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Startup That Builds Biological Parts

Ginkgo BioWorks aims to push synthetic biology to the factory level.
October 2, 2009

In a warehouse building in Boston, wedged between a cruise-ship drydock and Au Bon Pain’s corporate headquarters, sits Ginkgo BioWorks, a new synthetic-biology startup that aims to make biological engineering easier than baking bread. Founded by five MIT scientists, the company offers to assemble biological parts–such as strings of specific genes–for industry and academic scientists.

Biological parts: Ginkgo BioWorks, a synthetic-biology startup, is automating the process of building biological machines. Shown here is a liquid-handling robot that can prepare hundreds of reactions.

“Think of it as rapid prototyping in biology–we make the part, test it, and then expand on it,” says Reshma Shetty, one of the company’s cofounders. “You can spend more time thinking about the design, rather than doing the grunt work of making DNA.” A very simple project, such as assembling two pieces of DNA, might cost $100, with prices increasing from there.

Synthetic biology is the quest to systematically design and build novel organisms that perform useful functions, such as producing chemicals, using genetic-engineering tools. The field is often considered the next step beyond metabolic engineering because it aims to completely overhaul existing systems to create new functionality rather than improve an existing process with a number of genetic tweaks.

Scientists have so far created microbes that can produce drugs and biofuels, and interest among industrial chemical makers is growing. While companies already exist to synthesize pieces of DNA, Ginkgo assembles synthesized pieces of DNA to create functional genetic pathways. (Assembling specific genes into long pieces of DNA is much cheaper than synthesizing that long piece from scratch.)

Ginkgo will build on technology developed by Tom Knight, a research scientist at MIT and one of the company’s cofounders, who started out his scientific career as an engineer. “I’m interested in transitioning biology from being sort of a craft, where every time you do something it’s done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things,” says Knight.

Scientists generally create biological parts by stitching together genes with specific functions, using specialized enzymes to cut and sew the DNA. The finished part is then inserted into bacteria, where it can perform its designated task. Currently, this process is mostly done by a lab technician or graduate student; consequently, the process is slow, and the resulting construct isn’t optimized for use in other projects. Knight developed a standardized way of putting together pieces of DNA, called the BioBricks standard, in which each piece of DNA is tagged on both sides with DNA connectors that allow pieces to be easily interchanged.

“If your part obeys those rules, we can use identical reactions every time to assemble those fragments into larger constructs,” says Knight. “That allows us to standardize and automate the process of assembly. If we want to put 100 different versions of a system together, we can do that straightforwardly, whereas it would be a tedious job to do with manual techniques.” The most complicated part that Ginkgo has built to date is a piece of DNA with 15 genes and a total of 30,000 DNA letters. The part was made for a private partner, and its function has not been divulged.

Assembling parts is only part of the challenge in building biological machines. Different genes can have unanticipated effects on each other, interfering with the ultimate function. “One of the things we’ll be able to do is to assemble hundreds or thousands of versions of a specific pathway with slight variations,” says Knight. Scientists can then determine which version works best.

So far, Knight says, the greatest interest has come from manufacturing companies making chemicals for cosmetics, perfumes, and flavorings. “Many of them are trying to replace a dirty chemical process with an environmentally friendly, biologically based process,” he says.

Ginkgo is one of just a handful of synthetic-biology companies. Codon Devices, a well-funded startup that synthesized DNA, ceased operations earlier this year. “The challenge now is not to synthesize genes; there are a few companies that do that,” says Shetty. “It’s to build pathways that can make specific chemicals, such as fuels.” And unlike Codon, Ginkgo is starting small. The company is funded by seed money and a $150,000 loan from Lifetech Boston, a program to attract biotech to Boston. Its lab space is populated with banks of PCR machines, which amplify DNA, and liquid-handling robots, mostly bought on eBay or from other biotech firms that have gone out of business. And the company already has a commercial product–a kit sold through New England Biolabs that allows scientists to put together parts on their own.

“If successful, they will be providing a very important service for synthetic biology,” says Chris Voigt, a synthetic biologist at the University of California, San Francisco. “There isn’t anybody else who would be characterizing and providing parts to the community. I think that this type of research needs to occur outside of the academic community–at either a company or a nonprofit institute.”

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