Sep 28, 2005
Squeezing DNA through nanopores
Researchers at the University of Illinois, US, have used an electric field to force molecules of DNA to move through a narrow pore. The technique might ultimately be able to probe the mechanical properties of DNA-protein assemblies.
"We are developing a solid-state device for recording sequences of single DNA molecules as they pass through a nanometre-diameter pore in a silicon membrane," researcher Aleksei Aksimentiev told nanotechweb.org. "The smaller the diameter of the pore, the more control we have over the conformations of DNA [inside the pore] and the better are our chances for reading the sequence of DNA nucleotides - the genetic code - of the molecules."
According to Aksimentiev, computer simulations suggested that applying a strong electric field would enable the researchers to push double-stranded DNA through a pore smaller than the diameter of the DNA molecules in solution. The team found that this was indeed the case - they forced double-stranded DNA through pores with a diameter of less than 2.5 nm. It appeared that the electric field was able to stretch out the DNA molecules, making them thinner.
The scientists carried out their tests in a membrane transport bicell with two compartments, each containing potassium-chloride electrolyte and an Ag/AgCl electrode. The team made nanopores in the 10 nm-thick silicon-nitride membrane separating the two compartments using an electron beam. The nanopores had diameters of 1-3 nm.
The team introduced molecules of double-stranded or single-stranded DNA in solution to the negative electrode, applied a voltage across the membrane and measured the current through the nanopore. Transport of DNA molecules through the pore temporarily blocked the electrolytic current. The scientists estimated that they were able to apply forces of 1-300 pN to the DNA as it travelled through the pores.
Molecular-dynamics simulations of the experiments showed that the threshold for permeation of double-stranded DNA through the pore depended on the radius of the pore and the applied transmembrane bias, a result that tied in with the experimental data.
"Potential applications could include a high-throughput technology for measuring forces between DNA and proteins in DNA-protein assemblies," said Aksimentiev. "By measuring the time it takes to strip the protein off the DNA [as it is forced through the pore] at different pulling forces, we should be able to infer the interaction energy between DNA and the protein." Aksimentiev believes that abnormalities in binding energies discovered in this way could indicate disease or suggest a target for treatment.
"Another area of application is high-throughput DNA sequencing," said Aksimentiev. "The fact that single DNA strands could fit into a 1 nm-diameter pore suggests a strong confinement of DNA bases. This, potentially, could help immobilize DNA in the nanopore for a time interval sufficient to measure the nucleotide type. But this is a long shot."
Now the researchers plan to record electrical signatures from DNA molecules passing through a nanopore in a multilayered silicon wafer. The aim is to understand the nanoscale processes taking place inside the pores.
The researchers reported their work in Nano Letters.
About the author
Liz Kalaugher is editor of nanotechweb.org.