DNA nanotweezers studied with a coarse-grained model of DNA.
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.
Ouldridge
Thomas E
TE
Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford, OX1 3NP, United Kingdom.
Louis
Ard A
AA
Doye
Jonathan P K
JP
D000465:Algorithms; D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D006860:Hydrogen Bonding; D008956:Models, Chemical; D009010:Monte Carlo Method; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D018583:Pliability; D013816:Thermodynamics; D054159:Torsion, Mechanical
D004277:DNA, Single-Stranded; D004247:DNA