ArticleThe Journal of chemical physics2017
DNA elasticity from coarse-grained simulations: The effect of groove asymmetry.
Article in The Journal of chemical physics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
- Effect of temperature on anisotropic bending elasticity of dsRNA: an all-atom molecular dynamics simulation.RSC advances · 2024Article
- The interplay of supercoiling and thymine dimers in DNA.Nucleic acids research · 2022Article
- Diameter Dependent Melting and Softening of dsDNA Under Cylindrical Confinement.Frontiers in chemistry · 2022Article
- Energetics of twisted DNA topologies.Biophysical journal · 2021Review
- 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
- Design Approaches and Computational Tools for DNA Nanostructures.IEEE open journal of nanotechnology · 2021Article
- Effects of Model Shape, Volume, and Softness of the Capsid for DNA Packaging of phi29.The journal of physical chemistry. B · 2020Article
- Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches.Nucleic acids research · 2020Article
- Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond.Physical review. E · 2019Article
- Coarse-grained modelling of the structural properties of DNA origami.Nucleic acids research · 2019Article
- Bend-Induced Twist Waves and the Structure of Nucleosomal DNA.Physical review letters · 2018Article
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4 authors.
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Abstract
It is well established that many physical properties of DNA at sufficiently long length scales can be understood by means of simple polymer models. One of the most widely used elasticity models for DNA is the twistable worm-like chain (TWLC), which describes the double helix as a continuous elastic rod with bending and torsional stiffness. An extension of the TWLC, which has recently received some attention, is the model by Marko and Siggia, who introduced an additional twist-bend coupling, expected to arise from the groove asymmetry. By performing computer simulations of two available versions of oxDNA, a coarse-grained model of nucleic acids, we investigate the microscopic origin of twist-bend coupling. We show that this interaction is negligible in the oxDNA version with symmetric grooves, while it appears in the oxDNA version with asymmetric grooves. Our analysis is based on the calculation of the covariance matrix of equilibrium deformations, from which the stiffness parameters are obtained. The estimated twist-bend coupling coefficient from oxDNA simulations is G=30±1 nm. The groove asymmetry induces a novel twist length scale and an associated renormalized twist stiffness κ
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