Simplification of DNA Topology Below Equilibrium Values by Type II Topoisomerases

Rybenkov, Valentin V.; Ullsperger, Christian J.; Vologodskii, Alexander; Cozzarelli, Nicholas R.

doi:10.1126/science.277.5326.690

Cited by 257 publications

(373 citation statements)

References 18 publications

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“…Since the publication by Rybenkov et al (1997) demonstrating that Type IIA topoisomerases (with the exception of DNA gyrase) reduce the level of DNA linking, knotting, and supercoiling to below thermal equilibrium vales, it has remained a puzzle how these enzymes simplify global topology. Energetically, below-equilibrium topology simplification by Topo IIA does not violate thermodynamics since these topoisomerases utilize ATP as an energy source, so they can work against the thermal equilibrium limit.…”

Section: Dna Twist (Torsion)-dependent Protein Activitymentioning

confidence: 99%

“…Topo IA and IB, on the other hand, do not utilize external energy, so they can only achieve thermodynamic equilibrium topological distributions. It remains unclear, however, how Topo IIA employ some of the energy of ATP hydrolysis to distinguish DNA juxtapositions in catenanes and knots and writhe of supercoils, from those occurring within or between DNA molecules due to thermal fluctuations (Rybenkov et al 1997). This implies that Topo IIA must Bsense^which juxtapositions simplify global DNA topology when unlinked.…”

Section: Dna Twist (Torsion)-dependent Protein Activitymentioning

confidence: 99%

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The dynamic interplay between DNA topoisomerases and DNA topology

Seol

Neuman

2016

Biophys Rev

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Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

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Section: Dna Twist (Torsion)-dependent Protein Activitymentioning

confidence: 99%

Section: Dna Twist (Torsion)-dependent Protein Activitymentioning

confidence: 99%

The dynamic interplay between DNA topoisomerases and DNA topology

Seol

Neuman

2016

Biophys Rev

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“…(1), (2), (14), (21). So far, it was (hopefully) clear from the context in every place which x we have in mind.…”

Section: B Winding Around a Disc (B > 0)mentioning

confidence: 99%

“…Moreover, apart from networks, there is now another large "consumer" for polymer topology, this is DNA physics. The DNA double helix is frequently found in a closed loop form, it forms knots of various kinds [19,20], and there are special enzymes spending energy to simplify the entanglements [21].…”

Section: Introductionmentioning

confidence: 99%

Winding angle distribution for planar random walk, polymer ring entangled with an obstacle, and all that: Spitzer–Edwards–Prager–Frisch model revisited

Grosberg

2003

J. Phys. A: Math. Gen.

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Using a general Green function formulation, we re-derive, both, (i) Spitzer and his followers results for the winding angle distribution of the planar Brownian motion, and (ii) Edwards-Prager-Frisch results on the statistical mechanics of a ring polymer entangled with a straight bar. In the statistical mechanics part, we consider both cases of quenched and annealed topology. Among new results, we compute exactly the (expectation value of) the surface area of the locus of points such that each of them has linking number n with a given closed random walk trajectory (= ring polymer). We also consider the generalizations of the problem for the finite diameter (disc-like) obstacle and winding within a cavity.

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“…Mechanistically operating on writhe, Top2 requires repartitioning of strain along the helical axis to relax twist. Though relaxation is an energetically favored event, the extra energy from ATP-hydrolysis sharpens the distribution of relaxed products more than can be explained by a thermal Boltzmann partition function (Bates and Maxwell 2005;Podtelezhnikov et al 1999;Rybenkov et al 1997;Vologodskii 2009;Yan et al 1999). There are two major Top2s, Top2A and Top2B (Nitiss 2009).…”

mentioning

confidence: 99%

Controlling gene expression by DNA mechanics: emerging insights and challenges

2016

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Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions. The double helix is a fiber that responds to flexural and torsional stress, which if accumulated, can affect promoter output as well as change DNA and chromatin structure. The relationship between DNA mechanics and the control of early transcription initiation events has been under-investigated. Genomic techniques to display topological stress and conformational variation in DNA across the mammalian genome provide an exciting new insight on the role of DNA mechanics in the early stages of the transcription cycle. Without understanding how torsional and flexural stresses are generated, transmitted, and dissipated, no model of transcription will be complete and accurate.

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Simplification of DNA Topology Below Equilibrium Values by Type II Topoisomerases

Cited by 257 publications

References 18 publications

The dynamic interplay between DNA topoisomerases and DNA topology

The dynamic interplay between DNA topoisomerases and DNA topology

Winding angle distribution for planar random walk, polymer ring entangled with an obstacle, and all that: Spitzer–Edwards–Prager–Frisch model revisited

Controlling gene expression by DNA mechanics: emerging insights and challenges

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