Overtwisting induces polygonal shapes in bent DNA
arXiv:1812.03701 · doi:10.1063/1.5084950
Abstract
By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend coupling, a cross interaction term discussed in the recent DNA literature, induces minimal energy shapes with a periodic alternance of parts with high and low curvature resembling rounded polygons. We briefly discuss the possible experimental relevance of these findings. We finally show that the twist and bending energies of minicircles are governed by renormalized stiffness constants, not the bare ones. This has important consequences for the analysis of experiments involving circular DNA meant to determine DNA elastic constants.
arXiv comment11 pages, 7 figures
References in corpus (20)
- Sequence-dependent thermodynamics of a coarse-grained DNA model
- Torsional Directed Walks, Entropic Elasticity, and DNA Twist Stiffness
- Elasticity model of a supercoiled DNA molecule
- DNA nanotweezers studied with a coarse-grained model of DNA
- Entropic Elasticity of Twist-Storing Polymers
- Scaling exponents and probability distributions of DNA end-to-end distance
- Twist-bend coupling and the torsional response of double-stranded DNA
- Coarse-Grained Simulation of DNA using LAMMPS
- Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA
- Bend-Induced Twist Waves and the Structure of Nucleosomal DNA
- DNA elasticity from coarse-grained simulations: the effect of groove asymmetry
- Twist-bend coupling and the statistical mechanics of the twistable worm-like chain model of DNA: perturbation theory and beyond
- Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS
- Anomalous dynamics of DNA hairpin folding
- Elastic Correlations in Nucleosomal DNA Structure
- A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA
- Effect of Bending Anisotropy on the 3D Conformation of Short DNA Loops
- Stretching An Anisotropic DNA
- Role of helicity in DNA hairping folding dynamics
- Nonlinear Mechanical Response of DNA due to Anisotropic Bending Elasticity
Cited by in corpus (7)
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- Length scale dependent elasticity in DNA from coarse-grained and all-atom models
- Twist-bend coupling, twist waves and the shape of DNA loops
- Mechanical properties of Nucleic Acids and the non-local Twistable Wormlike Chain model
- Equilibrium Fluctuations of DNA Plectonemes
- Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending
- Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+