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Stretching and unzipping nucleic acid hairpins using a synthetic nanopore

Zhao, Q., Comer, J., Dimitrov, V., Yemenicioglu, S., Aksimentiev, A., Timp, G.
Nucleic acids research 2008 v.36 no.5 pp. 1532-1541
DNA, chemical elements, electric field, molecular dynamics, nanopores, silicon nitride
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.