We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural properties of DNA: the helical pitch, persistence length and torsional stiffness of double-stranded molecules, as well as the comparative flexibility of unstacked single strands. We apply the model to calculate the detailed free-energy landscape of one full cycle of DNA 'tweezers', a simple machine driven by hybridization and strand displacement.
@article{arxiv.0911.0555,
title = {DNA nanotweezers studied with a coarse-grained model of DNA},
author = {Thomas E. Ouldridge and Ard A. Louis and Jonathan P. K. Doye},
journal= {arXiv preprint arXiv:0911.0555},
year = {2010}
}