Project

Better genome editing tools through bacterial sex – Laboratory evolution of DNA nucleases

Evolution has given us powerful tools like CRISPR-Cas. We might now use artificial evolution to further improve these tools.

Background

Laboratory evolution is a powerful tool for improving proteins. However, for CRISPR-Cas9 and similar enzymes, it is complicated to establish a continuous system. After all, these enzymes cleave DNA sequences, resulting in irreversible degradation of the cleaved product. We might overcome this hurdle by having bacteria transfer genes between them. By including this horizontal gene transfer (HGT) step, we could create a continuous selection system for DNA cleaving enzymes.

Aim

The aim of this project is to establish a selection system using the transfer of plasmid DNA (plasmid conjugation) between bacteria. This system will be tested and optimized for the selection of DNA cleaving enzymes like Cas9. If successful, the selection can be combined with random mutagenesis to provide enzymes with improved traits.

Techniques

Depending on the phase of the project, BSc or MSc students will have the opportunity to work with:

  • Molecular cloning
  • Plasmid conjugation
  • Genome editing in bacteria
  • Laboratory evolution
  • Random mutagenesis
  • Flow cytometry of bacterial cells
Laboratory evolution of DNA nucleases

Contact

Due to the current Covid-19 situation no thesis projects can be offered at the moment. However, if the above text sparks your interest, contact Thomas Swartjes to arrange a BSc or MSc thesis as soon as a laboratory-based project can be arranged again (thomas.swartjes@wur.nl).