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DNA Sequencing, Without the Fuss

25 March 2012 1:00 pm
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J. Gundlach/U. of Washington

Reading DNA the nano way. DNA traveling through a protein pore can now be deciphered.

DNA sequencing technology has been improving by leaps and bounds in recent years, with several techniques vying for supremacy. Now an upstart technology, called nanopore sequencing, looks ready to jump to the front of the pack. Researchers have demonstrated for the first time that they can continuously read the chemical letters of DNA as it travels through a tiny pore, paving the way for a new kind of sequencing machine that decodes DNA much like an announcer reading a ticker tape. The advance might drop the cost of sequencing a complete human genome below $1000, which is expected to revolutionize personalized medicine and help usher in a new era of genetic-based diagnostics and medicines.

Most sequencing techniques require days of work. Machines copy DNA strands and modify them with fluorescent labels and other compounds to enable them to read DNA's sequence letters, or bases. Nanopore sequencing promises to do away with these added steps by sequencing single unmodified DNA strands, and thereby possibly becoming the fastest and cheapest sequencing method on the market.

The idea of passing a DNA strand through a small pore and then reading out its chemical letters was first suggested by researchers in Massachusetts and California in 1996. Since then scientists have figured out how to drive DNA through proteins with tiny pores embedded in a film using an electrical charge. As DNA's bases pass through the pore, they change the electrical charge. Sensitive electronics detect these changes and identify the bases.

One major problem, however, has been that when an electric voltage is applied across the film, DNA tends to move through the nanopore too quickly to read off all the bases in sequence. Two years ago, Mark Akeson and colleagues at the University of California, Santa Cruz, hit upon a possible solution. They added a protein called phi29 to a nanopore setup. The protein loosely grabbed onto a DNA strand as it was moving through the nanopore, slowing its progress.

Now, a team led by Jens Gundlach, a physicist at the University of Washington, Seattle, reports today in Nature Biotechnology that it has incorporated Akeson's phi29 protein into its nanopore setup, which uses a different pore protein that's more adept at quickly identifying all four chemical bases. The phi29 protein slows the DNA down so that only 20 to 30 nucleotide bases move through the pore each second, making it possible to electrically identify each one as it passes. "It's really the holy grail of nanopore sequencing," Gundlach says.

The advance promises to juice up the competition with a nanopore sequencing company called Oxford Nanopore Technologies. In February, officials with that company told attendees at a sequencing technology meeting in Florida that they had already snagged this grail. The company said it could not only electrically read out the full sequence of nucleotides in DNA as they streamed through an individual pore, but that by early 2013 it would be selling machines with thousands of nanopores running in parallel, making it possible to sequence a full genome in as little as 15 minutes, for around $1000.

Most genome researchers agree that would be an impressive feat if true. But they are still waiting for proof. "Oxford Nanopore was the first announcement, but they've been roundly criticized for not showing much data," says chemist Geoffrey Barrall, president of Electronic BioSciences in San Diego, California, which is also developing nanopore sequencing. By contrast, Barrall says, the results by Gundlach and colleagues look convincing. "This is the first paper where somebody has actually sequenced DNA."

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