The effect of salt concentration on DNA conformation transition: a molecular-dynamics study |
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Authors: | Chen Song Yueyuan Xia Mingwen Zhao Xiangdong Liu Feng Li Yanju Ji Boda Huang Yanyan Yin |
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Institution: | (1) School of Physics and Microelectronics, Shandong University, Jinan, Shandong, 250100, China;(2) School of Information Science and Engineering, Shandong University, Jinan, Shandong, 250100, China |
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Abstract: | We performed three 3-ns molecular dynamics simulations of d(CGCGAATTCGCG)2 using the AMBER 8 package to determine the effect of salt concentration on DNA conformational transitions. All the simulations
were started with A-DNA, with different salt concentrations, and converged with B-DNA with similar conformational parameters.
However, the dynamic processes of the three MD simulations were very different. We found that the conformation transition
was slow in the solution with higher salt concentration. To determine the cause of this retardation, we performed three additional
1.5-ns simulations starting with B-DNA and with the salt concentrations corresponding to the simulations mentioned above.
However, astonishingly, there was no delayed conformation evolution found in any of the three simulations. Thus, our simulation
conclusion is that higher salt concentrations slows the A → B conformation transition, but have no effect on the final stable
structure.
Figure A-DNA and B-DNA. (a) is the canonical A-DNA, and (b) is the canonical B-DNA. Looking from the central major groove |
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Keywords: | DNA conformation transition Molecular dynamics simulation Salt concentration Sugar pucker Minor groove width |
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