title: A coarse grain model for DNA.
abstract: Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using thermal denaturation experimental data at a fixed salt concentration. The validity of the model is established by its ability to predict several aspects of DNA behavior, including salt-dependent melting, bubble formation and rehybridization, and the mechanical properties of the molecule as a function of salt concentration.
authors.affiliation: Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, USA. thomas.knotts@byu.edu
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Knotts
authors.forename: Nitin
authors.initials: N
authors.lastname: Rathore
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
authors.forename: Juan J
authors.initials: JJ
authors.lastname: de Pablo
mesh_terms: D020029:Base Pairing; D002241:Carbohydrates / Q000737:chemistry*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009711:Nucleotides / Q000737:chemistry*; D010755:Organophosphates / Q000737:chemistry; D012492:Salts / Q000737:chemistry
chemical_list: D002241:Carbohydrates; D009711:Nucleotides; D010755:Organophosphates; D012492:Salts; D004247:DNA