title: Melting dynamics of short dsDNA chains in saline solutions.
abstract: DNA melting has attracted much attention due to its importance in understanding the life-reproduction and metabolism and in the applications of modern DNA-based technologies. While numerous works have been contributed to the determination of melting profiles in diverse environments, the understanding of DNA melting dynamics is still limited. By employing three-site-per-nucleotide (3SPN) double-stranded DNA (dsDNA) model, we here demonstrate the melting dynamics of an isolated short dsDNA under different conditions (different temperatures, ionic concentrations and DNA chain lengths) can be accessed by coarse-grained simulation studies. We particularly show that at dilute ionic concentration the dsDNA, regardless being symmetric or asymmetric, opens at both ends with roughly equal probabilities, while at high ionic concentration the asymmetric dsDNA chain opens at the A-T-rich end. The comparisons of our simulation results to available data are discussed, and overall good agreements have been found.
authors.affiliation: State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237 China.
authors.forename: Yichen
authors.initials: Y
authors.lastname: He
authors.affiliation: State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237 China.
authors.forename: Yazhuo
authors.initials: Y
authors.lastname: Shang
authors.affiliation: State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237 China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237 China.
authors.forename: Shuangliang
authors.initials: S
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237 China.
authors.forename: Honglai
authors.initials: H
authors.lastname: Liu
keywords: DNA; Ionic concentration; Melting dynamics; Molecular simulation