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

Journal article

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.

Authors: Ouldridge, T; Louis, A; Doye, J

• Journal: Physical Review Letters
• Volume: 104
• Issue: 17
• Pages: 178101
• Publication date: 2010-04-01
• DOI: 10.1103/physrevlett.104.178101
• EISSN: 1079-7114
• ISSN: 0031-9007
• Language: English
• Keywords: Nucleic Acid Conformation; Algorithms; Hydrogen Bonding; DNA; Pliability; Nanostructures; Monte Carlo Method; DNA, Single-Stranded; Models, Chemical; Thermodynamics; Base Pairing; Torsion, Mechanical; Nucleic Acid Hybridization