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Design-Build-Test-Learn Cycle of Synthetic Biology Innovation

April 16, 2024

The Design-Build-Test-Learn (DBTL) cycle embodies the essence of synthetic biology, guiding researchers on a journey of discovery and innovation. By seamlessly integrating design principles, molecular engineering, empirical testing, and iterative learning, this process empowers scientists to engineer biological systems with unprecedented functionality. 

DESIGN. The process starts with clearly defining the problem to be solved or the goal to be achieved including identifying the desired biological function or trait to be engineered. Researchers design the DNA sequences needed to encode the desired biological functions including designing new genes, modifying existing genes, or assembling genetic circuits.

  • Computer with software for DNA design and modeling (e.g., Geneious, Benchling, SnapGene)
  • Access to biological databases for sequence analysis (e.g., NCBI, UniProt)

BUILD. Researchers synthesize DNA or isolate and purify genomic DNA which is then assembled into larger DNA constructs or vectors. This may involve techniques such as polymerase chain reaction (PCR), Gibson assembly, or Golden Gate assembly. The assembled DNA is then cloned into a suitable host organism, such as bacteria or yeast. The cloned DNA constructs are introduced into the host organism through a process called transformation (for bacteria) or transfection (for eukaryotic cells). This step is crucial for getting the engineered DNA into the cells where it will be expressed.

  • Oligonucleotide synthesizer (for designing primers and probes)
  • PCR machine / thermocycler 
  • Gel electrophoresis & imaging
  • Enzymes and reagents for DNA manipulation (e.g., DNA polymerase, restriction enzymes)
  • DNA sequencer
  • Competent cells for transformation (for bacteria) or transfection reagents (for eukaryotic cells)
  • Incubators for cell culture
  • Microcentrifuge for cell pellet preparation
  • Water bath for heat shock transformation (for bacteria) or electroporation (for eukaryotic cells)

TEST. In vitro characterization techniques allow researchers to observe how the engineered system behaves in living cells. By conducting a battery of assays and experiments, scientists assess the system’s function, performance, and robustness. This phase provides valuable insights into the system’s behavior under various conditions.

  • Microscopes for observing cell morphology
  • Spectrophotometer for measuring optical density and absorbance
  • Plate reader for fluorescence-based assays
  • Chromatography equipment for analyzing metabolites or proteins

LEARN. DNA sequences and experimental conditions may need to be optimized to improve the performance of the engineered system. These insights inform iterative refinements to the design, guiding subsequent cycles of the DBTL process. Each iteration brings scientists closer to optimizing the biological system for its intended application.

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