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Speed-Reading the Genome

New techniques that can draw DNA through nanopores might lead to faster and cheaper sequencing.

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.

Meller has not yet demonstrated his sequencing technology, but he says it relies on a combination of proven techniques and, unlike electrical nanopore sequencing techniques, there are no fundamental problems remaining. His group has fabricated 25-nanopore arrays and demonstrated the effectiveness of the fluorescent probes. Now, with a three-year, $2.2-million NIH grant, he believes they’ll be able to put the pieces together.

If this technique works, it could mean DNA sequencing at extremely high throughput. Meller says arrays of 100 by 100 nanopores could sequence an entire human genome in an hour.

Current sequencing techniques rely on many repeated biochemical steps, including replicating the DNA, adding probes, and chopping it into pieces. It takes weeks for computers to process the resulting sequence fragments and piece them back together. Moreover, the computer processing is expensive and cannot piece together long sections of the genome in which the same sequence is repeated. Today’s techniques also cannot be used to find rearrangements–movements of large stretches of DNA from one part of a chromosome to another. Yet rearranged and repeated segments are believed to be important elements of genomics.

“Research is beginning to show that long-range rearrangements have disease effects,” says Jeffery Schloss, director of technology development at the genome institute. Yet current sequencing techniques cannot get at these. “If [nanopore sequencing] works at all, you ought to be able to sequence long stretches” because the DNA is read continuously in real time, he says.

Another exciting possibility, according to Schloss, is using nanopore sequencing to read molecular modifications to DNA that regulate gene expression. Inside cells, for example, genes are sometimes covered in hydrocarbon molecules, called methyl groups, effectively silencing them. (It’s how females operate with two X chromosomes: in each cell, one is covered with methyl groups and inactivated.) While traditional sequencing strips off methyl groups and other modifications, this step may not be necessary using nanopores. “I really like the idea of being able to read the native DNA,” says Schloss.

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