The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
j5 DNA Assembly Design Automation Software
Abstract
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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Cites
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Cited by
Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development
Paddon, C. J., & Keasling, J. D. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3240 · Cited by 675
Self-citationSynthetic biology of cyanobacteria: unique challenges and opportunities
Berla, B. M., Saha, R., Immethun, C. M., Maranas, C. D., Moon, T. S., & Pakrasi, H. B. (2013) · Frontiers in Microbiology · doi:10.3389/fmicb.2013.00246 · Cited by 305
Bricks and blueprints: methods and standards for DNA assembly.
Casini, A., Storch, M., Baldwin, G. S., & Ellis, T. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4014 · Cited by 286
Courbet, A., Endy, D., Renard, E., Molina, F., & Bonnet, J. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa3601 · Cited by 266
Realizing the potential of synthetic biology
Church, G. M., Elowitz, M. B., Smolke, C. D., Voigt, C. A., & Weiss, R. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3767 · Cited by 226
Metadata
- Authors
- Hillson, N. J., Rosengarten, R. D., & Keasling, J. D.
- Venue
- ACS Synthetic Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2011-12-20
- Volume
- 1
- Issue
- 1
- Pages
- 14-21
- ISSN
- 2161-5063 (ISSN-L)
- OpenAlex
- W2321143980
- Cited by
- 316
- References
- 34
- FWCI
- 7.88
- Type
- journal article
- Language
- en
- Open access
- closed
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