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.
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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Acknowledgements
This work was supported by the National Natural Science Foundation of China under Grant No. 90203013, and supported by the Education Ministry of China under Grant No. 20020422012. We thank David. A. Case and the AMBER group for making the AMBER 8 package available to us.
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Song, C., Xia, Y., Zhao, M. et al. The effect of salt concentration on DNA conformation transition: a molecular-dynamics study. J Mol Model 12, 249–254 (2006). https://doi.org/10.1007/s00894-005-0023-9
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DOI: https://doi.org/10.1007/s00894-005-0023-9