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Sequencing When It Rains, It Nanopores

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When Celera said it would sequence the human genome in three years, skeptics said it couldn’t be done. But for some, even that isn’t fast enough. “Today sequencing is too slow, too expensive, and inaccessible,” says Stephen Laderman, who heads the molecular diagnostic department at Agilent Technologies.

With Agilent’s funding, Harvard biologist Daniel Branton and physicist Jene Golovchenko, along with David Beamer of the University of California at Santa Cruz, are in the early stages of developing a technology they say would sequence an entire human genome in less than two hours.

Inspired by their cell membrane work, Branton and Beamer use a lipid bilayer, an ion gradient, and a membrane protein to take advantage of DNA’s negative charge. A DNA strand is piped through the membrane by changes in electrical charge. The idea is, as it shuttles through a 1.5 nanometer pore in the protein, each base identifies itself with a distinct electrical current.

The nanopore sequencer is likely up to a decade away from commercial viability. For one thing, the researchers are looking to replace the unstable protein pore with a solid-state material. “We’d like to use higher temperatures in order to keep the molecules single-stranded. But that’s not possible with a protein, which will be cooked like an egg,” says Branton. Another kink is the speed at which DNA flies through the pore: at a million bases a second, it’s too fast for today’s detectors to handle.

— Aaron J. Sender

 

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