DNA footprinting is a technique for identifying exactly where a protein binds to DNA. Knowing where a protein binds to DNA often aids in understanding how gene expression is regulated. Consequently, DNA footprinting is often part of a larger study to determine how a particular gene is controlled.

How It Works

DNA footprinting is based on the observation that when a protein binds to DNA, the DNA is protected from chemicals that would otherwise cleave it. In a typical DNA footprinting experiment, a DNA fragment with a suspected protein-binding site is first isolated, then labeled with a radioactive nucleotide or other chemical that will allow it to be detected later on.

Once labeled, the DNA is then mixed in a test tube with a DNA-binding protein and a chemical that cleaves DNA, such as the enzyme DNase I. In a separate test tube, more of the...