Stretching and unzipping nucleic acid hairpins using a synthetic nanopore

Q. Zhao, J. Comer, V. Dimitrov, S. Yemenicioglu, A. Aksimentiev, G. Timp

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)1532-1541
Number of pages10
JournalNucleic acids research
Issue number5
StatePublished - Mar 2008

ASJC Scopus subject areas

  • Genetics


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