Sep 17, 2003
Nanopore ‘microscope’ spies on DNA
Scientists from Harvard University, US, have examined the properties of single DNA molecules using a solid-state nanopore membrane. Ultimately, the technique could provide rapid DNA sequencing.
To carry out the procedure, Jene Golovchenko and colleagues used ion-beam sculpting to create 3 or 10 nm pores in a 5-10 nm thick silicon nitride membrane. Then they positioned the membrane between two chambers containing conducting electrolyte solution and applied a 120 mV bias across the nanopore to set up open-pore ionic conduction. Adding dsDNA to the negatively charged chamber resulted in momentary reductions in current flow as individual DNA molecules moved through the pore. The expected current blockage for a single molecule is linearly dependent on the cross-sectional area of the molecule.
For the 3 nm pore, all the current blockage events appeared relatively straightforward. In contrast, around 40% of the blockages for the 10 nm pore showed more complex patterns, an observation that the researchers attributed to folding of the molecules. The DNA molecules were about 2 nm wide, and so were unable to pass through the 3 nm pore whilst folded.
Although earlier studies have used biopore detectors, solid-state nanopores have the advantage that scientists can choose their diameters, enabling the study of molecules such as RNA, hybridized DNA and proteins. Solid-state nanopores are also more physically robust, and could be used at high or low temperatures and under voltage and pH conditions that would destroy biopore-membrane systems.
According to the researchers, who reported their work in Nature Materials, the solid-state pores provide a new way of studying the folding and pairing configurations of single long-chain molecules, the differences between chemically identical molecules in a statistical ensemble, and induced changes in molecular structure.
Now the scientists plan to add electrical contacts to the nanopores, a feature that should enable techniques such as electronic tunnelling and near-field optical studies of molecules as they pass through the nanopore. Such local single-molecule spectroscopy could increase longitudinal resolution, perhaps even up to the single-base level for DNA, allowing extremely rapid sequencing of long molecules.
About the author
Liz Kalaugher is editor of nanotechweb.org.