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Sticky DNA

But sensors with nanoscale features can only succeed if they are “sticky” enough to grab onto molecules of interest. Northwestern’s Mirkin sees value in gold: specifically, nanoscale gold particles, to which he affixes multiple fragments of DNA that can latch onto DNA targets. Each gold particle becomes “like Velcro,” he says. In the next 18 months, Mirkin says, he and his colleagues will build a simple, doctor’s-office diagnostic device capable of instantly diagnosing diseases or predispositions to disease, depending on what DNA fragments are used on the device. “Chips will be built for panels of diseases,” says Mirkin, including sexually transmitted diseases, cystic fibrosis and genetic predispositions to colon cancer and blood hypercoagulation (blood that clots excessively).

Mirkin’s prototype chip, under development by Northbrook, IL-based Nanosphere, a company he cofounded, uses DNA deposited between electrodes on a microchip to recognize targets of interest. A sample is mixed with those “Velcro” gold particles and washed over the chip. If the sample contains the targeted DNA-say, genetic material from the syphilis bacterium-the DNA will bind to those sticky gold particles and then to the DNA fragments between the electrodes. The gold particles close the circuit and produce a detectable signal. The more electrode sensing elements per chip, the more diseases-or genetic predispositions-can be detected.

Mirkin’s group is adapting a process known as dip-pen nanolithography to gain the ability to literally “print” DNA molecules between electrodes just 200 nanometers apart. Mirkin hopes to pack hundreds, even thousands, of electrode sensing elements on one chip.

Printing Molecules
In dip-pen nanolithography, molecules are printed directly on a chip surface.
Arrays of cantilevers (above) deposit millions, even billions, of different molecules on a surface; in cases where the printed molecules bind to specific genes or proteins, the chip can be used to diagnose diseases or discover drugs. Each cantilever, or “pen,” has a silicon tip (left) just a few atoms wide at its end. As the tip moves laterally, molecules attached to its sides are drawn down to the surface by a water meniscus that forms under the tip. The vertical motion of each cantilever is controlled thermally, allowing individual pens to start and stop printing.

Mirkin’s technology can find specifically targeted DNA in a sample. But if you could actually grab a single piece of DNA and directly “read” its genes, you could, in theory, identify any gene, or even complex gene patterns. Using tools adapted from semiconductor manufacture, physicist Harold Craighead of Cornell’s Center for Nanobiotechnology and his former postdoc Stephen Turner built a silicon chip containing tiny channels, each 50 nanometers in width and depth (see ” DNA Pipeline ,” below) . The channel is so small that a single strand of DNA can barely squeeze through-and that’s just the point. An electric field causes the normally coiled ball of DNA to bump into the channel, uncoil and thread its way down.

Once grabbed, the DNA needs to be “read”-to see, for example, if it contains a specific sequence. To make a sequence legible, researchers add fluorescent-labeled DNA probes to the sample beforehand; the probes bind to the target sequences. As each molecule of DNA wiggles its way down the channel, an optical detector identifies the fluorescent labels passing by. “We’re treating the DNA like it’s a recording medium,” says Turner, who is now president of Nanofluidics, a startup trying to commercialize the Cornell technology. “And just like a tape player, we’re playing the DNA.” While the Cornell researchers currently use an external optical microscope to read the “tape,” they hope to build an optical reader directly onto the chip using optical fibers. Turner expects to have a working device within the next few years.

Because the tools for making these tiny channels rely on the same standard equipment used to fabricate silicon chips for microelectronics, Turner envisions making nanofluidic chips with thousands and even millions of channels and optical fibers. With such devices, Turner says, doctors could one day take a drop of blood from a patient, drop it on the microchip and rapidly scan the DNA in the sample for genetic markers of disease. The device could also help doctors choose just the right drugs for the patient.

DNA Pipeline
To identify a particular sequence on a strand of DNA, researchers first mix the DNA with fluorescent probes that attach to that sequence. Then, on a microchip (above), an electrical field draws DNA through a channel 50 nanometers wide. An embedded optical reader detects any attached probes, identifying the sequence.

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