Using quantum-dot-labeled DNA and total internal reflection fluorescence microscopy, we can investigate the reaction mechanism of restriction endonucleases while using unlabeled protein. This single-molecule technique allows for massively multiplexed observation of individual protein-DNA interactions, and data can be pooled to generate well-populated dwell-time distributions.
Etson, C. M., Todorov, P., Shatery Nejad, N., Shrestha, N., Walt, D. R. Single-Molecule Dwell-Time Analysis of Restriction Endonuclease-Mediated DNA Cleavage. J. Vis. Exp. (168), e62112, doi:10.3791/62112 (2021).