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Cheap, fast genome sequencing could some day become a part of routine patient care–but researchers say it will take a novel approach.

Last week, the National Human Genome Research Institute in Bethesda, MD, announced more than $12 million in grants for researchers who are developing technologies to slash the costs of mapping a mammalian genome from around $10 million to $1,000. Some scientists believe that new twists on a decade-old idea, called nanopore sequencing, could speed up the sequencing process and provide a more complete map of the genome.

In nanopore sequencing, strands of DNA move through a small hole in a membrane with sensors that read off the base pairs of genetic code one by one. The hole, or nanopore, is about the size of a DNA molecule, or 1 to 2 nanometers in diameter, and the membrane separates positively and negatively charged solutions.

Because DNA has a strong negative charge, when it’s placed on the positive side, its tip finds the hole and gets sucked across the membrane. As the DNA moves through the nanopore, researchers should be able to “identify each base as it goes by” using electrical or optical techniques, says David Deamer, professor emeritus of chemistry at the University of California-Santa Cruz. Deamer and Harvard biology professor Daniel Branton came up with the nanopore sequencing concept in the mid-1990s.

The “membrane” in their setup is a silicon semiconductor. And the probes on the nanopores they’re developing send electrons through each base as it passes through the hole. Branton says they’re effectively designing a new kind of electron tunneling microscope, an instrument that uses a probe to send electrons through a molecule, thereby providing detailed information about its structure. In their DNA microscope, however, the molecule will move past the probe instead of the probe moving past the molecule.

But they still have a long way to go. “We can’t sequence anything yet,” says Branton. He projects that his group will be able to provide a short sequence in about five years.

Amit Meller, associate professor of biomedical engineering at Boston University, believes he’s much closer to demonstrating nanopore sequencing, using an entirely different approach. He’s designing a DNA sequencer based on a modified fluorescence microscope and arrays of many nanopores.

First, the DNA is incubated with four different fluorescent labels. The labels make the strand too big to go through the hole, so they have to pop off for the strand to advance. As the DNA moves through the nanopore base by base, the microscope will detect the labels as they pop off. Meller says the sequence data will be processed by a computer as each base is read off.

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Tagged: Biomedicine

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