ReviewQuarterly reviews of biophysics2012
Bullied no more: when and how DNA shoves proteins around.
Review in Quarterly reviews of biophysics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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.
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.
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Who cites it
46 citing papers in PubMed.
- Mapping the Conformational Landscape of DNA Minicircles Through Atomic Force Microscopy and Shape Space Analysis.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- Article
- Non-canonical DNA structures in the human ribosomal DNA.Histochemistry and cell biology · 2023Review
- Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions.International journal of molecular sciences · 2023Article
- DNA supercoiling-induced shapes alter minicircle hydrodynamic properties.Nucleic acids research · 2023Article
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability.Polymers · 2023Review
- A 2.8 Å Structure of Zoliflodacin in a DNA Cleavage Complex withInternational journal of molecular sciences · 2023Article
- DNA supercoiling-induced shapes alter minicircle hydrodynamic properties.bioRxiv : the preprint server for biology · 2023Article
- The interplay of supercoiling and thymine dimers in DNA.Nucleic acids research · 2022Article
- Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain.International journal of molecular sciences · 2022Article
- Atomistic Molecular Dynamics Simulations of DNA in Complex 3D Arrangements for Comparison with Lower Resolution Structural Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF.Computational and structural biotechnology journal · 2022Article
- Supercoiling and looping promote DNA base accessibility and coordination among distant sites.Nature communications · 2021Article
- Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides.Nature communications · 2021Article
- Traveling Salesman Finds Random Walk: A Curve Reconstruction Algorithm for Supercoiled DNA.Biophysical journal · 2020Article
- Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces.Accounts of chemical research · 2020Article
- Chromosomal Organization and Regulation of Genetic Function inEcoSal Plus · 2020Article
- BIOPHYSICS MEETS GENE THERAPY: HOW EXPLORING SUPERCOILING-DEPENDENT STRUCTURAL CHANGES IN DNA LED TO THE DEVELOPMENT OF MINIVECTOR DNA.Technology and innovation · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The predominant protein-centric perspective in protein-DNA-binding studies assumes that the protein drives the interaction. Research focuses on protein structural motifs, electrostatic surfaces and contact potentials, while DNA is often ignored as a passive polymer to be manipulated. Recent studies of DNA topology, the supercoiling, knotting, and linking of the helices, have shown that DNA has the capability to be an active participant in its transactions. DNA topology-induced structural and geometric changes can drive, or at least strongly influence, the interactions between protein and DNA. Deformations of the B-form structure arise from both the considerable elastic energy arising from supercoiling and from the electrostatic energy. Here, we discuss how these energies are harnessed for topology-driven, sequence-specific deformations that can allow DNA to direct its own metabolism.
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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.