Human topoisomerase II–DNA interaction study by using atomic force microscopy

Type II topoisomerases (Topo II) are unique enzymes that change the DNA topology by catalyzing the passage of two double-strands across each other by using the energy from ATP hydrolysis. In vitro, human Topo II relaxes positive supercoiled DNA around 10-fold faster than negative supercoiled DNA. By using atomic force microscopy (AFM) we found that human Topo II binds preferentially to DNA cross-overs. Around 50% of the DNA crossings, where Topo II was bound to, presented an angle in the range of 80–90°, suggesting a favored binding geometry in the chiral discrimination by Topo II. Our studies with AFM also helped us visualize the dynamics of the unknotting action of Topo II in knotted molecules.

► Human Topo II binds preferentially to DNA cross-overs.
► 50% of the DNA crossings where Topo II was bound had an angle in the range of 80–90°.
► We observed the untangling action of human Topo II on knotted DNA molecules.