A coarse-grained DNA model for the prediction of current signals in DNA translocation experiments

J Chem Phys. 2016 Nov 21;145(19):194106. doi: 10.1063/1.4967458.

Abstract

We present an implicit solvent coarse-grained double-stranded DNA (dsDNA) model confined to an infinite cylindrical pore that reproduces the experimentally observed current modulations of a KaCl solution at various concentrations. Our model extends previous coarse-grained and mean-field approaches by incorporating a position dependent friction term on the ions, which Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] identified as an essential ingredient to correctly reproduce the experimental data of Smeets et al. [Nano Lett. 6, 89 (2006)]. Our approach reduces the computational effort by orders of magnitude compared with all-atom simulations and serves as a promising starting point for modeling the entire translocation process of dsDNA. We achieve a consistent description of the system's electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.

MeSH terms

  • Base Pairing
  • DNA / chemistry*
  • DNA / metabolism*
  • Kinetics
  • Molecular Dynamics Simulation*
  • Movement / drug effects
  • Potassium Chloride / pharmacology
  • Reproducibility of Results
  • Solvents / chemistry

Substances

  • Solvents
  • Potassium Chloride
  • DNA