I et al 2006 Biochemistry 45 141
[32] Crespo-Hernandez C E, Cohen B and Kohler B 2005 Nature 436 1141
[33] Middleton C T et al 2009 Annu. Rev. Phys. Chem. 60 217
[34] Yang W 2006 DNA Repair 5 654
[35] Wu Y L 2012 J. Nucleic Acids 2012 140601
[36] Elbaz J et al 2010 Nat. Nanotechnol. 5 417
[37] Zhang X et al 2012 Proc. Natl. Acad. Sci. USA 109 8103 |
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