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Crafty Genomic Shoehorn May Yield Warp-Speed Whole-Genome Sequencing

SANTA CLARA, Calif., Feb. 27 - The technology to sequence a long strand of DNA by sending it through a 10 -9-meter hole at a speed of 1 billion bases per second may only be two years away, according to Daniel Branton.


Branton, a professor of molecular and cellular biology at Harvard, together with colleagues in Cambridge, Mass., and at the University of California, Santa Cruz, has already designed solid-state nanopores big enough through which a DNA molecule can be threaded but small enough to send the bases by only one at a time.


"DNA is a long, floppy, molecule," Branton said during the 2002 Genome Tri-Conferene meeting here. "But as it goes through the nanopore it has to proceed in single file order. We asked ourselves what kind of probe we could apply to detect the differences in bases."


The answer, it initially turned out, was to use a beam of ions sent across the pore to measure differences in bases. While this worked to distinguish between groups of bases, the number of ions that could be sent across the pore was limited by the size of the nanopore, said Branton. This limited sensitivity needed to measure distinctions down to the individual base.


"We could either slow down the DNA molecule to count the ions, or use an alternative probe," said Branton. "Our preference right now is to do it with tunneling," which would send enough electrons across the pore to distinguish differences down to single base pairs while maintaining the high-throughput rate of one base per millisecond and allowing the sequencing of DNA strands without the need for amplification.


By operating 100 electron-tunneling nanopore sequencers in parallel, Branton estimates it would take at most three hours to sequence an entire human genome. Though he pointed out that more realistic applications would be to focus on sequencing specific polymorphic regions of humans' chromosomes and sequencing smaller genomes of other organisms.


Branton and his colleagues will have to first perfect a method of making synthetic nanopores to use the tunneling method rather than ion flow to measure different bases. Demonstrating this first step along with actually using electrons to sequence DNA, or coming to the conclusion that it is not feasible, will take approximately two years, he said.


Meanwhile, the researchers are also developing the ion method for use in detecting haplotypes, Branton said. If successful, this work, assisted by a co-development deal with Agilent, which is designing algorithms for the ion-nanopore sequencer, will most likely yield the first application of the technology, according to Branton.

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