Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore

Nano Lett. 2009 Dec;9(12):4441-5. doi: 10.1021/nl9027318.


Using solid-state nanopores with optical tweezers, we perform force spectroscopy on DNA molecules that are coated with RecA proteins. We observe that the electrophoretic force is 2-4 times larger for RecA-DNA filaments than for uncoated DNA molecules and that this force increases at lower salt concentrations. The data demonstrate the efficacy of solid-state nanopores for locally probing the forces on DNA-bound proteins. Our results are described quantitatively by a model that treats the electrophoretic and hydrodynamic forces. The conductance steps that occur when RecA-DNA enters the nanopore change from conductance decreases at high salt to conductance increases at low salt, which allows the apparent charge of the RecA-DNA filament to be extracted. The combination of conductance measurements with local force spectroscopy increases the potential for future solid-state nanopore screening devices.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • DNA / chemistry*
  • DNA / ultrastructure*
  • Electrochemistry / methods*
  • Electrophoresis / methods*
  • Microscopy, Atomic Force / methods*
  • Models, Chemical*
  • Models, Molecular
  • Protein Binding
  • Rec A Recombinases / chemistry*
  • Rec A Recombinases / ultrastructure
  • Semiconductors
  • Stress, Mechanical


  • DNA
  • Rec A Recombinases