Reporter assay using the beta-galactosidase (lacZ) gene. The lacZ gene is typically fused to the promoter of interest. Differential regulation of the promoter mediated by the TF is assessed by induction of the system and evaluation of lacZ expression. Bacteria expressing lacZ appear blue when grown on a X-gal medium. The assay is often performed using a plasmid borne construction on a lacZ(def) strain.

Target-specific mutation, as opposed to non-specific mutation. In the context of TF-binding sites, site-directed mutagenesis is typically used to establish/confirm the specific sequence and location of a site, often in tandem with EMSA. Different positions of a putative binding site are mutated to non-consensus (or random) bases and binding to the mutated site is evaluated through EMSA or other means. Often implemented only in conserved motif positions or serially through all positions of a site.

While DNase is by far the most commonly used tool for fragmenting DNA, it is not the only one. DNA footprinting can also be performed using other methods that cause non-specific breaks in the DNA, such as hydroxyl radicals, or UV radiation. There is little difference between these alternate methods of DNA cleavage and the more common DNase-mediated procedure aside from variant resolving power (hydroxyl radicals have a higher resolution) and small procedural changes. The data looks very similar, and is analyzed the same way.

Visual inspection of promoter region to identify putative binding sites based on previous knowledge