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, and William P. Smith
Phys. Chem. Chem. Phys. 15, 20395-20414 (2013)
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.
The full paper is available from PCCP and arXiv.org.