"As the size and number of parts to be incorporated into the plasmid increases, traditional construction of recombinant DNA assemblies becomes ever more difficult," says Hillson. "The process must often be repeated from scratch for alternate combinations of parts, and every time you clone a different gene or fragment, you might have to use a different pair of restriction sites. This has been a labor-intensive and time-consuming process."
With modern DNA construction techniques, Hillson says, a small number of enzymes can be used over and over again, independent of the DNA sequence fragments being assembled, and thereby enabling automation with robotic platforms. However, designing protocols for these modern DNA construction approaches can be as labor-intensive, time-consuming and error-prone as the traditional approach. Furthermore, it is now increasingly important to consider outsourcing portions of DNA construction - to companies that chemically synthesize long sequences of DNA as a cost-effective alternative. To address these considerations Hillson created the j5 software package.
"The j5 software package is a Web-based computer application that automatically designs and optimizes state-of-the-art DNA construction protocols," Hillson says. "Within minutes it can determine the optimal flanking sequences that should be attached to each DNA part to produce the desired recombinant DNA at the least expense, in a manner that is executable by hand or robotics."
As a result, researchers can direct their resources to investigating their primary interests, rather than preparing the DNA that is merely a tool in their experiments.
"At JBEI, we want researchers spending their time designing their DNA constructs and assaying their function," Hillson says. "We don't want them to waste their time building these things in the lab, so we're trying to go after ways of tak
|Contact: Lynn Yarris|
DOE/Lawrence Berkeley National Laboratory