DNA Supercoiling Catalyzed by Bacterial Gyrase.

Samika Joshi, Neil Osheroff

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing 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

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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

1 citing paper in PubMed.

Synthesis and molecular docking of novel pyrazole, pyrimidine, and pyridine derivatives as potent antimicrobial, antibiofilm, and anticancer agents.Scientific reports · 2026
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

2 authors.

Samika JoshiDepartment of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.

Neil OsheroffDepartment of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA. neil.osheroff@vanderbilt.edu.

Funding

Mechanistic Studies of Gyrase/Topoisomerase IV-Targeted AntibacterialsR01AI170546 · NIAID · VANDERBILT UNIVERSITY · PI NEIL OSHEROFF · 2023 to 2026

$2.7M

Mechanistic Studies of Type II Topoisomerases and Topoisomerase-Targeted AgentsR01GM126363 · NIGMS · VANDERBILT UNIVERSITY · PI OSHEROFF, NEIL · 2018 to 2025

$2.6M

NIAID NIH HHS R01 AI170546NIGMS NIH HHS R01 GM126363

6 · The paper itself

Abstract

DNA gyrase is an essential type II topoisomerase that is conserved across bacteria species and has an essential function of resolving overwound (positive supercoiled) DNA and introducing negative supercoils into relaxed DNA. The overall catalytic activity of gyrase can be determined using in vitro assays utilizing purified enzyme subunits and a DNA substrate. As gyrase is the only topoisomerase that can introduce negative supercoils into relaxed DNA, the inhibition of this catalytic activity is a good indicator of the efficacy and potency of potential antibacterial compounds. This chapter outlines a protocol for a purified enzyme assay with relaxed DNA that utilizes gel electrophoresis to monitor the ability of gyrase to introduce negative supercoils into DNA. The protocol focuses on the DNA supercoiling activity of Escherichia coli wild-type gyrase. However, it can be easily modified for use with gyrase from other bacterial species.

Indexed as

DNA, BacterialDNA GyraseDNA, SuperhelicalEscherichia coliDNA, BacterialDNA GyraseDNA, SuperhelicalBacterial type II topoisomeraseDNA GyraseDNA supercoilingEscherichia coliNegative supercoilingOverwindingPositive supercoiling

Identifiers

PMID40372635

DOI10.1007/978-1-0716-4550-5_4

PMCPMC12154256

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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.