Emmanuel College 1 article published in JoVE Biology Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage Emily K. Matozel1, Nathaniel Dale1, Allen C. Price2 1Department of Biology, Emmanuel College, 2Department of Chemistry and Physics, Emmanuel College A highly parallel method for measuring the site-specific cleavage of DNA at the single molecule level is described. This protocol demonstrates the technique using the restriction endonuclease NdeI. The method can easily be modified to study any process that results in site-specific DNA cleavage.