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DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism.

Abstract:

Inverted repeat (IR) sequences in DNA can form noncanonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. First, a twist-induced denaturation bubble must diffuse so that its midpoint is near the center of symmetry of the IR sequence. Second, bubble fluctuations must be large enough to allow one of the arms to form...

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Publication status:
Published
Peer review status:
Peer reviewed
Version:
Accepted Manuscript

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Publisher copy:
10.1021/jp3080755

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Institution:
University of Oxford
Role:
Author
More by this author
Institution:
University of Oxford
Department:
Oxford, MPLS, Physics
Role:
Author
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Institution:
University of Oxford
Role:
Author
More by this author
Institution:
University of Oxford
Department:
Oxford, MPLS, Chemistry, Physical and Theoretical Chem
Role:
Author
More by this author
Institution:
University of Oxford
Department:
Oxford, MPLS, Physics, Theoretical Physics
Role:
Author
Studienstiftung des Deutschen Volkes More from this funder
Stiftung Maximilianeum More from this funder
Publisher:
American Chemical Society Publisher's website
Journal:
The journal of physical chemistry. B Journal website
Volume:
116
Issue:
38
Pages:
11616-11625
Publication date:
2012-09-05
DOI:
EISSN:
1520-5207
ISSN:
1520-6106
URN:
uuid:d5cd8424-1153-42e9-b65a-a85f0a405375
Source identifiers:
340086
Local pid:
pubs:340086

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