The atomistic simulation of DNA

Abstract

We review the current state of the art relating to the atomistic simulation of the structure and dynamics of DNA. We begin with a brief historical overview to set the scene and introduce some of the key issues that had to be addressed to progress the field and then we divide our discussion of the current situation into two sections. First, we overview the role that simulation has played, closely intertwined with experimental studies, in increasing our understanding of the biomechanical properties of DNA, for example, the way in which its structure responds to perturbations such as stretching and over- and under-twisting. Second, we discuss how atomistic simulations are contributing to our deeper understanding of nucleic acid recognition-both by proteins and by small-molecule ligands. In both areas, we emphasize not only where simulation has been particularly successful but also where thorny problems remain to tax the ingenuity of computational scientists in close collaboration with their experimental colleagues. © 2011 John Wiley & Sons, Ltd.