Mechanism of topology simplification by type II DNA topoisomerases

Type II DNA topoisomerases actively reduce the fractions of knotted and cat enated circular DNA below thermodynamic equilibrium values. To explain this surprising finding, we designed a model in which topoisomerases introduce a sharp bend in DNA. Because the enzymes have a specific orientation relati ve to the bend, they act like Maxwell's demon, providing unidirectional str and passage. Quantitative analysis of the model by computer simulations pro ved that it can explain much of the experimental data. The required sharp D NA bend was demonstrated by a greatly increased cyclization of short DNA fr agments from topoisomerase binding and by direct visualization with electro n microscopy.