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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.