Molecular Simulations of DNA Counterion Distributions

Authors

Alexander Lyubartsev Division of Physical Chemistry, Stockholm University

Publication Date

4/13/04

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Abstract

One of the remarkable physical properties of a DNA molecule is that it is a strongly charged polyelectrolyte. In solution, DNA dissociates, forming a negatively charged polyion surrounded by an atmosphere of mobile, positively charged counterions. Although positive counterions are attracted to DNA, they screen the negative charge of DNA, decreasing the attractive force for other positive counterions. Additionally, ions of different valency and size interact with DNA in a different manner, leading to effects of competition between ions of different species. There is always a delicate balance of forces forming the equilibrium ion distribution around DNA. The functionality of DNA in the cell is, in a decisive degree, determined by electrostatic forces, which in turn are dependent on the presence of different charged components in the surrounding solution. It is clear that understanding of DNA functionality is impossible without an understanding of electrostatic interactions of DNA with the environment.

The aim of the present review is to show how molecular computer simulations can contribute to our understanding of the basic features of the interaction of DNA with its ionic environment, what kind of information can be obtained by computer simulations, and how this information can be used to bridge experimental and theoretical studies of DNA. First, some common polyelectrolyte models of DNA will be briefly reviewed, and a survey of available computer simulation techniques will be given. Then, applications of computer simulations to describe the ionic environment of DNA on different levels of precision will be discussed: Monte Carlo (MC) and Brownian dynamics (BD) simulations within the continuum dielectric models, molecular dynamics (MD) simulations with explicit treatment of solvent, as well as a combination of these techniques, giving rise to the “multiscale modeling” approach.

Several reviews devoted to different aspects of DNA–ion interactions and computer simulations of DNA have recently appeared. A more general and detailed review of the computer simulation of polyelectrolytes is presented in Ref. .