CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY |
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DNA Conformational Variations Induced by Stretching 3'5'-Termini Studied by Molecular Dynamics Simulations |
QI Wen-Peng1,2, LEI Xiao-Ling2**
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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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Cite this article: |
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.
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Keywords:
87.10.Tf
87.15.A-
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Received: 15 December 2010
Published: 29 March 2011
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PACS: |
87.10.Tf
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(Molecular dynamics simulation)
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87.15.A-
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(Theory, modeling, and computer simulation)
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