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Thermodynamics and Kinetics of Adaptive Binding in the Malachite Green RNA Aptamer

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dc.contributor.authorDa Costa, Jason B.
dc.contributor.authorAndreiev, Aurelia I.
dc.contributor.authorDieckmann, Thorsten
dc.date.accessioned2018-05-04T19:29:05Z
dc.date.available2018-05-04T19:29:05Z
dc.date.issued2013-09-24
dc.descriptionThis document is the Accepted Manuscript version of a Published Work that appeared in final form in Biochemistry, copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see http://dx.doi.org/10.1021/bi400549sen
dc.description.abstractAdaptive binding, the ability of molecules to fold themselves around the structure of a ligand and thereby incorporating it into their three-dimensional fold, is a key feature of most RNA aptamers. The malachite green aptamer (MGA) has been shown to bind several closely related triphenyl dyes with planar and nonplanar structures in this manner. Competitive binding studies using isothermal titration calorimetry and stopped flow kinetics have been conducted with the aim of understanding the adaptive nature of RNA–ligand interaction. The results of these studies reveal that binding of one ligand can reduce the ability of the aptamer pocket to adapt to another ligand, even if this second ligand has a significantly higher affinity to the free aptamer. A similar effect is observed in the presence of Mg2+ ions which stabilize the binding pocket in a more ligand bound-like conformation.en
dc.description.sponsorshipNational Science and Engineering Research Council (NSERC) [326911-2009]en
dc.description.sponsorshipCanada Foundation for Innovation (CFI)en
dc.identifier.urihttp://dx.doi.org/10.1021/bi400549s
dc.identifier.urihttp://hdl.handle.net/10012/13234
dc.language.isoenen
dc.publisherAmerican Chemical Societyen
dc.subjectIsothermal Titration Calorimetryen
dc.subjectLigand-Bindingen
dc.subjectCross-Relaxationen
dc.subjectRiboswitchen
dc.subjectRecognitionen
dc.subjectFluorescenceen
dc.subjectSpectroscopyen
dc.subjectSuppressionen
dc.subjectPolymeraseen
dc.subjectNetworksen
dc.titleThermodynamics and Kinetics of Adaptive Binding in the Malachite Green RNA Aptameren
dc.typeArticleen
dcterms.bibliographicCitationHeart and Stroke Foundation of Canada grant-in-aiden
dcterms.bibliographicCitationNatural Sciences and Engineering Research Council of Canada Discovery grantsen
dcterms.bibliographicCitationBritish Heart Foundationen
dcterms.bibliographicCitationLabEx “Ion Channel Science and Therapeutics” and ANR-10-BLAN-1601en
dcterms.bibliographicCitationNational Institutes of Health Grant NS067456en
dcterms.bibliographicCitationNSERC Canada Graduate Scholarshipen
dcterms.bibliographicCitationResearch incentive funds from University of Waterloo.en
uws.contributor.affiliation1Faculty of Scienceen
uws.contributor.affiliation2Chemistryen
uws.peerReviewStatusRevieweden
uws.scholarLevelFacultyen
uws.typeOfResourceTexten

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