Sizing DNA using a nanometer-diameter pore

Jiunn B. Heng, Chuen Ho, Taekyung Kim, Rolf Timp, Aleksei Aksimentiev, Yelena V. Grinkova, S Sligar, Klaus Schulten, and Gregory Timp
Biophys J 87(4) 2905-11 (2004)
DOI:10.1529/biophysj.104.041814  PMID:15326034  BibTex

Each species from bacteria to human has a distinct genetic fingerprint. Therefore, a mechanism that detects a single molecule of DNA represents the ultimate analytical tool. As a first step in the development of such a tool, we have explored using a nanometer-diameter pore, sputtered in a nanometer-thick inorganic membrane with a tightly focused electron beam, as a transducer that detects single molecules of DNA and produces an electrical signature of the structure. When an electric field is applied across the membrane, a DNA molecule immersed in electrolyte is attracted to the pore, blocks the current through it, and eventually translocates across the membrane as verified unequivocally by gel electrophoresis. The relationship between DNA translocation and blocking current has been established through molecular dynamics simulations. By measuring the duration and magnitude of the blocking current transient, we can discriminate single-stranded from double-stranded DNA and resolve the length of the polymer.