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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Citations
Cites
Primer3 on the WWW for General Users and for Biologist Programmers
Rozen, S., & Skaletsky, H. (2003) · Bioinformatics Methods and Protocols · doi:10.1385/1-59259-192-2:365 · Cited by 15,013
Enzymatic assembly of DNA molecules up to several hundred kilobases
Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009) · Nature Methods · doi:10.1038/nmeth.1318 · Cited by 9,996
A Greedy Algorithm for Aligning DNA Sequences
Zhang, Z., Schwartz, S., Wagner, L., & Miller, W. (2000) · Journal of Computational Biology · doi:10.1089/10665270050081478 · Cited by 5,478
Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R.-Y., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., et al. (2010) · Science · doi:10.1126/science.1190719 · Cited by 2,638
A One Pot, One Step, Precision Cloning Method with High Throughput Capability
Engler, C., Kandzia, R., & Marillonnet, S. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003647 · Cited by 2,389
Automated design of synthetic ribosome binding sites to control protein expression
Salis, H. M., Mirsky, E. A., & Voigt, C. A. (2009) · Nature Biotechnology · doi:10.1038/nbt.1568 · Cited by 1,844
The Bioperl Toolkit: Perl Modules for the Life Sciences
Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G. R., Korf, I., Lapp, H., et al. (2002) · Genome Research · doi:10.1101/gr.361602 · Cited by 1,654
A Modular Cloning System for Standardized Assembly of Multigene Constructs
Weber, E., Engler, C., Gruetzner, R., Werner, S., & Marillonnet, S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016765 · Cited by 1,377
Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes
Engler, C., Gruetzner, R., Kandzia, R., & Marillonnet, S. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005553 · Cited by 1,023
Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC
Li, M. Z., & Elledge, S. J. (2007) · Nature Methods · doi:10.1038/nmeth1010 · Cited by 953
Engineering BioBrick vectors from BioBrick parts
Shetty, R. P., Endy, D., & Knight, T. F. (2008) · Journal of Biological Engineering · doi:10.1186/1754-1611-2-5 · Cited by 760
DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways
Shao, Z., Zhao, H., & Zhao, H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn991 · Cited by 678
Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways
Quan, J., & Tian, J. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006441 · Cited by 517
Synthetic chromosome arms function in yeast and generate phenotypic diversity by design
Dymond, J. S., Richardson, S. M., Coombes, C. E., Babatz, T., Muller, H., Annaluru, N., Blake, W. J., Schwerzmann, J. W., Dai, J., Lindstrom, D. L., et al. (2011) · Nature · doi:10.1038/nature10403 · Cited by 473
BglBricks: A flexible standard for biological part assembly
Anderson, J. C., Dueber, J. E., Leguia, M., Wu, G. C., Goler, J. A., Arkin, A. P., & Keasling, J. D. (2010) · Journal of Biological Engineering · doi:10.1186/1754-1611-4-1 · Cited by 429
Self-citationQuan, J., & Tian, J. (2011) · Nature Protocols · doi:10.1038/nprot.2010.181 · Cited by 361
GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules.
Sarrion-Perdigones, A., Falconi, E. E., Zandalinas, S. I., Juárez, P., Fernández-del-Carmen, A., Granell, A., & Orzaez, D. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021622 · Cited by 348
DNA assembly for synthetic biology: from parts to pathways and beyond
Ellis, T., Adie, T., & Baldwin, G. S. (2011) · Integrative Biology · doi:10.1039/c0ib00070a · Cited by 305
Khlebnikov, A., Keasling, J. D., Wanner, B. L., Skaug, T., & Datsenko, K. A. (2001) · Microbiology · doi:10.1099/00221287-147-12-3241 · Cited by 289
Self-citationUSERTM friendly DNA engineering and cloning method by uracil excision
Bitinaite, J., Rubino, M., Varma, K. H., Schildkraut, I., Vaisvila, R., & Vaiskunaite, R. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm041 · Cited by 186
Combinatorial engineering of microbes for optimizing cellular phenotype
Santos, C. N. S., & Stephanopoulos, G. (2008) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2008.01.017 · Cited by 171
Cytoplasmic degradation of ssrA‐tagged proteins
Farrell, C. M., Grossman, A. D., & Sauer, R. T. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.04798.x · Cited by 170
Synergies between synthetic biology and metabolic engineering
Nielsen, J., & Keasling, J. D. (2011) · Nature Biotechnology · doi:10.1038/nbt.1937 · Cited by 156
Self-citationBilitchenko, L., Liu, A., Cheung, S. F., Weeding, E. M. B., Xia, B., Leguía, M., Anderson, J. C., & Densmore, D. M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018882 · Cited by 129
Rapid and efficient construction of markerless deletions in the Escherichia coli genome
Yu, B., Kang, K. H., Lee, Y., Sung, B. H., Kim, M. S., & Kim, S. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn359 · Cited by 96
Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler
Shao, Z., Luo, Y., & Zhao, H. (2011) · Molecular BioSystems · doi:10.1039/c0mb00338g · Cited by 90
SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags
Hersch, G. L., Baker, T. A., & Sauer, R. T. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404733101 · Cited by 69
GeneDesign 3.0 is an updated synthetic biology toolkit
Richardson, S. M., Nunley, P. W., Yarrington, R. M., Boeke, J. D., & Bader, J. S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq143 · Cited by 67
Developer's and User's Guide to Clotho v2.0
Xia, B., Bhatia, S. P., Bubenheim, B., Dadgar, M., Densmore, D. M., & Anderson, J. C. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-385120-8.00005-x · Cited by 58
Algorithms for automated DNA assembly
Densmore, D. M., Hsiau, T. H.-C., Kittleson, J. T., DeLoache, W., Batten, C., & Anderson, J. C. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq165 · Cited by 54
Ramon, A., & Smith, H. O. (2010) · Biotechnology Letters · doi:10.1007/s10529-010-0455-x · Cited by 51
Automated Assembly of Standard Biological Parts
Leguía, M., Brophy, J. A. N., Densmore, D. M., & Anderson, J. C. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-385120-8.00016-4 · Cited by 28
GLAMM: Genome-Linked Application for Metabolic Maps
Bates, J. T., Chivian, D. C., & Arkin, A. P. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr433 · Cited by 26
DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems
Hillson, N. J. (2011) · Springer eBooks · doi:10.1007/978-1-4419-6766-4_14 · Cited by 20
Self-citation
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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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