New nanosize detector picks through DNA

Researchers have developed a new technology for rapidly distinguishing between almost identical DNA molecules.

Nanopore detector (left) pulls in a hairpin DNA molecule, which gets stuck (center). Once it uncoils, the molecule can go farther into the narrowing passage (right). A characteristic current change indicates which molecule is in the detector. Vercoutere et al./Nature Biotechnology

The highly sensitive device, called a nanopore detector, might eventually be able to sort through DNA and identify a small variation that predisposes a person to some disease. The technique might even permit DNA sequencing at unprecedented speeds, report Wenonah Vercoutere and her colleagues at the University of California, Santa Cruz in the March Nature Biotechnology.

The researchers created the detector by making a tiny membrane with a single pore just large enough for a DNA molecule to slip into. To test it, they synthesized many different molecules of so-called hairpin DNA, in which a single strand doubles back onto itself to create a tiny loop at one end.

In each molecule, the four types of nucleotide bases–the chemical units that code for genetic information in DNA–followed a sequence chosen by the researchers. Along the intertwined stem of each hairpin, the bases paired up, while the loop at the top contained four unpaired bases.

The researchers placed a membrane between two volumes of a salt solution and added DNA molecules with a single, known base sequence to one side. Applying a voltage across the membrane drew hairpin DNA molecules into the pore one at a time. Initially, each molecule got stuck in the pore, which narrows from 2.5 nanometers in diameter to 1.5 nm. But then the hairpin spontaneously untwisted into a single strand, thin enough to zip farther into the channel.

Each DNA molecule created a characteristic electrical signal as it blocked the pore and then moved on, says team member David Deamer. The researchers created a computer program that learned these signatures.

“We’re pulling [the molecules] into the pore and tasting them,” Deamer says.

The computer program can differentiate the DNA molecules in a solution of many different types, adds team member Mark Akeson. “We can tell eight to nine different guys apart in one set,” he says. The device can differentiate between hairpin molecules that vary by as little as one base pair in their stem or one unpaired base in their loop, he adds.

Although scientists have been experimenting with such detectors for several years, “this is the first time that nanopore technology has demonstrated this kind of resolution,” comments Daniel Branton, whose team at Harvard University also experiments with the technique.

Such sensitivity is an important step toward eventually using nanopore detectors to rapidly sequence DNA, says Branton. Researchers should now also work toward building stronger, longer-lasting devices, he says, since the current structures are relatively delicate.

In the current design, DNA molecules move through the pore too quickly to allow identification of individual bases, says Deamer. The team is looking for ways to slow the hairpin molecules, he says.

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