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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 pinn...

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Publication status:
Published
Peer review status:
Peer reviewed

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Publisher copy:
10.1038/srep07655

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Institution:
University of Oxford
Division:
MPLS
Department:
Physics
Sub department:
Theoretical Physics
Role:
Author
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Engineering and Physical Sciences Research Council More from this funder
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Funding agency for:
Ouldridge, T
Publisher:
Nature Publishing Group Publisher's website
Journal:
Scientific Reports Journal website
Volume:
5
Article number:
7655
Publication date:
2015-01-01
DOI:
EISSN:
2045-2322
ISSN:
2045-2322
Source identifiers:
462838
Language:
English
Keywords:
Subjects:
Pubs id:
pubs:462838
UUID:
uuid:647ef7b6-ed11-456e-a351-059375615a29
Local pid:
pubs:462838
Deposit date:
2014-05-30

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