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Plectoneme tip bubbles: coupled denaturation and writhing in supercoiled DNA.

ABSTRACT: 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.

SUBMITTER: Matek C

PROVIDER: S-EPMC5224516 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

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Plectoneme tip bubbles: coupled denaturation and writhing in supercoiled DNA.

Matek Christian C Ouldridge Thomas E TE Doye Jonathan P K JP Louis Ard A AA

Scientific reports 20150107

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 ...[more]

PMID: 25563652

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