Evidence map›Paper›PMID 41698922›Full record

ArticleNature communications2026

Supercoiled DNA recognition and cleavage control in topoisomerase VI.

Daniel E Richman, Timothy J Wendorff, Fahad Rashid, Curtis Beck, Qianyun Yan, Haley R Johnson, Ryan A Eckerty, Jonathan M Fogg, Matthew L Baker, Lynn Zechiedrich and 1 more

Abstract read
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Controlling Meiotic Double-Strand Break Formation in Mice: A Web of Multivalent Protein-Protein Interactions.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026
    Review
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Daniel E RichmanDepartment of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Timothy J WendorffDepartment of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Fahad RashidDepartment of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0003-3898-3842
Curtis BeckDepartment of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Qianyun YanDepartment of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Haley R JohnsonGraduate Program in Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.ORCID http://orcid.org/0009-0000-3444-1910
Ryan A EckertyDepartment of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA.
Jonathan M FoggDepartment of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA.
Matthew L BakerDepartment of Biochemistry & Molecular Biology, UTHealth Houston, Houston, TX, USA.ORCID http://orcid.org/0000-0001-9039-8523
Lynn ZechiedrichGraduate Program in Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.ORCID http://orcid.org/0000-0003-0533-1637
James M BergerDepartment of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. jmberger@jhmi.edu.ORCID http://orcid.org/0000-0003-0666-1240

Funding

Understanding and exploiting DNA topoisomerases in cancer biologyR35CA263778 · NCI · JOHNS HOPKINS UNIVERSITY · PI James M. Berger · 2021 to 2026
$5.0M
Harnessing Supercoiling to Regulate DNA ActivityR35GM141793 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI ZECHIEDRICH, LYNN · 2021 to 2025
$2.1M
NCI NIH HHS R35 CA263778NIGMS NIH HHS R35 GM141793U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R35CA263778
6 · The paper itself

Abstract

Type II topoisomerases modulate DNA supercoiling and resolve chromosome entanglements. Type IIB topoisomerases, exemplified by DNA topoisomerase VI (Top6), are used by plants and archaea to support endoreduplication and cell proliferation, respectively; homologs of Top6 further serve to initiate meiotic recombination in eukaryotes and constitute the nuclease portion of MksBEFG/Wadjet/Gabija bacterial defense systems. To understand how such factors act upon DNA, we determine structures of Top6 bound to supercoiled minicircles in cleaved and uncleaved states using single-particle electron cryo-microscopy. The structures show that Top6 binds a curved 74 bp region of the supercoiled minicircle DNA and that it cuts at a distinct deformability motif, explaining its preference for supercoiled substrates and highlighting the role of DNA plasticity in cleavage site selection. Dynamic protein-DNA interactions and an unanticipated tension sensor help recognize bent DNA and couple ATPase disposition to cleavage state activation. Our observations explain how DNA recognition and cleavage by type II topoisomerases are regulated by interdependent structural changes in DNA and the enzyme.

Indexed as

DNA, SuperhelicalDNA Topoisomerases, Type IIArchaeal ProteinsCryoelectron MicroscopyDNA CleavageModels, MolecularProtein BindingArchaeal ProteinsDNA, SuperhelicalDNA Topoisomerases, Type IIDNA topoisomerase VI

Identifiers

PMID41698922
PMCPMC13040014

What OpenQuestion holds

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Registered trials

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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 OpenQuestion graph.