title: Sequence-dependent thermodynamics of a coarse-grained DNA model.
abstract: 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)] 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.
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, United Kingdom.
authors.forename: Petr
authors.initials: P
authors.lastname: Šulc
authors.forename: Flavio
authors.initials: F
authors.lastname: Romano
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Ouldridge
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Rovigatti
authors.forename: Jonathan P K
authors.initials: JP
authors.lastname: Doye
authors.forename: Ard A
authors.initials: AA
authors.lastname: Louis
mesh_terms: D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D013816:Thermodynamics
chemical_list: D004247:DNA