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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