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    Research Article|October 01 2012

    Sequence-dependent thermodynamics of a coarse-grained DNA model

    Petr Šulc;
    Petr Šulc
    1Rudolf Peierls Centre for Theoretical Physics,
    University of Oxford
    , 1 Keble Road, Oxford, OX1 3NP,
    United Kingdom
    Search for other works by this author on:
    Flavio Romano;
    Flavio Romano
    2Physical and Theoretical Chemistry Laboratory, Department of Chemistry,
    University of Oxford
    , South Parks Road, Oxford, OX1 3QZ,
    United Kingdom
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    Thomas E. Ouldridge;
    Thomas E. Ouldridge
    1Rudolf Peierls Centre for Theoretical Physics,
    University of Oxford
    , 1 Keble Road, Oxford, OX1 3NP,
    United Kingdom
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    Lorenzo Rovigatti;
    Lorenzo Rovigatti
    3Dipartimento di Fisica,
    Sapienza–Università di Roma
    , Piazzale A. Moro 5, 00185 Roma,
    Italy
    Search for other works by this author on:
    Jonathan P. K. Doye;
    Jonathan P. K. Doye
    2Physical and Theoretical Chemistry Laboratory, Department of Chemistry,
    University of Oxford
    , South Parks Road, Oxford, OX1 3QZ,
    United Kingdom
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    Ard A. Louis
    Ard A. Louis
    1Rudolf Peierls Centre for Theoretical Physics,
    University of Oxford
    , 1 Keble Road, Oxford, OX1 3NP,
    United Kingdom
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    Crossmark: Check for Updates
    J. Chem. Phys. 137, 135101 (2012)
    Article history
    Received:
    July 15 2012
    Accepted:
    August 28 2012
    Citation

    Petr Šulc,Flavio Romano,Thomas E. Ouldridge,Lorenzo Rovigatti,Jonathan P. K. Doye,Ard A. Louis; Sequence-dependent thermodynamics of a coarse-grained DNA model.J. Chem. Phys. 7 October 2012; 137 (13): 135101.https://doi.org/10.1063/1.4754132

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      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)] https://doi.org/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.

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      © 2012 American Institute of Physics.
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