ArticleJournal of chemical theory and computation2019
Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Enzyme-Responsive Cyclic Gapmer Antisense Oligonucleotides via ThymidineBioconjugate chemistry · 2026Article
- Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2022Article
- DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.Nucleic acids research · 2021Article
- Supercoiling and looping promote DNA base accessibility and coordination among distant sites.Nature communications · 2021Article
- Structural Landscape of the Transition from an ssDNA Dumbbell Plus Its Complementary Hairpin to a dsDNA Microcircle Via a Kissing Loop Intermediate.Molecules (Basel, Switzerland) · 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
- Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches.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
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. While the wormlike chain model provides a good description of small to moderate bending fluctuations, it is expected to break down for large bending. Recent cyclization experiments on strongly bent shorter molecules indeed suggest enhanced flexibility over and above that expected from the wormlike chain. Here, we use a coarse-grained model of DNA to investigate the subtle thermodynamics of DNA cyclization for molecules ranging from 30 to 210 base pairs. As the molecules get shorter, we find increasing deviations between our computed equilibrium
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