期刊
JOURNAL OF CHEMICAL PHYSICS
卷 137, 期 13, 页码 -出版社
AIP Publishing
DOI: 10.1063/1.4754132
关键词
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资金
- Engineering and Physical Sciences Research Council
- Scatcherd European Scholarship
- University College (Oxford)
- Engineering and Physical Sciences Research Council [EP/I001352/1] Funding Source: researchfish
- EPSRC [EP/I001352/1] Funding Source: UKRI
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. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4754132]
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