Determining the topology of stable protein–DNA complexes

Difference topology is an experimental technique that can be used to unveil the topological structure adopted by two or more DNA segments in a stable protein–DNA complex. Difference topology has also been used to detect intermediates in a reaction pathway and to investigate the role of DNA supercoiling. In the present article, we review difference topology as applied to the Mu transpososome. The tools discussed can be applied to any stable nucleoprotein complex.