Coarse-graining DNA for simulations of DNA nanotechnology

Jonathan P.K. Doye, Thomas E. Ouldridge, Ard A. Louis, Flavio Romano, Petr Šulc, Christian Matek, Benedict E.K. Snodin, Lorenzo Rovigatti, John S. Schreck, Ryan M. Harrison, William P.J. Smith

Research output: Contribution to journalReview article

90 Scopus citations

Abstract

To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse-graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

Original languageEnglish (US)
Pages (from-to)20395-20414
Number of pages20
JournalPhysical Chemistry Chemical Physics
Volume15
Issue number47
DOIs
StatePublished - Dec 21 2013

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ASJC Scopus subject areas

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

Cite this

Doye, J. P. K., Ouldridge, T. E., Louis, A. A., Romano, F., Šulc, P., Matek, C., Snodin, B. E. K., Rovigatti, L., Schreck, J. S., Harrison, R. M., & Smith, W. P. J. (2013). Coarse-graining DNA for simulations of DNA nanotechnology. Physical Chemistry Chemical Physics, 15(47), 20395-20414. https://doi.org/10.1039/c3cp53545b