Dude, where's my DNA?

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Teams taking part in this year's International Genetically Engineered Machine (iGEM) came up against an inadvertent initiative test. And it was one that set a lot of teams back weeks or even months as they vied for the top prizes.

One of the big promises of synthetic biology in the world of iGEM is that you can glue off-the-shelf bits of DNA together to make new 'circuits' that effectively reprogram a microbe such as Escherichia coli. Most of the time, people use a mixture of readymade parts and bits they assemble themselves. The student teams who take part have to provide the DNA components they build to a registry of parts that can be used by future teams. That way, the registry of 'Biobrick' parts keeps growing.

But there's a scaling problem. As more Biobricks are made and more teams take part, it gets trickier to send out the DNA. In the previous year's competition, the Biobricks were sealed in 96-well plates before being delivered. If you multiply a couple of thousand parts by 80-odd teams, that's a whole stack of well plates. So, the organisers decided to try sending out DNA spotted onto books of filter paper and then dried. It was a much cheaper and, apparently, more practical option.

Unfortunately, there was a snag: it didn't work. The phrase of the competition this year was "we tried to extract the DNA for this part from the Biobrick book but we couldn't". Teams ended up cadging DNA from each other - often from the samples delivered the previous year that they had kept in the fridge.

When iGEM organiser Randy Rettberg asked for a show of hands on who had trouble extracting the DNA, I don't think a single hand stayed down. When asked who did succeed, only the members of one team - Caltech - thrust their hands into the air.

I asked Josh Michener of the Caltech how they managed it. The approach they took was to ignore the protocol published in the book and use some super-competent cells from a commercial supplier to get enough DNA to work with. The trouble, as Rettberg said later, was that the ordinary cells recommended for iGEM work would work but deliver less than one colony of active bacteria. For most people, that meant no positive result. This is one of the factors that is likely to lead to a shift in the way that the DNA in the Biobrick registry is delivered and, ultimately, stored.

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...because a bunch of stuff has gone up at my synthetic and systems biology blog in the wake of the iGEM competition over the weekend in Boston. In this contests, students from around the world try to tweak simple lifeforms... Read More

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This page contains a single entry by Chris Edwards published on November 11, 2008 2:20 AM.

The winners at iGEM was the previous entry in this blog.

Eurocores joins the synthetic-biology research club is the next entry in this blog.

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