By Monica Heger
Carbon nanotubes could serve as the nanopore in nanopore sequencing, researchers from Arizona State University reported in Science earlier this month.
The team demonstrated for the first time that single-stranded DNA can translocate through a single-walled carbon nanotube. In the process, they found that the properties of the tubes could make them a useful device for single-molecule sequencing because they slow the rate of translocation to a speed where reading the sequence may actually be possible.
Stuart Lindsay, director of Arizona State's Center for Single Molecule Biophysics at the Biodesign Institute, and his colleagues designed a device that ran a carbon nanotube between two fluid reservoirs, one of which contained single-stranded DNA. When an electric field was applied, the DNA passed through the carbon nanotube, producing current.
Eventually, Lindsay said, he wants to pair this method for translocating DNA with a method he is developing that can read the resulting current. Previously, he thought that four different readers would be needed (see In Sequence 3/31/2009) — one for each base — but now, he said, the goal is to have one readout that detects the different voltage spikes produced by each base.
Lindsay and his colleagues made carbon nanotubes that were between one and two nanometers in diameter. "We pursued carbon nanotubes because they are simultaneously both a good electrode and a nanopore," said Lindsay.
The nanotube spanned two fluid reservoirs and lay over an electrode at either end of the tube. The nanotube was also surrounded by a layer of water, which Lindsay said was key to coaxing the hydrophilic DNA into the hydrophobic tube. When an electric field was applied, the DNA passed through the tube, producing a current pulse.
Oddly, some of these pulses were much higher than Lindsay expected. "What we saw was an incredible current spike," he said. The large current could be due to the metallic nature of the carbon nanotubes and the water surrounding them, which would produce an electro-osmotic effect, driving ions through the nanotube, he explained.
The team then used PCR to verify that the carbon nanotubes showing the exceptionally large current spikes were actually translocating the DNA. "The number of spikes corresponded to the amount of DNA that went through," Lindsay said.
The carbon nanotubes demonstrated some other interesting properties that could make them especially useful for single-molecule sequencing. One problem that has hindered nanopore sequencing is that the rate of translocation is so fast that it is difficult to accurately read the sequence, but in this study, the DNA translocated through the nanotubes much slower than it typically passes through a nanopore, said Amit Meller, a physicist at Boston University who is working on an unrelated nanopore sequencing method.
The single-stranded DNA took around tens of milliseconds to thread through the tube, compared to just hundreds of microseconds that it takes to pass through a nanopore. Meller attributed the slower time to the length of the nanotube.
"In nanopores, the 'length' of the pore is about twice its diameter, but in the carbon tubes, it is roughly 1,000 [times its diameter]," he said. "[The DNA] has to pass this long length, and it has a lot of friction, so the average speed is much slower," he said. "They slow it down to the point where if someone were to use it for future devices for DNA sequencing, it would provide more time to interrogate the molecules."
Aside from a slower rate of translocation, the carbon nanotubes allow for even greater control over the translocation. Lindsay said that translocation can be stopped by simply removing the electric field. In nanopores, when the electric field is removed, the DNA diffuses through the nanopore within milliseconds, he said. But, in his device, when he removed the electric field, the DNA stayed put in the nanotube. "The DNA is in a cave," Lindsay said. "When you remove the electric field, it just sits there."
The next step is to couple this method of translocation with a method to read the bases. One approach that Lindsay is looking at involves using lithography to cut a gap in the portion of the carbon nanotube that lies between the two electrodes. Then, as the DNA passes through the tube from one reservoir to another, it would pass over that gap, and the current would tunnel out so that it can be read. Each base would produce a slightly different current. The tricky part, he said, is making a precise and accurate enough gap.
Lindsay said that he is not presently working with any industry partners, but that Arizona State has filed a number of patents based on the technique.