The topoisomerase II N-terminal ATPase clamp stabilization assay can determine the relative stability of the topoisomerase–DNA interaction. After allowing the protein and purified DNA to interact for a fixed amount of time, the protein:DNA complexes are then bound to a glass fiber filter where a series of washes of increasing stringency are applied. These washes can disrupt the protein:DNA interaction depending on the strength of the complex and whether the N-terminal domain, referred to here as the “clamp,” has closed around the DNA. The DNA flow through from each step can be concentrated and then quantified using gel electrophoresis. This approach enables researchers to examine what conditions tend to stabilize the enzyme:DNA complexes.