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      Streamlining the Design-to-Build Transition with Build-Optimization Software Tools

      1 , 1 , 1 , 2 , 1
      ACS Synthetic Biology
      American Chemical Society (ACS)

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          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.

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          Author and article information

          Journal
          ACS Synthetic Biology
          ACS Synth. Biol.
          American Chemical Society (ACS)
          2161-5063
          2161-5063
          November 17 2016
          March 17 2017
          December 22 2016
          March 17 2017
          : 6
          : 3
          : 485-496
          Affiliations
          [1 ]DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, United States
          [2 ]Fuels Synthesis and Technology Divisions, DOE Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
          Article
          10.1021/acssynbio.6b00200
          28004921
          94d2da4f-1796-4e09-ab97-b90f305dc926
          © 2017
          History

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