Coarse-graining DNA for simulations of DNA nanotechnology

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

Research output: Contribution to journalReview article

86 Citations (Scopus)

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
Externally publishedYes

Fingerprint

nanotechnology
Nanotechnology
deoxyribonucleic acid
DNA
simulation
nucleotides
Self assembly
self assembly
Nucleotides

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., Sulc, P., Matek, C., ... 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

Coarse-graining DNA for simulations of DNA nanotechnology. / Doye, Jonathan P.K.; Ouldridge, Thomas E.; Louis, Ard A.; Romano, Flavio; Sulc, Petr; Matek, Christian; Snodin, Benedict E.K.; Rovigatti, Lorenzo; Schreck, John S.; Harrison, Ryan M.; Smith, William P.J.

In: Physical Chemistry Chemical Physics, Vol. 15, No. 47, 21.12.2013, p. 20395-20414.

Research output: Contribution to journalReview article

Doye, JPK, Ouldridge, TE, Louis, AA, Romano, F, Sulc, P, Matek, C, Snodin, BEK, Rovigatti, L, Schreck, JS, Harrison, RM & Smith, WPJ 2013, 'Coarse-graining DNA for simulations of DNA nanotechnology', Physical Chemistry Chemical Physics, vol. 15, no. 47, pp. 20395-20414. https://doi.org/10.1039/c3cp53545b
Doye JPK, Ouldridge TE, Louis AA, Romano F, Sulc P, Matek C et al. Coarse-graining DNA for simulations of DNA nanotechnology. Physical Chemistry Chemical Physics. 2013 Dec 21;15(47):20395-20414. https://doi.org/10.1039/c3cp53545b
Doye, Jonathan P.K. ; Ouldridge, Thomas E. ; Louis, Ard A. ; Romano, Flavio ; Sulc, Petr ; Matek, Christian ; Snodin, Benedict E.K. ; Rovigatti, Lorenzo ; Schreck, John S. ; Harrison, Ryan M. ; Smith, William P.J. / Coarse-graining DNA for simulations of DNA nanotechnology. In: Physical Chemistry Chemical Physics. 2013 ; Vol. 15, No. 47. pp. 20395-20414.
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