DNA nanotweezers studied with a coarse-grained model of DNA

Phys Rev Lett. 2010 Apr 30;104(17):178101. doi: 10.1103/PhysRevLett.104.178101. Epub 2010 Apr 26.

Abstract

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.

MeSH terms

  • Algorithms
  • Base Pairing
  • DNA / chemistry*
  • DNA, Single-Stranded / chemistry
  • Hydrogen Bonding
  • Models, Chemical*
  • Monte Carlo Method
  • Nanostructures / chemistry*
  • Nucleic Acid Conformation*
  • Nucleic Acid Hybridization
  • Pliability
  • Thermodynamics
  • Torsion, Mechanical

Substances

  • DNA, Single-Stranded
  • DNA