BIOFABs directors Drew Endy (left) and Adam Arkin hope that their facility will help to industrialize synthetic biology.

Margot Hartford

The latest shopping website is open for business, offering unusual wares: DNA tools to help biologists to engineer life.

The DNA sequences which allow precise control of gene activity in the bacterium Escherichia coli are the first output of BIOFAB, based in Emeryville, California, which calls itself the worlds first biological design-build facility. Launched in 2009 with a US$1.4-million grant from the US National Science Foundation, BIOFAB aims to advance synthetic biology by creating standard biological parts in the form of DNA sequences that control gene expression. These standard sequences should allow biologists to engineer cells that can make medicines and perform other useful tasks simply by plugging in various sets of genes.

The sequences are meant to overcome a key barrier to synthetic biology: genes inserted into an organism do not behave predictably, even in such a well-understood workhorse as E. coli. You would think after a generation of genetic engineering, expressing genes with precision in an organism as well utilized as E. coliwould be pretty straightforward. It turns out its not, says BIOFAB co-director Drew Endy, a synthetic biologist at Stanford University in California.

For a cell to express a gene that is, transcribe it into an RNA molecule and then translate that RNA into a protein other sequences recognized by the cells machinery must precede it. A promoter sequence is needed to make an RNA transcript, and a ribosome binding site (RBS) is crucial for protein translation.

Over the past three decades, scientists have amassed collections of these sequences and used them to express genes in which they are interested. Some sequences tend to be strong and others weak, resulting in varying levels of RNA and protein being produced.

But a team led by Endy and BIOFAB co-director Adam Arkin, of Lawrence Berkeley National Laboratory in Berkeley, California, has found that the activities of those sequences are far from predictable. In two papers published online this week in Nature Methods1, 2, the team reports inserting many different combinations of promoters and RBS sequences in front of genes encoding fluorescent proteins, and then measuring the level of protein that was made. It was a bloody mess, says Arkin, with each promoterRBS combination having varying effects depending on the gene.

He and Endy also cite an earlier finding that a scientist hoping to express a protein at a particular level has just a 50% chance of producing the required amount within a factor of two. Such hit-or-miss expression poses a major challenge to synthetic biologists who would like to create genetic circuits involving dozens of genes.

As a solution, the BIOFAB team designed promoter and RBS sequences for E. colithat do not interfere with downstream DNA, so that their effects are independent of the specific gene they are paired with. The sequences should provide scientists with a much tighter grip on gene expression, offering around a 93% chance of hitting a desired level of expression within a factor of two2. Researchers can obtain the sequences for free online (see http://www.biofab.org/data), and Arkin says that some of his colleagues are already finding them useful.

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DNA tool kit goes live online

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