ArticleNucleic acids research2020
Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 25 citations in OpenAlex.
- Visualizing poloidal orientation in DNA minicircles.Biophysical journal · 2026Article
- DNA Cut-Ligation Cyclization Surpasses Jacobson-Stockmayer J-Factor Expectations by over Threefold.Biomolecules · 2026Article
- Phase-transition-like behaviors of sequence-selective dynamic bonds.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- DNA Circle-sequencing lowers the single molecule sequencing error threshold and identifies ultrasonication as a source of DNA damage.bioRxiv : the preprint server for biology · 2025Article
- Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations.Biosensors · 2025Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2024Article
- Article
- Single cohesin molecules generate force by two distinct mechanisms.Nature communications · 2023Article
- Weak tension accelerates hybridization and dehybridization of short oligonucleotides.Nucleic acids research · 2023Article
- Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2022Article
- Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability.Molecules and cells · 2022Review
- Kinetics of DNA looping by Anabaena sensory rhodopsin transducer (ASRT) by using DNA cyclization assay.Scientific reports · 2021Article
- Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding.The journal of physical chemistry. B · 2021Article
- Measuring DNA mechanics on the genome scale.Nature · 2021Article
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules.Sensors (Basel, Switzerland) · 2020Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization (unlooping) rates (kloop and kunloop) of DNA with sticky ends over three helical periods (100-130 bp) using single-molecule fluorescence resonance energy transfer (FRET). kloop showed a nontrivial undulation as a function of DNA length whereas kunloop showed a clear oscillation with a period close to the helical turn of DNA (∼10.5 bp). The oscillation of kunloop was almost completely suppressed in the presence of gaps around the sticky ends. We explain these findings by modeling double-helical DNA as a twisted wormlike chain with a finite width, intrinsic curvature, and stacking interaction between the end base pairs. We also discuss technical issues for converting the FRET-based cyclization/decyclization rates to an equilibrium quantity known as the J factor that is widely used to characterize DNA bending mechanics.
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