Watching Cas9 Edit DNA: Nanopores Track Enzymes in Real Time

Nanopore sensing is best known for high-resolution DNA sequencing, but it is rapidly expanding into an exciting new frontier: probing the specific interactions between enzymes and DNA. Historically, measuring how proteins behave on long DNA templates has been difficult due to high translocation speeds and signal noise. Now, researchers have reported the accurate position detection of catalytically active Cas9 bound to target sites on DNA.

By analysing specific electrical signals—specifically the 'event charge deficit' (ECD)—as the complex passes through a glass nanopore, the team could effectively 'fingerprint' the protein's location. This novel approach allowed them to quantify the kinetics of the reaction in real time, observing precisely when the wild-type Cas9 nuclease cleaved its target. This breakthrough enables single-molecule sensing of DNA-protein complexes, which could significantly improve our understanding of protein localisation and enhance Cas9-based targeting in genome engineering applications.