Molecular dynamics applied to nucleic acids

Abstract

In this Account, we focus on molecular dynamics (MD) simulations involving fully solvated nucleic acids. Historically, MD simulations were first applied to proteins and several years later to nucleic acids. The first MD simulations of DNA were carried out in vacuo, but nowadays fully solvated systems are common practice. Recently, technical improvements have made it possible to conduct accurate MD simulations of highly charged nucleic acids. The state-of-the-art of MD simulations and a number of applications on various nucleic acid systems are discussed.