Advance in Nanopore Gene Sequencing

Magnets help in the quest for the $1000 genome

Illustration: Emily Cooper

Electromagnetic

Opposing forces pull DNA through a nanopore so that the genetic sequence can be read as changes in current.

Your DNA sequence could be the ultimate addition to your medical records, revealing disease risks and offering the possibility of tailored treatments. But first, researchers need to make the sequencing of your entire genome affordable. The National Institutes of Health, in Bethesda, Md., are pushing researchers to come up with technology that would sequence a person’s entire genome for just US $1000. One of the front-runners in that race is called nanopore sequencing, and physicists at Brown University, in Providence, R.I., recently took a big step toward getting nanopore sequencing down to the $1000 mark.

Genetic information is encoded on DNA as the sequence in which four chemicals, called bases, are strung together. Using today’s techniques, sequencing someone’s genome can take days and cost about $100 000. Nanopore sequencing promises to speed up and simplify reading the 3 billion bases. The idea is to use an electric field to pull a DNA strand through a nanometer-scale pore. The pore is in a silicon nitride film immersed in a salt solution. A voltage drives current, in the form of ions in the water, through the nanopore, sucking the DNA through it like a child eating a noodle. As each base passes through the pore, it blocks the current to a degree specific to each of the four types of bases. The hope is to read the minute changes in current and thereby identify the sequence of bases.

However, ”there’s a big catch-22,” says Xinsheng Sean Ling, the Brown University physics professor who led the work, which was published in the 6 May issue of the journal Nanotechnology . ”You need a large electric field to draw the DNA molecule into the pore, but the same electric field also pushes the DNA too quickly.” That reduces the technology’s ability to tell one base from another.

So Ling and his colleagues attach DNA to an iron oxide bead 2.8 micrometers wide. An electric field pulls the free end of the strand through a 12¿Äënanometer silicon nitride pore, and a magnetic field drags the bead in the other direction. Without the opposing magnetic field, DNA would typically zip through the pore at the rate of one base per microsecond, but the tug-of-war between the two fields results in a rate of one per millisecond. ”So there would be less chance of error in reading the bases,” says John Kasianowicz, the biophysicist at the U.S. National Institute of Standards and Technology, in Gaithersburg, Md., who invented nanopore sequencing. ”This is a significant advance.”

So far the researchers have demonstrated the mechanics of pulling DNA through the pore, but they have yet to prove that their trick really improves DNA sequencing accuracy. And there may turn out to be better ways to slow down DNA.

Another group has tried tugging on the DNA with highly focused laser beams. And Oxford Nanopore Technologies, in Kidlington, England, recently demonstrated that DNA squiggles through a narrower pore made from a bacterial protein at 1/25th the speed it would take to move through a silicon-based pore, according to James Clarke, a scientist at Oxford Nanopore.

Silicon pores, however, are more stable and would make for a better commercial product, says Dan Branton, a nanopore researcher at Harvard. ”If you’re using a protein pore, it has to be embedded in a lipid layer, and those break and are very delicate,” he says.

Controlling the DNA’s speed through a pore is one of the biggest challenges facing nanopore technology, Branton says, and the magnetic technique addresses that issue well. However, he thinks that the process of attaching the magnetic bead could cost time and money, possibly defeating the main purpose of using nanopores: cheap sequencing.

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