title: Martini Coarse-Grained Force Field: Extension to DNA.
abstract: We systematically parameterized a coarse-grained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nucleobases between polar and nonpolar solvents as well as base-base potential of mean force calculations. The bonded interactions are fit to single-stranded DNA (ssDNA) atomistic simulations and an elastic network is used to retain double-stranded DNA (dsDNA) and other specific DNA conformations. We present the implementation of the Martini DNA model and demonstrate the properties of individual bases, ssDNA as well as dsDNA, and DNA-protein complexes. The model opens up large-scale simulations of DNA interacting with a wide range of other (bio)molecules that are available within the Martini framework.
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Jaakko J
authors.initials: JJ
authors.lastname: Uusitalo
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Helgi I
authors.initials: HI
authors.lastname: Ingólfsson
authors.affiliation: Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4.
authors.forename: Parisa
authors.initials: P
authors.lastname: Akhshi
authors.affiliation: Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4.
authors.forename: D Peter
authors.initials: DP
authors.lastname: Tieleman
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Siewert J
authors.initials: SJ
authors.lastname: Marrink
mesh_terms: D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D004277:DNA, Single-Stranded; D011506:Proteins; D004247:DNA