Stretching and unzipping nucleic acid hairpins using a synthetic nanopore

Q Zhao, Jeffrey Comer, Valentin Dimitrov, S Yemenicioglu, Aleksei Aksimentiev, and Gregory Timp
Nucleic Acids Res 36(5) 1532-41 (2008)
DOI:10.1093/nar/gkm1017  PMID:18208842  BibTex

We have explored the electromechanical properties of DNA by using an electric field to force single hairpin molecules to translocate through a synthetic pore in a silicon nitride membrane. We observe a threshold voltage for translocation of the hairpin through the pore that depends sensitively on the diameter and the secondary structure of the DNA. The threshold for a diameter 1.5 < d < 2.3 nm is V > 1.5 V, which corresponds to the force required to stretch the stem of the hairpin, according to molecular dynamics simulations. On the other hand, for 1.0 < d < 1.5 nm, the threshold voltage collapses to V < 0.5 V because the stem unzips with a lower force than required for stretching. The data indicate that a synthetic nanopore can be used like a molecular gate to discriminate between the secondary structures in DNA.