1. Stretching and unzipping nucleic acid hairpins using a synthetic nanopore
- Author
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Jeffrey Comer, Qian Zhao, G. Timp, Sukru Yemenicioglu, V. Dimitrov, and Aleksei Aksimentiev
- Subjects
Models, Molecular ,Nanostructure ,02 engineering and technology ,Biology ,010402 general chemistry ,01 natural sciences ,Molecular dynamics ,chemistry.chemical_compound ,Structural Biology ,Electric field ,Genetics ,Molecule ,Protein secondary structure ,Silicon Compounds ,Electric Conductivity ,Biological Transport ,Membranes, Artificial ,DNA ,021001 nanoscience & nanotechnology ,Nanostructures ,0104 chemical sciences ,Threshold voltage ,Nanopore ,Biochemistry ,chemistry ,Biophysics ,Nucleic Acid Conformation ,0210 nano-technology - Abstract
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.
- Published
- 2008
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