ArticleNucleic acids research2013
Comparison of DNA decatenation by Escherichia coli topoisomerase IV and topoisomerase III: implications for non-equilibrium topology simplification.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Type II topoisomerase substrate geometry revealed through combined experiment and computation.bioRxiv : the preprint server for biology · 2026Article
- Geometry of braided DNA dictates supercoiling partitioning.Nature communications · 2026Article
- Geometry of Braided DNA Dictates Supercoiling Partition.bioRxiv : the preprint server for biology · 2024Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2024Article
- MukBEF-dependent chromosomal organization in widenedFrontiers in microbiology · 2023Article
- Single-nucleotide resolution detection of Topo IV cleavage activity in theFrontiers in microbiology · 2023Article
- Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2022Article
- Duplex DNA and BLM regulate gate opening by the human TopoIIIα-RMI1-RMI2 complex.Nature communications · 2022Article
- Single-molecule measurements reveal that PARP1 condenses DNA by loop stabilization.Science advances · 2021Article
- Unravelling the mechanisms of Type 1A topoisomerases using single-molecule approaches.Nucleic acids research · 2021Review
- DNA-Topology Simplification by Topoisomerases.Molecules (Basel, Switzerland) · 2021Review
- Mechanisms for Chromosome Segregation in Bacteria.Frontiers in microbiology · 2021Review
- Topoisomerase IV can functionally replace all type 1A topoisomerases in Bacillus subtilis.Nucleic acids research · 2019Article
- Genome-wide mapping of Topoisomerase I activity sites reveal its role in chromosome segregation.Nucleic acids research · 2019Article
- Kinetic pathways of topology simplification by Type-II topoisomerases in knotted supercoiled DNA.Nucleic acids research · 2019Article
- Direct observation of topoisomerase IA gate dynamics.Nature structural & molecular biology · 2018Article
- Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices.Physical review letters · 2017Article
- Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase.PLoS genetics · 2017Article
- Torque and buckling in stretched intertwined double-helix DNAs.Physical review. E · 2017Article
- The dynamic interplay between DNA topoisomerases and DNA topology.Biophysical reviews · 2016Review
Corrections and comments
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Authors and funding
5 authors.
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Abstract
Type II topoisomerases are essential enzymes that regulate DNA topology through a strand-passage mechanism. Some type II topoisomerases relax supercoils, unknot and decatenate DNA to below thermodynamic equilibrium. Several models of this non-equilibrium topology simplification phenomenon have been proposed. The kinetic proofreading (KPR) model postulates that strand passage requires a DNA-bound topoisomerase to collide twice in rapid succession with a second DNA segment, implying a quadratic relationship between DNA collision frequency and relaxation rate. To test this model, we used a single-molecule assay to measure the unlinking rate as a function of DNA collision frequency for Escherichia coli topoisomerase IV (topo IV) that displays efficient non-equilibrium topology simplification activity, and for E. coli topoisomerase III (topo III), a type IA topoisomerase that unlinks and unknots DNA to equilibrium levels. Contrary to the predictions of the KPR model, topo IV and topo III unlinking rates were linearly related to the DNA collision frequency. Furthermore, topo III exhibited decatenation activity comparable with that of topo IV, supporting proposed roles for topo III in DNA segregation. This study enables us to rule out the KPR model for non-equilibrium topology simplification. More generally, we establish an experimental approach to systematically control DNA collision frequency.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.