Practice question

DNase I footprinting precisely maps nucleotide-resolution binding sites of proteins on DNA, essential for promoter and operator analysis. End-labeled DNA fragment is first incubated with purified protein to allow specific complex formation, then subjected to limited digestion with DNase I endonuclease which randomly cleaves accessible phosphodiester bonds. Protein-occupied regions resist cleavage, creating gap in otherwise continuous ladder after denaturing polyacrylamide gel electrophoresis and autoradiography. Comparing digestion patterns with and without protein reveals protected motifs, identifying binding sites for transcription factors, repressors or nucleosomes rather than measuring transcription directly.