Synthetic Evolution

The Diercks lab applies our T7 ORACLE continuous hypermutation and accelerated evolution technology to challenges in human health and synthetic biology. Key areas of interest are the development of protein therapeutics for targeted protein degradation, the directed evolution of enzyme therapies, as well as new technologies for genetic code expansion. The lab further aims to expand the concept of directed evolution from biomacromolecules to abiological materials and to create Darwinian Nanoparticles with a selectable genotype/phenotype non-viral gene delivery vehicles with improved tissue/cell type tropism, endosomal escape, and intracellular trafficking.

An orthogonal T7 Replisome for Continuous Hypermutation and Accelerated Evolution in E. coli

An Orthogonal Replication System in E. coli

We have developed an orthogonal replication system in E. coli based on the controlled bacterial expression of the replisome of bacteriophage T7. The orthogonality to host replication enables fundamental alteration of the T7 replisome's properties without compromising host fitness. This is exploited by our lab to (i) increase the T7 replisome's mutation rate for for continuous hypermutation and accelerated evolution of genes of interest (T7 Orthogonal Replisome Assisted Continuous Laboratory Evolution, T7 ORACLE), as well as (ii) to expand the genetic alphabet and replicate new-to nature genetic polymers in vivo.

Continuous Evolution of Enzyme Therapeutics

We have engineered T7 ORACLE for continuous hypermutation of genes of interest in E. coli at rates 100,000-fold faster than genomic replication We leverage this system for the continuous evolution of protein and enzyme therapeutics, high-affinity binders (e.g., monobodies, scFvs, FABs), as well as for repurposing the cell's macromolecular machinery for genetic code expansion. These areas remain underexplored in the context of directed evolution because conventional technologies render high-throughput evolution too laborious and time consuming for an academic setting. T7 ORACLE addresses this limitation and reduces directed evolution campaigns to mere passaging of cells.

Directed Evolution of Botox Protease for Targeted Protein Degradation

Developing generalizable strategies to degrade "undruggable proteins" represents a path towards cures for currently untreatable diseases. We aim to evolve botulinum neurotoxin type A (BonT/A)—a bacterial protease used by millions for cosmetic and therapeutic applications—to change its substrate specificity and selectively cleave proteins that cannot be targeted by small molecules. The extended binding site and concomitant high sequence specificity of Botox for its intrinsically disordered target protein SNAP25 supports the great promise of this approach. Efforts in our lab focus on applying this strategy to targets in oncology and in pain.

Darwinian Nanoparticles for Gene Delivery

We are developing a system for the directed evolution of “Darwinian Nanoparticles”. By endowing abiotic nanomaterials with a selectable genotype-phenotype link we aim to harness the concept of Darwinian evolution for the optimization of non-viral gene delivery vehicles. This will serve as a general high throughput diversification and screening strategy to supplement existing rational design approaches to optimize synthetic nanoparticles for applications in vivo. Iterative rounds replication, diversification, and selection of libraries of such "Darwinian Nanoparticles" will be used to develop next generation drug- and gene delivery vehicles.