title: A coarse-grain three-site-per-nucleotide model for DNA with explicit ions.
abstract: The "three sites per nucleotide" (3SPN) model provides a coarse-grained representation of nucleic acids for simulation of molecular processes. Previously, this model has relied on an implicit representation of the surrounding ionic environment at the level of Debye-Hückel theory. In this work, we eliminate this limitation and present an explicit representation of ions, both monovalent and divalent. The coarse-grain ion-ion and ion-phosphate potential energy functions are inferred from all-atom simulations and parameterized to reproduce key features of the local structure and organization of ions in bulk water and in the presence of DNA. The resulting model, 3SPN.1-I, is capable of reproducing the local structure observed in detailed atomistic simulations, as well as the experimental melting temperature of DNA for a range of DNA oligonucleotide lengths, CG-content, Na(+) concentration, and Mg(2+) concentration.
authors: Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors: Gordon S
authors: GS
authors: Freeman
authors: Daniel M
authors: DM
authors: Hinckley
authors: Juan J
authors: JJ
authors: de Pablo
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D007477:Ions / Q000737:chemistry*; D008954:Models, Biological; D008956:Models, Chemical; D009691:Nucleic Acid Denaturation; D009711:Nucleotides / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D007477:Ions; D009711:Nucleotides; D014867:Water; D004247:DNA