DNase footprinting assay

A DNase footprinting assay is a technique from molecular biology that detects DNA-protein interaction using the fact that a protein bound to DNA will often protect that DNA from enzymatic cleavage. The method uses restriction enzymes or other deoxyribonucleases (DNases, for short) to cut the DNA, followed by gel electrophoresis to detect the resulting cleavage pattern. To examine DNA-protein interactions, the cleavage pattern of isolated DNA is compared with the cleavage pattern of DNA in the presence of the putative binding protein. If the protein binds the DNA, the binding site is protected against restriction enzyme cleavage and fewer cleavage sites are detected. From the position of the cleavage sites missing in the assay containing the binding protein, the position and extension of the binding site can be inferred.