title: Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.
abstract: We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na(+)] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
authors.forename: Benedict E K
authors.initials: BE
authors.lastname: Snodin
authors.affiliation: Life Sciences Interface Doctoral Training Center, South Parks Road, Oxford OX1 3QU, United Kingdom.
authors.forename: Ferdinando
authors.initials: F
authors.lastname: Randisi
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
authors.forename: Majid
authors.initials: M
authors.lastname: Mosayebi
authors.affiliation: Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.
authors.forename: Petr
authors.initials: P
authors.lastname: Šulc
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
authors.forename: John S
authors.initials: JS
authors.lastname: Schreck
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
authors.forename: Flavio
authors.initials: F
authors.lastname: Romano
authors.affiliation: Department of Mathematics, Imperial College, 180 Queen's Gate, London SW7 2AZ, United Kingdom.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Ouldridge
authors.affiliation: Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel.
authors.forename: Roman
authors.initials: R
authors.lastname: Tsukanov
authors.affiliation: Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel.
authors.forename: Eyal
authors.initials: E
authors.lastname: Nir
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, United Kingdom.
authors.forename: Ard A
authors.initials: AA
authors.lastname: Louis
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
authors.forename: Jonathan P K
authors.initials: JP
authors.lastname: Doye
mesh_terms: D004247:DNA / Q000737:chemistry*; D004548:Elasticity; D031541:Fluorescence Resonance Energy Transfer; D008957:Models, Genetic; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012492:Salts / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics; D044366:Transition Temperature
chemical_list: D012492:Salts; D004247:DNA