APPLICATIONS OF TECHNOLOGY: 

  • Synthetic biology 
  • Genomics
  • Gene characterization
  • Drug discovery

BENEFITS: 

  • Accelerates gene discovery and characterization toward practical applications
  • Significantly reduces cost and turnaround time of DNA sequence synthesis
  • Automatically detects and redesigns difficult sequences for DNA synthesis with higher success rates, eliminating trial-and-error processes
  • Converts files among common synthetic biology software formats

BACKGROUND: 

Synthetic biology enables the design and synthesis of DNA sequences that are difficult to find in nature, as well as sequences that are not known to occur naturally, with potential applications in diverse fields, such as fuels, chemical production, and cellular engineering, among others. However, not every DNA sequence can be readily manufactured due to current limitations of biological design software tools and constraints of DNA synthesis.

TECHNOLOGY OVERVIEW: 

Researchers at Berkeley Lab and the U.S. Department of Energy Joint Genome Institute have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. The BOOST library offers a wide range of capabilities, including:

  • Reverse translation and codon juggling
  • Detection and resolution of constraint violations
  • Polishing of individual sequences
  • Sequence partitioning

The detection of constraint violations preempts the need for sequence redesign by users. In addition, by optimizing the design of DNA sequences, the BOOST library can significantly reduce the cost and turnaround time of DNA synthesis, compared to commercial DNA design software tools.

DEVELOPMENT STAGE: Proven principle 

RELATED TECHNOLOGIES: 

ART: A machine learning Automated Recommendation Tool for guiding synthetic biology 2020-011

Toaster Software: Optimizing CRISPR Technologies for Genome Editing 2016-056

PRINCIPAL INVESTIGATORS: Ian Blaby, Gautham Mani, Ernst Oberortner, Jan-Fang Cheng, Nathan J. Hillson, Samuel Deutsch

FOR MORE INFORMATION:

“Streamlining the Design-to-Build Transition with Build-Optimization Software Tools,” ACS Synth. Biol. 2017, 6, 3, 485–496, December 6, 2016

“New Software Tools Streamline DNA Sequence Design-and-Build Process,” Joint Genome Institute

OPPORTUNITIES: Available for licensing or collaborative research