ArticleBiochemistry2006
Effect of DNA supercoiling on the geometry of holliday junctions.
Article in Biochemistry, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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.
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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
29 citing papers in PubMed, 56 citations in OpenAlex.
- Recent progress in probing small molecule interactions with DNA.Biophysical reviews · 2025Review
- Crossover recombination between homologous chromosomes in meiosis: recent progress and remaining mysteries.Trends in genetics : TIG · 2025Review
- Polymorphic potential of SRF binding site ofRSC advances · 2024Article
- In Vivo Genomic Supercoiling Mapping Using Psora-seq.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Non-canonical DNA structures in the human ribosomal DNA.Histochemistry and cell biology · 2023Review
- Review
- Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription.Nucleic acids research · 2022Article
- Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures.Molecules (Basel, Switzerland) · 2020Article
- The structural ensemble of a Holliday junction determined by X-ray scattering interference.Nucleic acids research · 2020Article
- Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability.Bioinformatics (Oxford, England) · 2018Article
- Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes.Journal of physics D: Applied physics · 2018Article
- Recognition of Local DNA Structures by p53 Protein.International journal of molecular sciences · 2017Review
- Review
- Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments.Scientific reports · 2016Article
- Imaging of DNA and Protein-DNA Complexes with Atomic Force Microscopy.Critical reviews in eukaryotic gene expression · 2016Review
- The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeat.BMC genomics · 2015Article
- Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability.DNA repair · 2014Review
- Nanoscale Nucleosome Dynamics Assessed with Time-lapse AFM.Biophysical reviews · 2014Article
- DNA repair mechanisms and Toxoplasma gondii infection.Archives of microbiology · 2014Review
- Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region.Biophysical journal · 2011Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Unusual DNA conformations including cruciforms play an important role in gene regulation and various DNA transactions. Cruciforms are also the models for Holliday junctions, the transient DNA conformations critically involved in DNA homologous and site-specific recombination, repair, and replication. Although the conformations of immobile Holliday junctions in linear DNA molecules have been analyzed with the use of various techniques, the role of DNA supercoiling has not been studied systematically. We utilized atomic force microscopy (AFM) to visualize cruciform geometry in plasmid DNA with different superhelical densities at various ionic conditions. Both folded and unfolded conformations of the cruciform were identified, and the data showed that DNA supercoiling shifts the equilibrium between folded and unfolded conformations of the cruciform toward the folded one. In topoisomers with low superhelical density, the population of the folded conformation is 50-80%, depending upon the ionic strength of the buffer and a type of cation added, whereas in the sample with high superhelical density, this population is as high as 98-100%. The time-lapse studies in aqueous solutions allowed us to observe the conformational transition of the cruciform directly. The time-dependent dynamics of the cruciform correlates with the structural changes revealed by the ensemble-averaged analysis of dry samples. Altogether, the data obtained show directly that DNA supercoiling is the major factor determining the Holliday junction conformation.
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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.