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Faster, Cheaper DNA Sequencing Using New Nanopore Technique

Researchers at Boston University, and colleagues, have developed a silicon nanopore-based method that promises to make future genome sequencing faster and cheaper by dramatically reducing the amount of DNA required, thus eliminating the expensive, time-consuming, and error-prone step of DNA amplification. The technique uses electrical fields to feed long strands of DNA through four-nanometer-wide pores, much like threading a needle. The method uses sensitive electrical current measurements to detect single DNA molecules as they pass through the nanopores. "The current study shows that we can detect a much smaller amount of DNA sample than previously reported," said senior author Dr. Amit Meller. "When people start to implement genome sequencing or genome profiling using nanopores, they could use our nanopore capture approach to greatly reduce the number of copies used in those measurements," said Dr. Meller. The group harnessed electric fields around the opening of the nanopore to attract long, negatively charged DNA strands and to slide them through the nanopore, where the DNA sequence can be detected. In doing this work, the researchers made the counterintuitive discovery that the longer the DNA strand, the more quickly it found the pore opening. "That's really surprising," Dr. Meller said. "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.” Dr. Meller added, "DNA amplification technologies limit DNA molecule length to under a thousand basepairs. 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.” This work was reported online in Nature Nanotechnology on December 20. [Press release] [Nature Nanotechnology abstract]