Martini Coarse-Grained Force Field: Extension to DNA

• Published in: Journal of chemical theory and computation Vol. 11; no. 8; pp. 3932 - 3945
• Main Authors: Uusitalo, Jaakko J, Ingólfsson, Helgi I, Akhshi, Parisa, Tieleman, D. Peter, Marrink, Siewert J
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 11-08-2015
• Subjects: Beads; Bonding; Compatibility; Computer simulation; Deoxyribonucleic acid; DNA - chemistry; DNA, Single-Stranded - chemistry; Hydrogen Bonding; Molecular Dynamics Simulation; Nucleic Acid Conformation; Nucleotides; Protein Binding; Proteins - chemistry; Proteins - metabolism; Solvents
• ISSN: 1549-9618; 1549-9626
• DOI: 10.1021/acs.jctc.5b00286

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.