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Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.

Abstract:

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, ...

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

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Publisher copy:
10.1063/1.4921957

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Institution:
University of Oxford
Department:
Oxford, MPLS, Chemistry, Physical and Theoretical Chem
Role:
Author
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Institution:
University of Oxford
Department:
Oxford, MPLS, Theoretical Physics
Role:
Author
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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, Chemistry, Physical and Theoretical Chem
Role:
Author
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Engineering and Physical Sciences Research Council More from this funder
Publisher:
AIP Publishing Publisher's website
Journal:
The Journal of chemical physics Journal website
Volume:
142
Issue:
23
Pages:
234901
Publication date:
2015-06-05
DOI:
EISSN:
1089-7690
ISSN:
0021-9606
URN:
uuid:241ae8d5-2092-4b24-b1d0-3fb7482b7bcd
Source identifiers:
517512
Local pid:
pubs:517512
Language:
English
Keywords:

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