The DNA template labeled at the 3 or 5 end, depending on the location of the binding site(s).  Labels that can be used are: radioactivity and fluorescence. Radioactivity has been traditionally used to label DNA fragments for footprinting analysis, as the method was originally developed from the Maxam-Gilbert chemical sequencing technique.  Radioactive labeling is very sensitive and is optimal for visualizing small amounts of DNA. Fluorescence is a desirable advancement due to the hazards of using radio-chemicals.  However, it has been more difficult to optimize because it is not always sensitive enough to detect the low concentrations of the target DNA strands used in DNA footprinting experiments.  Electrophoretic sequencing gels or capillary electrophoresis have been successful in analyzing footprinting of fluorescent tagged fragments.