Cell-free screening of CRISPR-Cas activity by microfluidics-assisted in vitro compartmentalization

CRISPR-Cas systems are responsible for antiviral immunity of prokaryotic cells and have been repurposed as powerful genome-editing tools. Cell-free gene expression has been applied for the rapid characterization of CRISPR-Cas systems in microtiter plates. In vitro compartmentalization makes use of artificial microcompartments that individually act as bioreactors. Here, we performed cell-free reactions of CRISPR-Cas activity into microtiter plates, which we proceeded to encapsulate into double emulsion (DE) droplets generated by on-chip microfluidics. Emulsion droplets were screened for CRISPR-Cas activity based on relative fluorescence levels using a common cell sorter, and enrichment for the expected guide (g)RNA genotype was observed. Encapsulation of single gene copies per droplet is an important prerequisite for applying this technique to complex gene libraries. We show a proof-of-principle assay for efficient, compartmentalized gene amplification using magnetic microbeads. In conclusion, we demonstrate the feasibility of microfluidics-based, high-throughput, cell-free screening of CRISPR-Cas activity.