Sequence-dependent thermodynamics of a coarse-grained DNA model

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

Research output: Contribution to journalArticle

113 Citations (Scopus)

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)]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
Volume137
Issue number13
DOIs
StatePublished - Oct 7 2012
Externally publishedYes

Fingerprint

Melting point
deoxyribonucleic acid
melting
Thermodynamics
strands
thermodynamics
DNA
histograms
melting points
temperature
flexibility
tendencies
computer programs
Molecules
molecules
simulation
interactions

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Sulc, P., Romano, F., Ouldridge, T. E., Rovigatti, L., Doye, J. P. K., & Louis, A. A. (2012). Sequence-dependent thermodynamics of a coarse-grained DNA model. Journal of Chemical Physics, 137(13), [135101]. https://doi.org/10.1063/1.4754132

Sequence-dependent thermodynamics of a coarse-grained DNA model. / Sulc, Petr; Romano, Flavio; Ouldridge, Thomas E.; Rovigatti, Lorenzo; Doye, Jonathan P.K.; Louis, Ard A.

In: Journal of Chemical Physics, Vol. 137, No. 13, 135101, 07.10.2012.

Research output: Contribution to journalArticle

Sulc, P, Romano, F, Ouldridge, TE, Rovigatti, L, Doye, JPK & Louis, AA 2012, 'Sequence-dependent thermodynamics of a coarse-grained DNA model', Journal of Chemical Physics, vol. 137, no. 13, 135101. https://doi.org/10.1063/1.4754132
Sulc P, Romano F, Ouldridge TE, Rovigatti L, Doye JPK, Louis AA. Sequence-dependent thermodynamics of a coarse-grained DNA model. Journal of Chemical Physics. 2012 Oct 7;137(13). 135101. https://doi.org/10.1063/1.4754132
Sulc, Petr ; Romano, Flavio ; Ouldridge, Thomas E. ; Rovigatti, Lorenzo ; Doye, Jonathan P.K. ; Louis, Ard A. / Sequence-dependent thermodynamics of a coarse-grained DNA model. In: Journal of Chemical Physics. 2012 ; Vol. 137, No. 13.
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