Detection of local protein structures along DNA using solid-state nanopores

Nano Lett. 2010 Jan;10(1):324-8. doi: 10.1021/nl903631m.


Nanopores have been successfully employed as a new tool to rapidly detect single biopolymers, in particular DNA. When a molecule is driven through a nanopore by an externally applied electric field, it causes a characteristic temporary change in the trans-pore current. Here, we examine the translocation of DNA with discrete patches of the DNA-repair protein RecA attached along its length. Using the fact that RecA-coated DNA and bare DNA yield very different current-blockade signatures, we demonstrate that it is possible to map the locations of the proteins along the length of a single molecule using a solid-state nanopore. This is achieved at high speed and without any staining. We currently obtain a spatial resolution of about 8 nm, or 5 RecA proteins binding to 15 base pairs of DNA, and we discuss possible extensions to single protein resolution. The results are a crucial first step toward genomic screening, as they demonstrate the feasibility of reading off information along DNA at high resolution with a solid-state nanopore.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • Electrochemistry / methods
  • Microscopy, Atomic Force / methods
  • Microscopy, Electron, Transmission
  • Nanostructures / chemistry*
  • Nanotechnology / methods*
  • Nucleic Acid Conformation
  • Oxygen / chemistry
  • Polymers / chemistry
  • Porosity
  • Rec A Recombinases / chemistry
  • Surface Properties


  • Polymers
  • DNA
  • Rec A Recombinases
  • Oxygen