Repository-based plasmid design

Autoři: Joshua J. Timmons aff001;  Doug Densmore aff001
Působiště autorů: Lattice Automation Inc., Boston, Massachusetts, United States of America aff001;  Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America aff002;  Biological Design Center, Boston University, Boston, Massachusetts, United States of America aff003
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
prolekare.web.journal.doi_sk: 10.1371/journal.pone.0223935


There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. A challenge in biodesign remains how to use these and other repository-based sequences effectively, correctly, and seamlessly. This work describes an approach to plasmid design where a plasmid is specified as simply a DNA sequence or list of features. The proposed software then finds the most cost-effective combination of synthetic and PCR-prepared repository fragments to build the plasmid via Gibson assembly®. It finds existing DNA sequences in both user-specified and public DNA databases: iGEM, Addgene, and DNASU. Such a software application is introduced and characterized against all post-2005 iGEM composite parts and all Addgene vectors submitted in 2018 and found to reduce costs by 34% versus a purely synthetic plasmid design approach. The described software will improve current plasmid assembly workflows by shortening design times, improving build quality, and reducing costs.

Klíčová slova:

BLAST algorithm – Molecular cloning – Plasmid construction – Polymerase chain reaction – Sequence assembly tools – Sequence databases – Synthetic biology – Synthetic plasmids


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