title: Adaptive resolution simulation of oligonucleotides.
abstract: Nucleic acids are characterized by a complex hierarchical structure and a variety of interaction mechanisms with other molecules. These features suggest the need of multiscale simulation methods in order to grasp the relevant physical properties of deoxyribonucleic acid (DNA) and RNA using in silico experiments. Here we report an implementation of a dual-resolution modeling of a DNA oligonucleotide in physiological conditions; in the presented setup only the nucleotide molecule and the solvent and ions in its proximity are described at the atomistic level; in contrast, the water molecules and ions far from the DNA are represented as computationally less expensive coarse-grained particles. Through the analysis of several structural and dynamical parameters, we show that this setup reliably reproduces the physical properties of the DNA molecule as observed in reference atomistic simulations. These results represent a first step towards a realistic multiscale modeling of nucleic acids and provide a quantitatively solid ground for their simulation using dual-resolution methods.
authors.affiliation: Departamento de Físico-Química, Instituto de Química, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil.
authors.forename: Paulo A
authors.initials: PA
authors.lastname: Netz
authors.affiliation: Max Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany.
authors.forename: Raffaello
authors.initials: R
authors.lastname: Potestio
authors.affiliation: Max Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany.
authors.forename: Kurt
authors.initials: K
authors.lastname: Kremer
mesh_terms: D000465:Algorithms; D002712:Chlorides / Q000378:metabolism; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism*; D006860:Hydrogen Bonding; D007477:Ions / Q000378:metabolism; D008958:Models, Molecular; D009841:Oligonucleotides / Q000378:metabolism*; D012964:Sodium / Q000378:metabolism; D012997:Solvents / Q000378:metabolism; D055672:Static Electricity; D014867:Water / Q000378:metabolism
chemical_list: D002712:Chlorides; D007477:Ions; D009841:Oligonucleotides; D012997:Solvents; D014867:Water; D004247:DNA; D012964:Sodium