Molecular dynamics simulation of multivalent ion mediated DNA attraction
Biological Physics
2009-11-13 v1 Chemical Physics
Abstract
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e. multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.
Cite
@article{arxiv.0801.3067,
title = {Molecular dynamics simulation of multivalent ion mediated DNA attraction},
author = {Liang Dai and Yuguang Mu and Lars Nordenskiold and Johan R. C. van der Maarel},
journal= {arXiv preprint arXiv:0801.3067},
year = {2009}
}
Comments
4 pages, 5 figures, to be published in Physical Review Letters