Molecular dynamics applied to nucleic acids.
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.
Norberg
Jan
J
Center for Structural Biochemistry, Department of Biosciences at Novum Karolinska Institutet, S-141 57 Huddinge, Sweden. Jan.Norberg@biosci.ki.se
Nilsson
Lennart
L
D003198:Computer Simulation; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D020135:Peptide Nucleic Acids / Q000737:chemistry; D012995:Solubility
D009696:Nucleic Acids; D020135:Peptide Nucleic Acids