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dc.contributor.authorXu, Xinliang
dc.contributor.authorGe, Hao
dc.contributor.authorGu, Chan
dc.contributor.authorGao, Yi Qin
dc.contributor.authorWang, Siyuan S.
dc.contributor.authorThio, Beng Joo Reginald
dc.contributor.authorHynes, James T.
dc.contributor.authorXie, X. Sunney
dc.contributor.authorCao, Jianshu
dc.date.accessioned2014-07-01T14:57:52Z
dc.date.available2014-07-01T14:57:52Z
dc.date.issued2013-10
dc.identifier.issn1520-6106
dc.identifier.issn1520-5207
dc.identifier.urihttp://hdl.handle.net/1721.1/88163
dc.description.abstractWe report a study of DNA deformations using a coarse-grained mechanical model and quantitatively interpret the allosteric effects in protein–DNA binding affinity. A recent single-molecule study (Kim et al. Science 2013, 339, 816) showed that when a DNA molecule is deformed by specific binding of a protein, the binding affinity of a second protein separated from the first protein is altered. Experimental observations together with molecular dynamics simulations suggested that the origin of the DNA allostery is related to the observed deformation of DNA’s structure, in particular, the major groove width. To unveil and quantify the underlying mechanism for the observed major groove deformation behavior related to the DNA allostery, here we provide a simple but effective analytical model where DNA deformations upon protein binding are analyzed and spatial correlations of local deformations along the DNA are examined. The deformation of the DNA base orientations, which directly affect the major groove width, is found in both an analytical derivation and coarse-grained Monte Carlo simulations. This deformation oscillates with a period of 10 base pairs with an amplitude decaying exponentially from the binding site with a decay length lD ≈10 base pairs as a result of the balance between two competing terms in DNA base-stacking energy. This length scale is in agreement with that reported from the single-molecule experiment. Our model can be reduced to the worm-like chain form at length scales larger than lP but is able to explain DNA’s mechanical properties on shorter length scales, in particular, the DNA allostery of protein–DNA interactions.
dc.description.sponsorshipNational Science Foundation (U.S.) (NSF CHE-112825)
dc.description.sponsorshipSingapore University of Technology and Design (Start-Up Research Grant (SRG EPD 2012 022))
dc.description.sponsorshipSingapore University of Technology and Design (Research Fellowship)
dc.description.sponsorshipSingapore-MIT Alliance for Research and Technology
dc.description.sponsorshipUnited States. Dept. of Defense (DOD ARO W911NF-09-0480)
dc.description.sponsorshipChinese Academy of Sciences (Foundation for the Author of National Excellent Doctoral Dissertation of China (No. 201119)
dc.description.sponsorshipNational Institutes of Health (U.S.) (Director's Pioneer Award)
dc.description.sponsorshipNational Science Foundation (U.S.) (NSF CHE-1112564)
dc.language.isoen_US
dc.publisherAmerican Chemical Societyen_US
dc.relation.isversionofhttp://dx.doi.org/10.1021/jp4047243en_US
dc.rightsArticle is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.en_US
dc.sourceCao via Erja Kajosaloen_US
dc.titleModeling Spatial Correlation of DNA Deformation: DNA Allostery in Protein Bindingen_US
dc.typeArticleen_US
dc.identifier.citationXu, Xinliang, Hao Ge, Chan Gu, Yi Qin Gao, Siyuan S. Wang, Beng Joo Reginald Thio, James T. Hynes, X. Sunney Xie, and Jianshu Cao. “Modeling Spatial Correlation of DNA Deformation: DNA Allostery in Protein Binding.” The Journal of Physical Chemistry B 117, no. 42 (October 24, 2013): 13378–13387.en_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Chemistryen_US
dc.contributor.approverCao, Jianshuen_US
dc.contributor.mitauthorCao, Jianshuen_US
dc.contributor.mitauthorXu, Xinliangen_US
dc.relation.journalJournal of Physical Chemistry Ben_US
dc.eprint.versionAuthor's final manuscripten_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dspace.orderedauthorsXu, Xinliang; Ge, Hao; Gu, Chan; Gao, Yi Qin; Wang, Siyuan S.; Thio, Beng Joo Reginald; Hynes, James T.; Xie, X. Sunney; Cao, Jianshuen_US
dc.identifier.orcidhttps://orcid.org/0000-0001-7616-7809
mit.licensePUBLISHER_POLICYen_US


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