ArticleNucleic acids research2014
Probing the elastic limit of DNA bending.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Inferring DNA Kinkability from Biased MD Simulations.Journal of chemical theory and computation · 2026Article
- Phase-transition-like behaviors of sequence-selective dynamic bonds.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations.Biosensors · 2025Article
- DNAcycP2: improved estimation of intrinsic DNA cyclizability through data augmentation.Nucleic acids research · 2025Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2024Article
- Twist-stretch relations in nucleic acids.European biophysics journal : EBJ · 2023Article
- Etoposide promotes DNA loop trapping and barrier formation by topoisomerase II.Nature chemical biology · 2023Article
- Weak tension accelerates hybridization and dehybridization of short oligonucleotides.Nucleic acids research · 2023Article
- Temperature-dependent elastic properties of DNA.Biophysical reports · 2022Article
- Non-linear Hamiltonian models for DNA.European biophysics journal : EBJ · 2022Review
- Cytosine methylation regulates DNA bendability depending on the curvature.Chemical science · 2022Article
- Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2022Article
- DNAcycP: a deep learning tool for DNA cyclizability prediction.Nucleic acids research · 2022Article
- Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability.Molecules and cells · 2022Review
- DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.Nucleic acids research · 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
- Revealing thermodynamics of DNA origami folding via affine transformations.Nucleic acids research · 2020Article
- Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.Nucleic acids research · 2020Article
- Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment.Frontiers in physics · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule Fluorescence Resonance Energy Transfer. The relationship of loop lifetime to loop size revealed a critical transition in bending stress. Above the critical loop size, the loop lifetime changed with loop size in a manner consistent with elastic bending stress, but below it, became less sensitive to loop size, indicative of softened dsDNA. The critical loop size increased from ∼ 60 bp to ∼ 100 bp with the addition of 5 mM magnesium. We show that our result is in quantitative agreement with the kinkable worm-like chain model, and furthermore, can reproduce previously reported looping probabilities of dsDNA over the range between 50 and 200 bp. Our findings shed new light on the energetics of sharply bent dsDNA.
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