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 computationa l studies of the ion atmosphere of DNA as related to issues of both st ructure and function. Manning's elementary yet elegant concept of ''co unterion condensation'' is revisited and shown to be well supported by current state-of-the-art molecular simulations. Studies of the ion at mosphere problem based on continuum electrostatics, integral equation methods, Monte Carlo simulation, molecular dynamics, and Brownian dyna mics are considered. Grand canonical Monte Carlo and non-linear Poisso n Boltzmann studies have recently focussed on the determination and si gnificance of the index of non-ideality in solution known as the ''pre ferential interaction coefficient,'' for which the relevant current li terature is cited. The review concludes with a survey of applications to ligand binding problems involving drug-DNA and protein-DNA interact ions.