ArticleNature structural & molecular biology2018
Direct observation of topoisomerase IA gate dynamics.
Article in Nature structural & molecular biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
32 citing papers in PubMed, 47 citations in OpenAlex.
- Hydrogen-deuterium exchange points to inter-domain interactions in reverse gyrase that modulate conformational changes in positive DNA supercoiling.The Journal of biological chemistry · 2026Article
- Topoisomerase III limits RecA-dependent DNA amplification in the chromosome terminus with RecG.Nucleic acids research · 2026Article
- Networked salt-bridges mediate magnesium-dependent conformational dynamics and functional regulation in type IA topoisomerases.Nature communications · 2026Article
- Investigation of potential hinge region forbioRxiv : the preprint server for biology · 2026Article
- Molecular dynamics simulations reveal DNA gate opening mechanisms for M. smegmatis topoisomerase 1A.Biophysical journal · 2026Article
- Mechanistic basis for relaxation of DNA supercoils by human topoisomerase IIIα-RMI1-RMI2.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Inhibition of DNA cleavage and strand passage activities of Mycobacterium tuberculosis topoisomerase I.Nucleic acids research · 2025Article
- Deciphering the human TopIIIα activity modulated by Rmi1 using magnetic tweezers.Nucleic acids research · 2025Article
- Structural insights into human topoisomerase 3β DNA and RNA catalysis and nucleic acid gate dynamics.Nature communications · 2025Article
- Insights into the DNA and RNA Interactions of Human Topoisomerase III Beta Using Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- Variation of Structure and Cellular Functions of Type IA Topoisomerases across the Tree of Life.Cells · 2024Review
- Characterization of human XPD helicase activity with single-molecule magnetic tweezers.Biophysical journal · 2024Article
- Characterization of a pathway of genomic instability induced by R-loops and its regulation by topoisomerases in E. coli.PLoS genetics · 2023Article
- Unraveling topoisomerase IA gate dynamics in presence of PPEF and its preclinical evaluation against multidrug-resistant pathogens.Communications biology · 2023Article
- What's on the Other Side of the Gate: A Structural Perspective on DNA Gate Opening of Type IA and IIA DNA Topoisomerases.International journal of molecular sciences · 2023Review
- The interaction between transport-segment DNA and topoisomerase IA-crystal structure of MtbTOP1 in complex with both G- and T-segments.Nucleic acids research · 2023Article
- Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β.Nature communications · 2022Article
- Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations.Scientific reports · 2022Article
- Mechanism of Bloom syndrome complex assembly required for double Holliday junction dissolution and genome stability.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Duplex DNA and BLM regulate gate opening by the human TopoIIIα-RMI1-RMI2 complex.Nature communications · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Type IA topoisomerases cleave single-stranded DNA and relieve negative supercoils in discrete steps corresponding to the passage of the intact DNA strand through the cleaved strand. Although type IA topoisomerases are assumed to accomplish this strand passage via a protein-mediated DNA gate, opening of this gate has never been observed. We developed a single-molecule assay to directly measure gate opening of the Escherichia coli type IA topoisomerases I and III. We found that after cleavage of single-stranded DNA, the protein gate opens by as much as 6.6 nm and can close against forces in excess of 16 pN. Key differences in the cleavage, ligation, and gate dynamics of these two enzymes provide insights into their different cellular functions. The single-molecule results are broadly consistent with conformational changes obtained from molecular dynamics simulations. These results allowed us to develop a mechanistic model of interactions between type IA topoisomerases and single-stranded DNA.
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Registered trials
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 OpenQuestion graph.