Biophysical Society Thematic Meeting| Lima 2019

Revisiting the Central Dogma of Molecular Biology at the Single-Molecule Level

Poster Abstracts

21-POS Board 21 KINETIC PATHWAYS IN KNOTTED SUPERCOILED DNA INDUCED BY TYPE-II TOPOISOMERASES AND SITE-SPECIFIC RECOMBINASES Andreas Hanke 1 ; Riccardo Ziraldo 2 ; Stephen D Levene 2 ; 1 University of Texas Rio Grande Valley, Physics and Astronomy, Brownsville, TX, USA 2 University of Texas at Dallas, Bioengineering, Richardson, TX, USA The topological state of covalently closed, double-stranded DNA is defined by the knot type K and the linking-number difference DLk relative to unknotted relaxed DNA. DNA topoisomerases are essential enzymes that control the topology of DNA in all cells. In particular, type-II topoisomerases change both K and DLk by a duplex-strand-passage mechanism and have been shown to simplify the topology of DNA to levels below thermal equilibrium at the expense of ATP hydrolysis. It remains a key question how small enzymes are able to preferentially select strand passages that result in topology simplification in much larger DNA molecules. Using numerical simulations, we consider the non-equilibrium dynamics of transitions between topological states (K, DLk) in DNA induced by type-II topoisomerases modeled as a hairpin-like gate segment. For a biological process that delivers DNA molecules in a given topological state (K, DLk) at a constant rate we fully characterize the pathways of topology simplification by type-II topoisomerases in terms of stationary probability distributions and probability currents on the network of topological states (K, DLk). Surprisingly, only a small number of intermediate topological states contribute to the pathways, namely those that dominate the conditional equilibrium distribution P(K|DLk), the distribution of K for given DLk. Our results show that topology simplification by type-II topoisomerases in DNA results from a combination of two effects: Enhanced juxtaposition probability between gate and transfer segments, and enhanced probability for an unknot to stay unknotted after strand passage. Another important class of enzymes capable of changing DNA topology are recombinase proteins, which change the degree of DNA supercoiling, and knot or catenane type, by a segment breakage and rejoining mechanism of specific DNA sites. Using numerical simulations, we fully characterize the distribution of topological states (K, DLk) of recombination products induced by tyrosine recombinases acting on inversely repeated DNA sites.

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