Biomedical engineers from Boston University have developed a new sequencing technique that eliminates the time-consuming, and often error-prone step of DNA amplification - which will make future genome sequencing both faster and less expensive than any current technologies.

Current genome sequencing technologies rely on DNA amplification to make literally billions of copies in order to produce a sample large enough to be analyzed. Not only is this process time-consuming - but making copies of copies often leads to errors in the base pairing, and thus results in less than perfect sequencing reads. Additionally, current DNA amplification methods limit the DNA molecule length to under a thousand base pairs - so multiple, overlapping reads must be processed and assembled to complete the picture.

Challenged by the "$1,000 Genome" program launched in 2004 by the National Human Genome Research Institute (NHGRI) at NIH - Amit Meller, a Biomedical Engineering professor focussed on single molecule biophysics and nano-technology to develop ultra fast and cheap DNA sequencing technologies.

Meller's team developed a novel sequencing technique based upon the optical readout of DNA molecule translocations through nanometer scale pores. The DNA is first converted into an expanded, digitized form by systematically substituting each and every base in the sequence with a specific ordered pair of concatenated oligonucleotides. This converted DNA is then hybridized with complementary molecular beacons of two colors.

Using an electrical field, the long strand of DNA sequence is drawn through nanopore sensors, where the DNA is 'unzipped'. The unzipping event releases the hybridized fluorophore, resulting in a series of photon flashes which can be recorded by a CCD camera.

A surprising benefit of the technology is that the longer the DNA strand, the more quickly it finds its way to the nanopore opening.

"That's really surprising," 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 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 technologies limit DNA molecule length to under a thousand basepairs," Meller added. "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."

The technique is described in a paper published in the December 20th online edition of Nature Nanotechnology.

Article: http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2009.379.html

Source: http://www.bu.edu/meller/research.html