Hydroxyl Radical Footprinting
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The basic principle of the DNA footprinting technique is the measuring of the accessibility of the DNA by a probe. The probe can be an enzyme or a chemical reagent that is able to cut the DNA backbone. The target is a DNA fragment with a signal-sequence for a sequence-specific binding protein. The sites on the DNA that interact with the protein are excluded from cutting by the probe. These sites appear after electrophoresis as blanks in the otherwise regular cutting pattern, which represent the characteristic footprint of the protein.
