Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson-Boltzmann approach.

ABSTRACT: The ion atmosphere created by monovalent (Na(+) ) or divalent (Mg(2+) ) cations surrounding a B-form DNA duplex were examined using atomistic molecular dynamics (MD) simulations and the nonlinear Poisson-Boltzmann (PB) equation. The ion distributions predicted by the two methods were compared using plots of radial and two-dimensional cation concentrations and by calculating the total number of cations and net solution charge surrounding the DNA. Na(+) ion distributions near the DNA were more diffuse in PB calculations than in corresponding MD simulations, with PB calculations predicting lower concentrations near DNA groove sites and phosphate groups and a higher concentration in the region between these locations. Other than this difference, the Na(+) distributions generated by the two met

SUBMITTER: Robbins TJ 

PROVIDER: S-EPMC4102171 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature