The effect of nucleic acid geometry on counterion association

The very high axial charge density of nucleic acids is a physical characteristic that substantially influences the thermodynamics of virtually all processes in which they are involved. This arises from long range electrostatic interacts between nucleic acids and the counter- and co-ions in solution so that salt concentration dramatically effects the activities of both reactants and products. A significant contributor to the resulting salt dependence for processes involving nucleic acids (e.g. ligand binding to a choice of nucleic acid substrates or a structural change), is the difference in arrangement of the sugar-phosphate backbone of competing structures. This article reviews the results of a set of Grand Canonical Monte Carlo (GCMC) simulations that explores the effect of nucleic acid geometry, varied as a function of oligomer length and four-way junction branch length, on counterion association and therefore many nucleic acid processes. These GCMC simulations, which utilize a "primitive" model description of the nucleic acid, are complemented by a number of simulations which numerically solve the non-linear Poisson-Boltzmann equation utilizing detailed models for nucleic acids and proteins. Simulations of this kind are particularly useful for the study of systems that have been well characterized structurally, as well as thermodynamically. What is sought in the current article is insight into how an extremely general feature of DNA, namely the geometric arrangement of its phosphate charges surrounded by an exclusion surface, might play a role in determining nucleic acid processes.