Practice question

In DNase I footprinting, limited digestion of labeled DNA normally generates ladder representing cleavage at every accessible phosphodiester bond. After denaturing gel electrophoresis, band pattern reflects random cuts. When DNA-binding protein occupies specific sequence, it sterically shields underlying backbone, preventing DNase I access and cleavage at those positions. Hence corresponding bands disappear, leaving clear window termed footprint. Location and length of absent bands map binding motif coordinates. This absence indicates protected protein-bound region, distinguishing sequence-specific occupancy from changes in gene expression, amplification or non-coding nature.