DNA Conformational Variations Induced by Stretching 3'5'-Termini Studied by Molecular Dynamics Simulations
QI Wen-Peng1,2, LEI Xiao-Ling2**
1Department of Physics, Shandong University, Jinan 250100 2Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800
DNA Conformational Variations Induced by Stretching 3'5'-Termini Studied by Molecular Dynamics Simulations
QI Wen-Peng1,2, LEI Xiao-Ling2**
1Department of Physics, Shandong University, Jinan 250100 2Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800
摘要Investigating the interaction between protein and stretched DNA molecules has become a new way to study the protein DNA interaction. The conformations from different stretching methods give us a further understanding of the interaction between protein and DNA. We study the conformational variations of a 22-mer DNA caused by stretching both 3'− and 5'−termini by molecular dynamics simulations. It requires 250 kJ/mol to stretch the DNA molecule by 3'5'−termini for 3.5 nm and the force plateau is at 123.8 pN. The stretching 3'5'−termini leads to large values of the angle opening and the dihedral propeller between bases in one base pair, the double helix untwists from 34° to 20° and the successive base pairs rolls to the side of the DNA major groove. The distances between successive base pairs increases from 3.2 Å to 5.6 Å.
Abstract：Investigating the interaction between protein and stretched DNA molecules has become a new way to study the protein DNA interaction. The conformations from different stretching methods give us a further understanding of the interaction between protein and DNA. We study the conformational variations of a 22-mer DNA caused by stretching both 3'− and 5'−termini by molecular dynamics simulations. It requires 250 kJ/mol to stretch the DNA molecule by 3'5'−termini for 3.5 nm and the force plateau is at 123.8 pN. The stretching 3'5'−termini leads to large values of the angle opening and the dihedral propeller between bases in one base pair, the double helix untwists from 34° to 20° and the successive base pairs rolls to the side of the DNA major groove. The distances between successive base pairs increases from 3.2 Å to 5.6 Å.
[1] Gore J et al 2006 Nature 439 100
[2] Gemmen G J, Millin R and Smith D E 2006 Proc. Natl. Acad. Sci. U. S.A. 103 11555
[3] Gemmen G J et al 2006 Nucleic Acids Res. 34 2864
[4] Leger J F et al 1999 Phys. Rev. Lett. 83 1066
[5] Danilowicz C et al 2009 Proc. Natl. Acad. Sci. U. S.A. 106 13196
[6] Albrecht C H, Neuert G, Lugmaier R A and Gaub H E 2008 Biophys. J. 94 4766
[7] Lebrun A and Lavery R 1996 Nucleic Acids Res. 24 2260
[8] Lavery R and Lebrun A 1999 Genetica 106 75
[9] Konrad M W and Bolonick J I 1996 J. Am. Chem. Soc. 118 10989
[10] Wang X F, Lei X L, Fang H P 2006 Chin. Phys. Lett. 23 1339
[11] Lei X L, Wang X F, Hu J, Fang H P 2005 Chin, Phys. Lett. 22 1540
[12] Xiu P, Zhou B, Qi W P, Lu H J, Tu Y S and Fang H P 2009 J. Am. Chem. Soc. 131 2840
[13] Gong X J, Li J Y, Lu H J, Wan R Z, Li J C, Hu J and Fang H P 2007 Nature Nanotechnol. 2 709
[14] Song B, Elster M and Guniberti G 2008 Nano Lett. 8 3217
[15] Harris S A, Sands Z A and Laughton C A 2005 Biophys. J. 88 1684
[16] Piana S 2005 Nucleic Acids Res. 33 7029
[17] Qi W P, Song B, Lei X L and Fang H P 2010 Chemphyschem 11 2146
[18] Lindahl E, Hess B and van der Spoel D 2001 J. Mol. Biol. 7 306
[19] Cornell W D, Cieplak P, Bayly C I, Gould I R, Merz K M, Ferguson D M, Spellmeyer D C, Fox T, Caldwell J W and Kollman P A 1996 J. Am. Chem. Soc. 118 2309
[20] Case D A, Darden T A, Cheatham T E, Simmerling C L, Wang J, Duke R E, Luo R, Merz K M, Wang B and Pearlman D A 2004 Amber 8 (San Francisco: University of California)
[21] Wing R, Drew H, Takano T, Broka C, Tanaka S, Itakura K and Dickerson R E 1980 Nature 287 755
[22] Jorgensen W L et al 1983 J. Chem. Phys. 79 926
[23] Darden T, York D and Pedersen L 1993 J. Chem. Phys. 98 10089
[24] Essmann U, Perera L, Berkowitz M L, Darden T, Lee H and Pedersen L G 1995 J. Chem. Phys. 103 8577
[25] Lavery R and Sklenar H 1988 J. Biomol. Struct. Dyn. 6 63
[26] Kumar S, Rosenberg J M, Bouzida D, Swendsen R H and Kollman P A 1995 J. Comput. Chem. 16 1339
[27] Roux B 1995 Comput. Phys. Commun. 91 275
[28] Calladine C R, Drew H R, Luisi B F and Travers A A 2004 Understanding DNA: The Molecule and How It Works (Amsterdan: Elsevier)
[29] Suck D and Oefner C 1986 Nature 321 620
2011, Vol. 28 
