DNA nanotweezers studied with a coarse-grained model of DNA

Details DNA nanotweezers studied with a coarse-grained model of DNA DNA nanotweezers studied with a coarse-grained model of DNA

2009-11-03

arxiv.org/abs/0911.0555v1

Phys. Rev. Lett. 104, 178101 (2010)

Physics

Condensed Matter

Soft Condensed Matter

4 pages, 5 figures

Scientific paper

10.1103/PhysRevLett.104.178101

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.

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