Hydroxyl Radical Interference

Interference studies are just the inverse approach of “footprinting ” experiments. In both types of experiments the effect of a chemical modification of a single base on the binding of a sequence-specific protein is determined, but the experiments differ in the sequence of the binding event and the modification procedure. The “interference ” approach is characterized first by chemical modification of the DNA and then by subsequent protein binding. These studies provide information about the change of the binding strength following single base modification. This change can be positive or negative. A quantification of the effect is possible by the gel shift assay (1 ).