July/August 2008

Sequencing a Single Molecule of DNA

Helicos Biosciences' novel machine could speed up sequencing and unearth new disease-linked genetic variations.

By Emily Singer

The HeliScope is the first commercial machine to sequence a single piece of DNA rather than one copied many times. Each “flow cell” (above) has 25 channels, each capable of holding 16 million strands of DNA for sequencing. A coating on the surface of the cell allows it to be washed clean between reactions. Credit: Porter Gifford

Multimedia   See how the HeliScope sequences DNA.   Watch Helicos Biosciences' process for sequencing a single molecule of DNA.   Stephen Quake, cofounder of Helicos Biosciences, talks about sequencing.

In the corner of Helicos BioSciences' ­offices in Cambridge, MA, a screen on the face of what looks like a giant refrigera­tor flashes a countdown: 10 days, five hours, and 51 minutes until it finishes reading the sequence of all the DNA that has been fed into it. The high-­throughput machine, a complex configuration of tubes, lasers, and chemi­cals, contains two plates, each with 25 ­microfluidic channels etched into it. Each channel is capable of holding and sequencing a separate DNA sample. Sequencing the samples in parallel, the machine takes just one hour to read 1.3 billion of the chemical "bases"--known as A, C, T, and G--that make up a strand of DNA.

Called the HeliScope, it is the first commercial instrument that can directly read the sequence of a single such strand, a capability that gives it the potential for unprecedented speed. In fact, says Stephen Quake, a bioengineer at Stanford University who cofounded the company in 2003, Helicos has "basically built the world's fastest DNA sequencer." Though it's not clear whether the machine will produce a complete sequence more rapidly than competing systems do (the data generated by a sequencing machine still has to be analyzed and stitched together, a computationally intensive task), Quake says it is "opening entire new areas of research."

The HeliScope, introduced earlier this year, is joining an intense race for faster and cheaper sequencing technologies. The price of sequencing a human genome has dropped in recent years, from the $300 million the Human Genome Project spent on its first draft to less than $100,000. The applications of cheap sequencing are almost limitless, from disease diagnostics to research that could yield microbes engineered to produce biofuels or medicines.

In other advanced sequencing technologies currently in use, including those from Illumina, Applied Biosystems, and 454 Life Sciences (which was acquired by Roche last year), the DNA to be sequenced must be amplified, or copied many times; the copies are then read simultaneously to make it easier to detect fluorescent signals that indicate the position of each DNA letter. Single-­molecule sequencing skips the copying step, meaning that many more unique samples can be packed into a single sequencing experiment.

In addition, single-molecule sequencing may be able to generate a more complete picture of the genome. That's because when DNA is amplified, some strings are likelier than others to be copied successfully, so they're more likely to be represented in the final sequence. Likewise, rare genetic mutations may go unrepresented because they don't get copied. "If at the end of the day you can just put a single strand of DNA onto a platform and sequence it directly, it's a huge advantage," says Elaine R. Mardis, codirector of the Genome Center at ­Washington University in St. Louis.

Awake at Night
With the Helicos technology, the DNA to be sequenced is first chopped into short pieces about 200 bases long and injected into a flow cell, a specialized glass slide. The flow cell is coated with tiny snippets of DNA that are designed to snag the fragments as they float by, anchoring them in place. The immobilized pieces of DNA are fluorescently labeled so that their position under a fluorescence microscope can be recorded by a camera. Nearly a billion pieces of DNA can be analyzed in a single sequencing experiment, compared with about 400,000 to 50 million for other technologies.

The flow cell is then nestled into the ­HeliScope, where the microscope sits ensconced in 400 pounds of Vermont granite. The added weight stops any vibrations from interfering with the signals the device must detect. A complex optical system and a tangle of tubing surround the microscope, connecting it to what looks like a miniature fridge filled with bottles of specially made chemicals.