j5 DNA Assembly Design Automation Software
journal contributionposted on 20.01.2012, 00:00 by Nathan J. Hillson, Rafael D. Rosengarten, Jay D. Keasling
Recent advances in Synthetic Biology have yielded standardized and automatable DNA assembly protocols that enable a broad range of biotechnological research and development. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. Here, we report the development and deployment of a web-based software tool, j5, which automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. Using a GFP expression testbed, we demonstrate that j5 designs can be executed with the SLIC, Gibson, or CPEC assembly methods, used to build combinatorial libraries with the Golden Gate assembly method, and applied to the preparation of linear gene deletion cassettes for E. coli. The DNA assembly design algorithms reported here are generally applicable to broad classes of DNA construction methodologies and could be implemented to supplement other DNA assembly design tools. Taken together, these innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design.
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combinatorial DNA constructionDNA assembly design algorithmsj 5 DNA Assembly Design Automation SoftwareRecent advancesSynthetic Biologyuser design errorsresearchers timeDNA assembly methodsDNA assembly design toolscombinatorial librariesassembly strategiesdecrease research costsGolden GateGFP expression testbedDNA construction methodologiesautomatable DNA assembly protocolsj 5 design processDNA assembly protocolsdesign specification rulesassembly errorsgene deletion cassettesSLICCPEC assembly methodsGolden Gate assembly methodcost optimizationDNA synthesisj 5 designsbiotechnological research