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Startup: Designer Life

Startup Codon Devices is creating entirely synthetic cells, proteins, and microorganisms. Someday they could be used to produce drugs or clean up pollution.
September 1, 2005

Last year, some 250 engineers, computer scientists, and biologists gathered at MIT for the first conference in a new field called synthetic biology. Their common goal: designing and building from scratch artificial biological systems such as cells or microorganisms that can do anything from producing drugs to cleaning up pollution. But conference goers agreed that to achieve such a goal, they will need better tools for synthesizing the long stretches of DNA required to build the synthetic organisms’ genomes.

Just a few months after the conference, some of the researchers founded a synthetic-biology startup called Codon Devices to provide those tools. With $13 million in venture capital funding, Codon is developing high-speed, low-cost DNA synthesis technology that could make synthetic biology a reality. By the end of this year, the company hopes to begin collaborating with academic researchers, helping them with DNA design and fabrication and delivering to them engineered DNA, proteins, or cells as products.

Codon’s technology could enable improved protein-based therapeutics and vaccines. Since synthetic biologists engineer genomes from scratch, instead of modifying naturally occurring ones, they should be able to create proteins and cells with novel and complex capabilities. Synthetic biologists say they want to design and build genomes in the same way that electrical engineers make integrated circuits. “They’ve been doing large-scale integrated circuits since I was a kid. Now we’re trying to do large-scale integrated biological circuits,” says Harvard Medical School geneticist George Church, Codon’s cofounder and chief scientific officer.

Although synthetic biologists can design DNA sequences for engineered organisms, they lack affordable tools that can quickly, automatically, and accurately turn those sequences into DNA molecules. With current methods, for instance, it can take many years, $10 million, and lots of manual handling and reagents to make a bacterial genome that is five million DNA letters long. And the process is prone to error: each letter of the final molecule has a 1 percent chance of being incorrect.

Within the next two years, Codon’s technology should reduce the time and cost of synthesizing DNA to about one-hundredth to one-thousandth of their current rates. That will enable the fabrication of longer stretches of DNA, says the company. And Codon aims to reduce the error rate to between one-thousandth and one-ten-thousandth of the current rate.

Codon researchers use the basic approach of conventional DNA synthesis but have streamlined the process to cut down on the number of steps, the volume of reagents, and the manual transferring of reagents between containers–all of which allows for more automation. Key to the system is the use of a gene chip on which thousands of small fragments of the desired DNA sequence are synthesized in parallel in one step. The company’s DNA-design software determines how to parcel out the sequence so that once the fragments are synthesized they can be pieced together with minimal labor.

The startup will face technical hurdles. For one, it may be difficult for Codon’s gene chip-based synthesis technology to handle certain types of sequences, such as very repetitive ones, says John Mulligan, CEO of Blue Heron Biotechnology, a Bothell, WA, gene synthesis company that is also looking to use gene chips.

And there are business challenges as well. Codon is the first startup to try to commercialize synthetic biology. “It may take a little while to shake out the business models,” says Mulligan. But the startup is right to focus on selling its DNA design capabilities, rather than just its DNA synthesis services, he says. “That’s where the high value is.” – By Corie Lok

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