![]() ![]() Plus, they assist researchers required by journals to make their materials publicly available. They enable inexpensive, reproducible, and collaborative experimental designs while handling the tedious processes of sample categorization and archiving. Įlectronically available plasmid repositories are centers for plasmid sharing. But the exogenous region of plasmids are increasingly complex genetic circuits in synthetic biology, for example, can comprise more than a dozen separate elements packaged together. Most are simple relative to their bacterial progenitors, containing just an origin of replication, resistance marker–combined together in a “backbone”–and an insert region of exogenous DNA. They are used for studying genes, encoding programs, and editing human cells. Plasmids are a common design element in molecular biology. The described software will improve current plasmid assembly workflows by shortening design times, improving build quality, and reducing costs. 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. It finds existing DNA sequences in both user-specified and public DNA databases: iGEM, Addgene, and DNASU. The proposed software then finds the most cost-effective combination of synthetic and PCR-prepared repository fragments to build the plasmid via Gibson assembly ®. This work describes an approach to plasmid design where a plasmid is specified as simply a DNA sequence or list of features. A challenge in biodesign remains how to use these and other repository-based sequences effectively, correctly, and seamlessly. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. ![]()
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