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.

Acceleration of DNA melting kinetics using alternating electric fields

“…We hence examine the melting of the individual base pair and found that they melt sequentially, starting with one of the end base pairs. In agreement with previous simulations, 47,48 we observe that the speed of base-pair dissociation generally becomes larger and larger during the melting process (see Fig. 6).…”