Chin. Phys. Lett.  2011, Vol. 28 Issue (4): 048702    DOI: 10.1088/0256-307X/28/4/048702
CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY |
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
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QI Wen-Peng, LEI Xiao-Ling 2011 Chin. Phys. Lett. 28 048702
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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.
Keywords: 87.10.Tf      87.15.A-     
Received: 15 December 2010      Published: 29 March 2011
PACS:  87.10.Tf (Molecular dynamics simulation)  
  87.15.A- (Theory, modeling, and computer simulation)  
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https://cpl.iphy.ac.cn/10.1088/0256-307X/28/4/048702       OR      https://cpl.iphy.ac.cn/Y2011/V28/I4/048702
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LEI Xiao-Ling
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