TY - JOUR
T1 - Sequence-dependent thermodynamics of a coarse-grained DNA model
AU - Šulc, Petr
AU - Romano, Flavio
AU - Ouldridge, Thomas E.
AU - Rovigatti, Lorenzo
AU - Doye, Jonathan P.K.
AU - Louis, Ard A.
N1 - Funding Information:
The authors would like to thank Erik Winfree, Filip Lankaš, Felix Ritort, and Agnes Noy for helpful discussions. The authors also acknowledge financial support from the Engineering and Physical Sciences Research Council, University College (Oxford), and from the Oxford Supercomputing Centre for computer time. P.Š. is grateful for the award of a Scatcherd European Scholarship.
PY - 2012/10/7
Y1 - 2012/10/7
N2 - 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.
AB - 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.
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U2 - 10.1063/1.4754132
DO - 10.1063/1.4754132
M3 - Article
C2 - 23039613
AN - SCOPUS:84867508975
SN - 0021-9606
VL - 137
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
IS - 13
M1 - 135101
ER -