Assembly standards

In 2003, Tom Knight published a technical report on a standard for physical composition of genetic parts. He called parts that adhered to the standard BioBricks. Tom’s key innovation is to design a standard that enabled any two parts (that adhered to the standard) to be assembled together. All of a sudden, this meant that two people on opposite sides of the world could design two parts and those parts would be compatible with one another. Moreover, since the same process could be used to assemble any two parts together, the process could then be refine and optimized. Now the collection of genetic parts that adhere to the original BioBrick standard has grown to over 3000, largely due to the efforts of undergraduate teams in the iGEM competition.

Of course, it’s no secret that Tom’s original standard isn’t perfect. Its biggest drawback is that it leaves an 8 bp scar site between adjacent parts. Thus, you can’t use Tom’s standard to assemble protein domains together. To address this limitation, new standards have been developed. For example, Ira Phillips and Pam Silver designed a modification to Tom’s standard that reduces the scar site to just 6 bp. As did Kristian Muller, Katja Arndt, Raik Grunberg and the 2007 Freiburg iGEM team. Others, like Chris Anderson and co. at UC Berkeley, have designed entirely new assembly standards that are not backwards-compatible with Tom’s standard. Even Tom has designed updates to his own standard.

All the standards have their pro’s and con’s and it is not yet clear which standard(s) should or will “win”. What is clear is that organizations like the BioBricks Foundation, iGEM, SynBERC, and the Registry of Standard Biological Parts (heck, even Ginkgo!) have to balance between two competing goals. The first is supporting innovation around new methods and standards for part assembly. The second is to gain the network advantages of having a large group of people all using the same standard and sharing and reusing parts. Standards setting and adoption isn’t a trivial task. We only have to look to the VHS vs. betamax format wars followed by the HD-DVD vs. Blu-ray wars to know that it’s not simply the first standard or even the technically superior standard that gets adopted.

Posted By: Reshma Shetty