Modeling DNA in aqueous solutions: theoretical and computer simulation studies on the ion atmosphere of DNA

This article provides a review of current theoretical and computational studies of the ion atmosphere of DNA as related to issues of both structure and function. Manning's elementary yet elegant concept of "counterion condensation" is revisited and shown to be well supported by current state-of-the-art molecular simulations. Studies of the ion atmosphere problem based on continuum electrostatics, integral equation methods, Monte Carlo simulation, molecular dynamics, and Brownian dynamics are considered. Grand canonical Monte Carlo and non-linear Poisson Boltzmann studies have recently focussed on the determination and significance of the index of non-ideality in solution known as the "preferential interaction coefficient," for which the relevant current literature is cited. The review concludes with a survey of applications to ligand binding problems involving drug-DNA and protein-DNA interactions.