Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA

@article{Matek2015PlectonemeTB,
  title={Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA},
  author={Christian Matek and Thomas E. Ouldridge and Jonathan P. K. Doye and Ard A. Louis},
  journal={Scientific Reports},
  year={2015},
  volume={5}
}
We predict a novel conformational regime for DNA, where denaturation bubbles form at the tips of plectonemes, and study its properties using coarse-grained simulations. For negative supercoiling, this regime lies between bubble-dominated and plectoneme-dominated phases, and explains the broad transition between the two observed in experiment. Tip bubbles cause localisation of plectonemes within thermodynamically weaker AT-rich sequences, and can greatly suppress plectoneme diffusion by a… 
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Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e. over- or under-wounded. They are ubiquitous in cellular DNA and their physical properties have…
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It is shown that the presence of soft sequences increases the number of plectoneme branches and that the edges of the branches tend to be localized at these sequences.
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TLDR
A statistical-mechanical model for stretched twisted double-helix DNA, where thermal fluctuations are treated explicitly from a Hamiltonian without using any scaling hypotheses is presented, and it is found that a defect can spatially pin a plectoneme domain via nucleation of a kinked end loop, in accord with experiments and simulations.
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TLDR
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TLDR
Computational simulations are used to study how well the rigidity of a driving DNA duplex can rupture a double-stranded DNA target into single-Stranded segments and how well this stress can discriminate between unzipping or shearing geometries.
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TLDR
A model to explain discontinuities in the increase of the length of a DNA plectoneme when the DNA filament is continuously twisted under tension is developed, similar to the Prandtl-Tomlinson model of atomic scale friction.
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