Stretching and unzipping nucleic acid hairpins using a synthetic nanopore.
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.
Zhao
Q
Q
Beckman Institute, University of Illinois, Urbana, IL 61801, USA.
Comer
J
J
Dimitrov
V
V
Yemenicioglu
S
S
Aksimentiev
A
A
Timp
G
G
D001692:Biological Transport; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004553:Electric Conductivity; D008567:Membranes, Artificial; D008958:Models, Molecular; D049329:Nanostructures / Q000648:ultrastructure*; D009690:Nucleic Acid Conformation; D017655:Silicon Compounds / Q000737:chemistry
D008567:Membranes, Artificial; D017655:Silicon Compounds; D004247:DNA; C032734:silicon nitride