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Dec 21, 2009

New Nanopore Technology Could Enable Faster DNA Sequencing without Amplification

  • Scientists in the U.S. have devised a nanopore capture method that they claim could lead to the development of a faster, cheaper DNA sequencing technology that negates the need for DNA amplification. The technique uses electrical fields to draw long strands of DNA through 4 nm silicone nanopore sensors. The individual DNA molecules are then detected using electrical current measurements as they pass through the nanopores.

    The new approach is being developed by researchers at Boston University College of Engineering and colleagues at New York University and Bar-Ilan University in Israel. Led by Amit Meller, Ph.D., associate professor at Boston University's biomedical engineering department, they used salt gradients to alter the electrical field around the pores, increasing the rate at which DNA molecules are captured, and shortenening the lag time between molecules. This reduces the quantity of DNA needed for accurate measurements, they claim.

    By boosting the capture rates by a few orders of magnitude and reducing the volume of the sample changer, the researchers were able to reduce the number of DNA molecules required by a factor of 10,000—from about 1 billion sample molecules to just 100,000. Their work is published in Nature Nanotechnology in a paper titled "Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient."

    The team's most surprising finding was that the longer the DNA strand, the more quickly it found the pore opening. This was an added bonus that they claim could make future genome sequencing using the new technique even faster than predicted.

    "That's really surprising," admits Dr. Meller. "You'd expect that if you have a longer 'spaghetti', then finding the end would be much harder. At the same time this discovery means that the nanopore system is optimized for the detection of long DNA strands—tens of thousands of basepairs or even more. This could dramatically speed future genomic sequencing by allowing analysis of a long DNA strand in one swipe, rather than having to assemble results from many short snippets.”

    DNA amplification techniques currently limit molecule length to under a thousand basepairs, Dr. Meller points out. "Because our method avoids amplification, it not only reduces the cost, time, and error rate of DNA replication techniques but also enables the analysis of very long strands of DNA—much longer than current limitations.”

     



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