Journal
SCIENTIFIC REPORTS
Volume 5, Issue -, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/srep07655
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Funding
- German Academic Exchange Service (DAAD)
- Studienstiftung des deutschen Volkes
- University College, Oxford
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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 pinning mechanism. They occur for supercoiling densities and forces that are typically encountered for DNA in vivo, and may be exploited for biological control of genomic processes.
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