The process typically involves several steps: 1. Labeling the DNA: A DNA fragment of interest is end-labeled with a radioactive or fluorescent marker. 2. Protein Binding: The labeled DNA is incubated with the protein of interest, allowing it to bind to specific sites on the DNA. 3. DNase I Digestion: The DNA-protein complex is treated with DNase I. The regions of DNA not bound by the protein will be cleaved by DNase I, while the bound regions will be protected. 4. DNA Fragment Analysis: The digested DNA is then separated on a polyacrylamide gel. The protected regions appear as gaps or "footprints" in the pattern of cleaved DNA.
