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Published on: November 10, 2016
Mechanism of topology simplification by type II DNA topoisomerases
A V Vologodskii1, W Zhang, V V Rybenkov
1Department of Chemistry, New York University, Washington Square, New York, NY 10003, USA. alex.vologodskii@nyu.edu
Abstract:
Type II DNA topoisomerases actively reduce the fractions of knotted and catenated 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 relative to the bend, they act like Maxwell's demon, providing unidirectional strand passage. Quantitative analysis of the model by computer simulations proved that it can explain much of the experimental data. The required sharp DNA bend was demonstrated by a greatly increased cyclization of short DNA fragments from topoisomerase binding and by direct visualization with electron microscopy.
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