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New Software Tools Streamline DNA Sequence Design-and-Build Process
Published: December 06, 2016
Posted: March 16, 2017

The goal of build optimization software tools is to streamline, in a scalable fashion, the process of designing readily synthesizable DNA fragments. [Image courtesy of the Department of Energy’s Joint Genome Institute]

These enhanced tools will accelerate gene discovery and characterization.

The Science                       
Synthetic DNA enables scientists to expand the breadth and depth of their genomic research. In a recent study, researchers developed a suite of build optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. BOOST can automatically detect “difficult” sequences of nucleotides and redesign them for DNA synthesis, addressing DNA sequences with certain problematic characteristics (e.g., extreme % guanine-cytosine content, sequence patterns, and repeats), which decrease the success rate of DNA synthesis.

The Impact
By improving the design and manufacture of synthetic DNA through enhanced tools, scientists can accelerate gene discovery and gene characterization toward practical applications for energy and the environment.

Summary
The ability to design and manufacture synthetic DNA has opened tremendous possibilities in genomic research. In addition to providing access to samples that are difficult to find in nature (as well as crafting genomic sequences not known to occur in the natural world), manufacturing DNA enables scientists to test any sequence in a wide variety of contexts and environments. Biological computer-aided design and manufacture (bioCAD/CAM) software tools help researchers design sequences that can be critical to discovering new solutions for energy and the environment. So far, however, the software has not been able to automatically fix problematic sequences, slowing down the transition from the design to the manufacturing process and delaying the synthesis of designed DNA.

To solve this problem, researchers at the U.S. Department of Energy’s (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility, developed the BOOST suite to automate the synthetic DNA design process—and do away with the trial-and-error process scientists currently utilize to determine a sequence that can be synthesized.

The new suite of tools is available as a web application, an executable JAVA Archive (JAR), and as a representational state transfer application program interface (RESTful API). Ultimately, BOOST will accelerate the use of synthetic DNAs to explore gene functions relevant to DOE’s energy and environmental missions.

Contact (BER PM)
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
daniel.drell@science.doe.gov

(PI Contact)
Samuel Deutsch
DOE Joint Genome Institute SDeutsch@lbl.gov

Funding
U.S. Department of Energy Office of Science

Publication
E. Oberortner, J.F. Cheng, N.J. Hillson, and S. Deutsch, “Streamlining the design-to-build transition with build-optimization software tools.” ACS Synthetic Biology (2016). DOI:10.1021/acssynbio.6b00200. (Reference link)

Related Links
BOOST
JGI: DNA Synthesis Science Program

Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: DOE Joint Genome Institute (JGI)
  • Research Area: DOE Bioenergy Research Centers (BRC)
  • Research Area: Biosystems Design
  • Research Area: Computational Biology, Bioinformatics, Modeling

Division: SC-33.2 Biological Systems Science Division, BER

 

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