DNase footprinting assay

This makes it possible to locate a protein binding site on a particular DNA molecule.

The method uses an enzyme, deoxyribonuclease (DNase, for short), to cut the radioactively end-labeled DNA, followed by gel electrophoresis to detect the resulting cleavage pattern.

For example, the DNA fragment of interest may be PCR amplified using a 32P 5' labeled primer, with the result being many DNA molecules with a radioactive label on one end of one strand of each double stranded molecule.

This protection will result in a clear area on the gel which is referred to as the "footprint".

This technique was developed by David J. Galas and Albert Schmitz at Geneva in 1977[2]

DNase I footprint of a protein binding to a radiolabelled DNA fragment. Lanes "GA" and "TC" are Maxam-Gilbert chemical sequencing lanes, see DNA Sequencing . The lane labelled "control" is for quality control purposes and contains the DNA fragment but not treated with DNase I.