DNase I Footprinting assay is a method of studying DNA -protein interaction and identifying the DNA-sequence to which a protein binds. First, a target DNA-fragment about 100-300 bp in length is either PCR generated or cut from a vector and then uniquely labeled (at only one end) and incubated with protein (usually nuclear extract), followed by controlled digestion with DNase I which cut the probe randomly but only once. The digested DNA is recovered from the reaction and resolved on a polyacrylamide gel along with G+A chemical sequencing reaction which uses the same probe as template. The regions bound by proteins will be protected from DNase I digestion and will be shown as a blank area on the gel track, while the exact protein-bound sequence can be read out by comparing the location of the blank with the sequencing reaction.
