ArticleNucleic acids research2009
Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 53 citations in OpenAlex.
- Cryo-EM structure of a 95-base-pair double-stranded DNA minicircle at 5.3 Å resolution.Nucleic acids research · 2026Article
- Apical localization of RNA polymerases modulates transcription dynamics and supercoiling domains revealed by cryo-ET.Molecular cell · 2026Article
- cgNA+min: computation of sequence-dependent dsDNA energy-minimizing minicircles.Nucleic acids research · 2026Article
- Apical Localization of RNA Polymerases Modulate Transcription Dynamics and Supercoiling Domains Revealed by Cryo-ET.bioRxiv : the preprint server for biology · 2026Article
- Visualizing the 4D Impact of Gold Nanoparticles on DNA.International journal of molecular sciences · 2023Article
- DNAcycP: a deep learning tool for DNA cyclizability prediction.Nucleic acids research · 2022Article
- Atomic force microscopy-A tool for structural and translational DNA research.APL bioengineering · 2021Review
- Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides.Nature communications · 2021Article
- A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.Frontiers in molecular biosciences · 2021Review
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- Probing hyper-negatively supercoiled mini-circles with nucleases and DNA binding proteins.PloS one · 2018Article
- Influence of DNA sequence on the structure of minicircles under torsional stress.Nucleic acids research · 2017Article
- Modulation of cyclobutane thymine photodimer formation in T11-tracts in rotationally phased nucleosome core particles and DNA minicircles.Nucleic acids research · 2017Article
- Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles.Nucleic acids research · 2017Article
- Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity.Nucleic acids research · 2017Article
- Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation.Nucleic acids research · 2016Article
- DNA minicircles clarify the specific role of DNA structure on retroviral integration.Nucleic acids research · 2016Article
- Simulation of DNA Supercoil Relaxation.Biophysical journal · 2016Article
- Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA.Biophysical journal · 2015Article
- Structural diversity of supercoiled DNA.Nature communications · 2015Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We use cryo-electron microscopy (cryo-EM) to study the 3D shapes of 94-bp-long DNA minicircles and address the question of whether cyclization of such short DNA molecules necessitates the formation of sharp, localized kinks in DNA or whether the necessary bending can be redistributed and accomplished within the limits of the elastic, standard model of DNA flexibility. By comparing the shapes of covalently closed, nicked and gapped DNA minicircles, we conclude that 94-bp-long covalently closed and nicked DNA minicircles do not show sharp kinks while gapped DNA molecules, containing very flexible single-stranded regions, do show sharp kinks. We corroborate the results of cryo-EM studies by using Bal31 nuclease to probe for the existence of kinks in 94-bp-long minicircles.
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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.