Practice question

DNase I footprinting visualizes specific protection from nuclease cleavage. Radiolabeled DNA digested with limiting DNase I normally yields continuous ladder of bands after denaturing electrophoresis. When sequence-specific DNA-binding protein occupies major groove, it physically blocks nuclease access to phosphate backbone within its recognition motif. Protected region therefore lacks cleavage products, appearing as blank gap or footprint within ladder. Mapping gap boundaries defines length and sequence of protein recognition element for transcription factors or repressors. This protection pattern represents protein-binding site rather than degradation, mutation or hybridization site.