Monday, May 19, 2008

DNA Sequencing in a Snap

An innnovative approach could target hard-to-sequence areas.

By Emily Singer

Seeing the sequence: This image shows a cluster of DNA molecules (black strands) that have been synthesized using bases that are specially labeled to be visible under an electron microscope. Scientists are using this technique to develop a novel sequencing technology. Credit: ZS Genetics

A novel sequencing technology being developed by a Massachusetts startup allows scientists to take photographs of the sequence of a DNA molecule. William Glover, president of ZS Genetics, based in North Reading, MA, says that his approach will allow scientists to read long stretches of DNA, enabling the sequencing of hard-to-read areas, such as highly repetitive regions in plants and some parts of the human genome. Longer sequences also allow scientists to distinguish between maternal and paternal chromosomes, which might have important diagnostic applications.

Scientists at a recent sequencing conference in San Diego--where details of the technology were presented for the first time--were intrigued by the approach because it is totally different than even the newest methods on the market. "It's surprising and potentially very powerful," says Vladimir Benes, head of the Genomics Core Facility at the European Molecular Biology Laboratory, in Germany.

The cost of DNA sequencing has plummeted since a working draft of the human genome was completed in 2001. Most of the newest technologies currently in use generate very short sequences, about 30 to 150 base pairs, which are then stitched together with special software. But this method doesn't always capture all the information in the genome, and some parts of the genome are difficult to sequence this way, says Glover.

ZS Genetics is a relative newcomer to the field and uses an approach vastly different than any other: electron microscopy. Glover predicts that by next year, the company's technology will be able to generate readable lengths of DNA that are thousands of base pairs long, and he believes that ZS Genetics' sequencing method will improve by a factor of 10 in the next couple of years, making the pieces even easier to assemble. The company was recently accepted as one of the teams in the Archon X Prize for Genomics, a $10 million award for the first privately funded team that can sequence 100 human genomes in 10 days.

"Any technology that can bring the read length to the 1,000 base-pairs range will definitely, at least for de novo sequencing, represent a major breakthrough," says Benes. He says that the approach might be particularly useful for sequencing the genomes of plants, which often have highly complex genomes littered with repetitive sequences that are difficult to assemble computationally.

At a width of 2.2 nanometers, DNA is invisible under an average light microscope.

But electron microscopes, which detect the difference in charge between atoms, have a subnanometer resolution. While the sequence of natural DNA lacks enough contrast to be resolved with electron microscopy, Glover and his colleagues developed a novel labeling system to make the molecules more visible.

Researchers synthesize a new complementary strand of the molecule to be sequenced using bases--the letters that make up DNA--labeled with iodine and bromine. The labeled bases appear as either large or small dots under the electron microscope, allowing scientists to read the sequence. (Three different labels will be required to read the sequence of the four bases found in DNA. Three of the bases will have different labels; the fourth will simply remain unlabeled.)