DNA Footprinting was developed in 1977 and is an analytical procedure in molecular biology for identifying the specific sequence of DNA (the binding site) that binds to a particular protein. DNA Footprinting is most commonly performed on proteins that are thought to play some significant functional role such as gene regulation. This method can be performed on proteins which bind both double and single-stranded DNA. Additionally, DNA-binding proteins can be split into two groups, namely site-specific DNA-binding proteins and non-specific DNA–binding proteins. DNA Footprinting uses a damaging agent such as a chemical reagent, radical or a nuclease that can cut or modify DNA at every base pair. However, where the ligand binds to DNA, the cleavage is restrained. DNA Footprinting discovers which specific parts of a DNA molecule have sites for specific proteins to attach to them. Using this technique, DNA that has first been in the presence of DNA-binding proteins and then exposed to a damaging agent, can be compared to DNA that was never exposed to the binding protein (and thus not protected against the damaging agent). The DNA sequence that is protected from cleaving can then be identified as the binding site.
DNA Footprinting can provide information that is, conceptually, much like fingerprinting in the sense that it can be used to identify a unique individual. DNA Footprinting can extract a banding pattern, or electropherogram, much like a bar code, that can identify a species or individual (some genes will be vary at the species level and others at the individual level)