Sequence-dependent thermodynamics of a coarse-grained DNA model

Petr Šulc, Flavio Romano, Thomas E. Ouldridge, Lorenzo Rovigatti, Jonathan P.K. Doye, Ard A. Louis

Research output: Contribution to journalArticlepeer-review

240 Scopus citations


We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)]10.1063/1.3552946 originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands, and (e) the structure of a kissing-loop complex. Where possible, we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as a free software.

Original languageEnglish (US)
Article number135101
JournalJournal of Chemical Physics
Issue number13
StatePublished - Oct 7 2012
Externally publishedYes

ASJC Scopus subject areas

  • General Physics and Astronomy
  • Physical and Theoretical Chemistry


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