Wednesday, August 17, 2011

Graphical software speeds up DNA construction

Biochemist Nathan Hillson at the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) has developed j5, the only DNA construction software that also identifies which recombinant DNA technology strategy would be the most cost-effective.

The Web-based j5 software package features a graphical interface that enables users to design a DNA construct or combinatorial libraries through the arrangement of individual part icons that abstractly represent underlying DNA sequences. Outputs are in the form of user-friendly spreadsheets that detail the resulting designed experimental protocols, providing instructions that can either be followed by a person in the laboratory or fed directly into a robotic platform for a machine to carry out.

“Our j5 is the only software package today that both standardizes and cost-optimizes the DNA construction process,” says Hillson. “Through the design of short DNA sequences that can be used to join longer sequences together in recombinant DNA assemblies, the j5 software improves the accuracy, scalability, and cost-effectiveness of DNA construction.”

“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,” continues Hillson.

In addition to identifying the most cost-effective strategies for DNA cloning, j5 also makes it possible to construct combinatorial libraries: collections of hundreds to millions of related DNA assemblies, each with a different combination of genes or parts that perform similar functions in different organisms.

“Combinatorial libraries can be screened to identify the gene combination that, when transferred into a desirable host organism, results in the most productive enzyme pathway,” says Hillson. “The j5 software is the only program that enables the combinatorial design of scarless DNA construction methods.”


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