Type II topoisomerases are essential enzymes common to all organisms. Their cellular functions includemaintaining the levels of chromosome compaction and ensuring proper segregation at cell division. Inaddition they are often used as targets for antimicrobial agents and anticancer drugs. Understanding theprocess by which topoisomerase II (topo II) simplifies the topological complexity of its DMA substrate is ofkey importance. By a cut-and-paste mechanism, which is well understood at the molecular level, topo II isable to pass a DMA segment through another. How topo II recognizes the two DMA segments is stillunclear. Topo II is known to unknot and decatenate DMA to levels below those expected by randomstrand-passage. These and other experimental observations suggest a chirality-driven non-randommechanism of topo II action. Numerous experimental and theoretical studies have addressed thesequestions. However a clear picture of the mechanism of topo II is still lacking. Our long-term goal is tofind an accurate model for the mechanism of topology simplification by topo II. We here focus on theprocess of DNA unknotting. Our objective is to verify whether topo II has the ability to unknot DMA in thesmallest possible number of strand-passages, or whether a chirality bias combined with other localinformation are sufficient to reach the experimentally observed unknotting levels. We propose aninterdisciplinary approach involving a sophisticated theoretical framework based on mathematical knottheory and Monte Carlo computer simulations, and followed by experimental validation. The computerimplementation is based on a novel idea which will greatly reduce computation time as compared to othercomputational models of unknotting.Relevance to Public Health: Our method will give us the ability to efficiently simulate wild-type topo IIon any distribution of DNA knots. Besides being of theoretical interest, such modeling is relevant to publichealth. Unknotting assays are used in the design of anti-cancer drugs to identify new topo II inhibitors.Our work will be applied to quantifying the unknotting capabilities of the topo II of a given organism withand without the presence of an inhibitor, thus establishing a precise measure of the inhibitor'seffectiveness.
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