sb2000116_si_001.pdf (7.73 MB)
j5 DNA Assembly Design Automation Software
journal contribution
posted on 2012-01-20, 00:00 authored by Nathan J. Hillson, Rafael D. Rosengarten, Jay D. KeaslingRecent 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
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