title: The effect of salt concentration on DNA conformation transition: a molecular-dynamics study.
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: see text].
authors.affiliation: School of Physics and Microelectronics, Shandong University, Jinan, Shandong, 250100, China. sc3210@gmail.com
authors.forename: Chen
authors.initials: C
authors.lastname: Song
authors.forename: Yueyuan
authors.initials: Y
authors.lastname: Xia
authors.forename: Mingwen
authors.initials: M
authors.lastname: Zhao
authors.forename: Xiangdong
authors.initials: X
authors.lastname: Liu
authors.forename: Feng
authors.initials: F
authors.lastname: Li
authors.forename: Yanju
authors.initials: Y
authors.lastname: Ji
authors.forename: Boda
authors.initials: B
authors.lastname: Huang
authors.forename: Yanyan
authors.initials: Y
authors.lastname: Yin
mesh_terms: D002241:Carbohydrates / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012965:Sodium Chloride / Q000494:pharmacology*
chemical_list: D002241:Carbohydrates; D012965:Sodium Chloride; D004247:DNA