Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

Benedict E.K. Snodin, Ferdinando Randisi, Majid Mosayebi, Petr Šulc, John S. Schreck, Flavio Romano, Thomas E. Ouldridge, Roman Tsukanov, Eyal Nir, Ard A. Louis, Jonathan P.K. Doye

Research output: Contribution to journalArticlepeer-review

220 Scopus citations


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.

Original languageEnglish
Article number234901
JournalJournal of Chemical Physics
Issue number23
StatePublished - 21 Jun 2015

ASJC Scopus subject areas

  • General Physics and Astronomy
  • Physical and Theoretical Chemistry


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