ArticlePhysical review. E, Statistical, nonlinear, and soft matter physics2013
Global force-torque phase diagram for the DNA double helix: structural transitions, triple points, and collapsed plectonemes.
Article in Physical review. E, Statistical, nonlinear, and soft matter physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- MACRO-MOLECULAR CROWDING FAVORS WRITHE IN UNWOUND DNA.bioRxiv : the preprint server for biology · 2026Article
- The Free Energy of Nucleosomal DNA Based on the Landau Model and Topology.Biomolecules · 2023Article
- Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates.Nucleic acids research · 2023Article
- Article
- DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases.Nucleic acids research · 2022Article
- Writhing and hockling instabilities in twisted elastic fibers.The European physical journal. E, Soft matter · 2021Article
- Nanomechanics of negatively supercoiled diaminopurine-substituted DNA.Nucleic acids research · 2021Article
- Force spectroscopy with electromagnetic tweezers.Journal of applied physics · 2021Article
- Energetics of twisted DNA topologies.Biophysical journal · 2021Review
- Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.Transcription · 2021Article
- Single-molecule micromanipulation studies of methylated DNA.Biophysical journal · 2021Article
- Nanomechanics of G-quadruplexes within the promoter of the KIT oncogene.Nucleic acids research · 2021Article
- Transfer-matrix calculations of the effects of tension and torque constraints on DNA-protein interactions.Nucleic acids research · 2018Article
- Protein-mediated loops in supercoiled DNA create large topological domains.Nucleic acids research · 2018Article
- Defect-facilitated buckling in supercoiled double-helix DNA.Physical review. E · 2018Article
- Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers.Nucleic acids research · 2017Article
- Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively.Nucleic acids research · 2017Article
- Theoretical Methods for Studying DNA Structural Transitions under Applied Mechanical Constraints.Polymers · 2017Review
- Supercoiling biases the formation of loops involved in gene regulation.Biophysical reviews · 2016Review
- Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation.Biophysical journal · 2016Article
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2 authors.
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Abstract
We present a free energy model for structural transitions of the DNA double helix driven by tensile and torsional stress. Our model is coarse grained and is based on semiflexible polymer descriptions of B-DNA, underwound L-DNA, and highly overwound P-DNA. The statistical-mechanical model of plectonemic supercoiling previously developed for B-DNA is applied to semiflexible polymer models of P- and L-DNA to obtain a model of DNA structural transitions in quantitative accord with experiment. We identify two distinct plectonemic states, one "inflated" by electrostatic repulsion and thermal fluctuations and the other "collapsed," with the two double helices inside the supercoils driven to close contact. We find that supercoiled B and L are stable only in the inflated form, while supercoiled P is always collapsed. We also predict the behavior and experimental signatures of highly underwound "Q"-DNA, the left-handed analog of P-DNA; as for P, supercoiled Q is always collapsed. Overstretched "S"-DNA and strand-separated "stress-melted" DNA are also included in our model, allowing prediction of a global phase diagram for forces up to 1000 pN and torques between ±60 pN nm, or, in terms of linking number density, from σ=-5 to +3.
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