DNase I footprinting is used to:
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, id
Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.
