DNA manufacturing vs. gene synthesis

After designing a DNA sequence, synthetic biologists need to make it. We prefer to refer to that step as “DNA manufacturing” rather than “gene synthesis“. In most cases, people need to produce sequences that are much longer than a gene. Manufacturing includes the de novo synthesis of gene-sized fragments but also techniques to assemble these fragments in larger constructs.

None of the individual steps of manufacturing processes are particularly challenging to perform on their own. It is possible to do gene synthesis using standard laboratory equipment and standard molecular biology protocols. The main challenge lies in the complexity of the DNA manufacturing workflows. Assembling a complex DNA molecule or a library of related molecules requires a lot of operations.  Orchestrating the overall process can quickly become overwhelming. Failure to manage the process can jeopardize the project success.

Informatics challenges

Some of the challenges we are trying to solve include:

  • Streamline quality control operations by developing algorithms that automate the comparison of a reference sequence and the physical sequence produced by the assembly of sequencing reads. (see Software for details)
  • Processes to manage laboratory information in a synthetic biology laboratory. In particular, processes to document the sequence of the samples handled by the laboratory (See LIMS for details).
  • Minimizing the cost of DNA manufacturing projects by maximizing reusability of genetic material and modeling the cost structure of various assembly strategies.
  • Maintaining the security of a DNA manufacturing operation by developing threat detection algorithms to monitor the biosecurity of the genetic material circulating in a facility (See Cyberbiosecurity for details).