title: Streamlining the Design-to-Build Transition with Build-Optimization Software Tools.
abstract: Scaling-up capabilities for the design, build, and test of synthetic biology constructs holds great promise for the development of new applications in fuels, chemical production, or cellular-behavior engineering. Construct design is an essential component in this process; however, not every designed DNA sequence can be readily manufactured, even using state-of-the-art DNA synthesis methods. Current biological computer-aided design and manufacture tools (bioCAD/CAM) do not adequately consider the limitations of DNA synthesis technologies when generating their outputs. Designed sequences that violate DNA synthesis constraints may require substantial sequence redesign or lead to price-premiums and temporal delays, which adversely impact the efficiency of the DNA manufacturing process. We have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. BOOST incorporates knowledge of DNA synthesis success determinants into the design process to output ready-to-build sequences, preempting the need for sequence redesign. The BOOST web application is available at https://boost.jgi.doe.gov and its Application Program Interfaces (API) enable integration into automated, customized DNA design processes. The herein presented results highlight the effectiveness of BOOST in reducing DNA synthesis costs and timelines.
authors.affiliation: DOE Joint Genome Institute , 2800 Mitchell Drive, Walnut Creek, California 94598, United States.
authors.forename: Ernst
authors.initials: E
authors.lastname: Oberortner
authors.affiliation: DOE Joint Genome Institute , 2800 Mitchell Drive, Walnut Creek, California 94598, United States.
authors.forename: Jan-Fang
authors.initials: JF
authors.lastname: Cheng
authors.affiliation: DOE Joint Genome Institute , 2800 Mitchell Drive, Walnut Creek, California 94598, United States.|Fuels Synthesis and Technology Divisions, DOE Joint BioEnergy Institute , 5885 Hollis Street, Emeryville, California 94608, United States.
authors.forename: Nathan J
authors.initials: NJ
authors.lastname: Hillson
authors.affiliation: DOE Joint Genome Institute , 2800 Mitchell Drive, Walnut Creek, California 94598, United States.
authors.forename: Samuel
authors.initials: S
authors.lastname: Deutsch
mesh_terms: D017076:Computer-Aided Design; D004247:DNA / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D005813:Genes, Synthetic / Q000235:genetics; D005818:Genetic Engineering / Q000379:methods*; D012984:Software; D058615:Synthetic Biology / Q000379:methods*
chemical_list: D004247:DNA
keywords: DNA synthesis; bioCAD/CAM; design−build−test; synthetic biology