DNA Footprinting

DNA footprinting is often used to locate the binding site for proteins that regulate transcription. For example, a researcher may suspect that a particular protein binds to a particular DNA fragment and inhibits transcription. After conducting a DNA footprinting experiment, the researcher will know the location of the exact sequence of DNA bound by that protein. If that sequence matches the sequence of a promoter the DNA footprinting experiment can help explain how that DNA-binding protein carries out its function.

Modified DNA footprinting experiments can also be performed to detect where proteins bind to DNA in a living cell. In these experiments, cells are grown under conditions where the protein of interest would be expected to bind to DNA. The cells are then treated with a chemical that causes proteins bound to DNA to become permanently attached to the DNA. The resulting DNA-protein complexes are then purified from the cell, and the DNA sequences are identified.

Since DNA footprinting is used to identify the specific sequences in DNA where a protein binds, the technique is likely to be of continuing usefulness in genetic research. For example, DNA footprinting is likely to be heavily used in characterizing the function of proteins identified in the Human Genome Project and other genome projects, making it an important component of a molecular geneticist's toolbox.