Hydroxyl Radical Footprinting

Abstract

The basic principle of the DNA footprinting technique is the measurement of accessibility of the DNA using a probe. The probe can be any enzyme or a chemical reagent that is able to cut the DNA backbone. When the target DNA is a fragment containing a signal sequence for a sequence-specific binding protein, sites on the DNA that interact with the protein are inaccessible to the probe. After electrophoretic separation based on molecular weight, these inaccessible sites appear as blanks in an otherwise regular DNA cleavage pattern, thus revealing the characteristic interaction footprint for the binding protein.