Figure 14.

Topoisomerase reaction cycle. A) The three steps in the vTopo reaction involve DNA binding, reversible DNA backbone cleavage described by the rate constants k_cl and k_r, and for supercoiled DNA substrates, supercoil relaxation while the enzyme is covalently attached to the phosphodiester backbone (k_sup). Relaxation occurs by a “free rotation” mechanism in which the noncovalently bound end swivels around the helix axis. The number of supercoils that are removed after a single cleavage event is dependent on the ratio k_sup/k_r: if k_r is rapid there is no opportunity for DNA rotation before the strand is resealed. B) Free energy reaction coordinate profile depicting the thermodynamic and kinetic barriers of the reaction. The rate constants and equilibrium constants refer to the free energy barriers defined by K = exp (−ΔG/RT) and k = (k_BT/h) exp(−ΔG^‡/RT).