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dc.creatorStopar, A
dc.creatorCoral, L
dc.creatorDi Giacomo, S
dc.creatorAdedeji, AF
dc.creatorCastronovo, M
dc.date.accessioned2021-01-22T14:29:43Z
dc.date.available2021-01-22T14:29:43Z
dc.date.issued2018-01-25
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.doihttp://dx.doi.org/10.34944/dspace/4824
dc.identifier.other29216375 (pubmed)
dc.identifier.urihttp://hdl.handle.net/20.500.12613/4842
dc.description.abstract© The Author(s) 2017. Controlling DNA nanostructure interaction with protein is essential in developing nanodevices with programmable function, reactivity, and stability for biological and medical applications. Here, we show that the sequence-specific action of restriction endonucleases towards sharp triangular or rectangular DNA origami exhibits a novel, binary 'on/off' behaviour, as canonical recognition sites are either essentially fully reactive, or strongly resistant to enzymatic cutting. Moreover, introduction of structural defects in the sharp triangle can activate an otherwise unreactive site, with a site-to-defect distance of ∼50 nm. We argue that site reactivity is dependent upon programmable, mechanical coupling in the two-dimensional DNA origami, with specific structural elements, including DNA nicks and branches proximal to the sites that can function as negative(anti) determinants of reactivity. Empirically modelling the constraints to DNA degrees of freedom associated with each recognition site in the sharp triangle can rationalize the pattern of suppressed reactivity towards nine restriction endonucleases, in substantial agreement with the experimental results. These results provide a basis for a predictive understanding of structure-reactivity correlates of specific DNA nanostructures, which will allow a better understanding of the behaviour of nucleic acids under nanoscale confinement, as well as in the rational design of functional nanodevices based on self-assembling nucleic acids.
dc.format.extent995-1006
dc.language.isoen
dc.relation.haspartNucleic Acids Research
dc.relation.isreferencedbyOxford University Press (OUP)
dc.rightsCC BY-NC
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.subjectBase Sequence
dc.subjectBinding Sites
dc.subjectDNA
dc.subjectDNA Cleavage
dc.subjectDNA Restriction Enzymes
dc.subjectModels, Molecular
dc.subjectNanostructures
dc.subjectNanotechnology
dc.subjectNucleic Acid Conformation
dc.subjectProtein Binding
dc.subjectProtein Domains
dc.titleBinary control of enzymatic cleavage of DNA origami by structural antideterminants
dc.typeArticle
dc.type.genreJournal Article
dc.relation.doi10.1093/nar/gkx1204
dc.ada.noteFor Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
dc.date.updated2021-01-22T14:29:38Z
refterms.dateFOA2021-01-22T14:29:43Z


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