Steps of DNA footprinting start by amplify region of interested DNA molecule by conventional PCR and label amplified DNA with radioactivity or fluorescence label probe and apply incubation with protein and immunoprecipitation After that apply DNA modification with DNA modifiers or cleavage agents such as (DNase-1 or Hydroxyl radicals) then run polyacrylamide gel electrophoresis with uniform ladder for control sample to allow prediction of exact location of binding site so footprinting is a gap pattern on polyacrylamide gel which mean protein bound DNA and protect DNA from cleavage agent (Watch Related Video in #geneticteacher)
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