ArticleScientific reports2018
Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- DNA Cut-Ligation Cyclization Surpasses Jacobson-Stockmayer J-Factor Expectations by over Threefold.Biomolecules · 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
- Laplace approximation of J factors for rigid base and rigid basepair models of DNA cyclization.Biophysical journal · 2025Article
- Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.Nucleic acids research · 2020Article
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We use Monte Carlo simulation to quantify the change in cyclization J-factor within a dramatically simplified model of DNA that involves parameters for uniform stiffnesses, intrinsic twist, and intrinsic bending (including nonplanar bending). Plots of J versus DNA length over multiple periods of helical repeat are fit to a simple functional form in order to project the behavior of J over a broad range of these model parameters. In some instances, this process allows us to find families of DNA molecules (within our model) with quite different material properties, but very similar plots of J versus length, so similar as to likely to be indistinguishable by experiments. This effect is seen both for the parameter-pair of bend angle and stiffness scaling, as well as for the parameter-trio of helical repeat, bend angle, and bend non-planarity.
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