Evidence map›Paper›PMID 40894068›Full record

ArticleResearch square2025

DNA deformability defines sequence-dependent capture of

Matthew L Baker, Haley R Johnson, Ryan A Eckerty, Jonathan M Fogg, Silvia L Summers, Marlène Vayssières, Nils Marechal, Valérie Lamour, Wilma K Olson, Lynn Zechiedrich

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Matthew L BakerDepartment of Biochemistry & Molecular Biology, University of Texas Health Sciences Center at Houston, Houston, TX USA.ORCID 0000-0001-9039-8523
Haley R JohnsonGraduate Program in Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.ORCID 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.
Silvia L SummersDepartment of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA.
Marlène VayssièresUniversité de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France.
Nils MarechalUniversité de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France.
Valérie LamourUniversité de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France.ORCID 0000-0001-7793-4029
Wilma K OlsonDepartment of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.ORCID 0000-0002-7803-1072
Lynn ZechiedrichGraduate Program in Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.ORCID 0000-0003-0533-1637

Funding

THEORETICFAL ASPECTS OF DNA SUPERCOILINGR01GM034809 · NIGMS · RUTGERS THE ST UNIV OF NJ NEW BRUNSWICK · PI OLSON, WILMA K · 1985 to 2019
$4.6M
Harnessing Supercoiling to Regulate DNA ActivityR35GM141793 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI ZECHIEDRICH, LYNN · 2021 to 2025
$2.1M
X3DNA-DSSR: a resource for structural bioinformatics of nucleic acidsR24GM153869 · NIGMS · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI Xiang-Jun Lu · 2024 to 2026
$1.5M
NIGMS NIH HHS R01 GM034809NIGMS NIH HHS R24 GM153869NIGMS NIH HHS R35 GM141793
6 · The paper itself

Abstract

Bacterial gyrase, unique among type II topoisomerases, introduces negative supercoils into DNA. Mechanistic details of gyrase still must be elucidated because of the complexity of the process and the difficulty in visualizing it. Specifically, the interplay among base sequence, local DNA deformability, and global DNA topology for gyrase site selection is unclear. To understand how gyrase interacts with DNA and selects a site of action, we created an

Indexed as

DNA base-pair step deformabilityDNA minicircleDNA site recognitionDNA supercoilingType II topoisomerase

Identifiers

PMID40894068
PMCPMC12393610

What OpenQuestion holds

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Registered trials

None linked

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.