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US Department of Energy Develops DNA Construction Software

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Despite advances in DNA construction technology, choosing and designing the right protocols can still be a labor-intensive and error-prone process. To help researchers focus their energies on their primary areas of interest instead of having to prepare DNA, Nathan Hillson, a researcher at the US Department of Energy's Joint Bioenergy Institute, has developed a software tool called j5 to help identify the most cost-effective and efficient method of DNA construction.

"With the price of directly synthesizing DNA becoming more and more economical, it is increasingly important to compare the cost of constructing the DNA in your own lab with the price of outsourcing the construction to companies. It was with these two considerations in mind that I started to develop j5," Hillson says. "The major differences between j5 and similar tools — like Life Technologies' DNA Oligo Designer — is that they do not additionally design Golden Gate-style DNA construction protocols, they do not perform any optimization around the cost of DNA construction, and they are not able to design the construction of large combinatorial libraries of related constructs."

Migrating the command-line version of j5 from Hillson's laptop to the broader research community has been challenging. Currently, Hillson says his team has registered users on six continents at more than 135 institutions, thanks to its current cloud-based graphical Web interface.

Future development plans for j5 include adding capabilities for in vivo yeast-based DNA construction protocols, and adding more extensive integration with robotics platforms and with next-generation microfluidic devices as they become available. According to Hillson, several commercial companies are already competing for exclusive distribution licensing rights for their software.

"We anticipate over the coming year that a polished commercial-grade version of the software will emerge and provide the community with a refined tool that's easier to use than the current version of j5, and will likely offer a refined feature set," he says. "I envision a lot of competition in this software and laboratory automation space going forward, which is exciting, because this will greatly benefit the biotechnology community as a whole."

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