Studying the Structural Dynamics and Aptamer-Ligand Interactions in the Cocaine-Binding Aptamer through Fluorescence Spectroscopy

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dc.contributor.advisorJohnson, Philip E.
dc.contributor.authorShoara, Amin Aron
dc.date.accessioned2022-12-14T16:36:25Z
dc.date.available2022-12-14T16:36:25Z
dc.date.copyright2022-08-08
dc.date.issued2022-12-14
dc.date.updated2022-12-14T16:36:25Z
dc.degree.disciplineChemistry
dc.degree.levelDoctoral
dc.degree.namePhD - Doctor of Philosophy
dc.description.abstractSince its first report in 1990, aptamers have been utilized in biosensor modeling technologies. One of the most important advantages of using aptamers is the structural flexibility and thermal stability of nucleic acids. These structural merits enable aptamers to be linked on solid surfaces, attached to chemical labels, or extended to build nanostructures for advanced therapeutic and diagnostic modeling purposes. The cocaine-binding aptamer was originally selected through a systematic evolution of ligands by exponential enrichment (SELEX) method to select cocaine molecules from cocaine metabolites in biological solutions. However, the aptamer showed binding to quinine and other antimalaria drugs tighter than its original ligand, cocaine. Work presented in this dissertation demonstrate how the cocaine-binding aptamer can be exploited as a model system for the structural analysis of aptamers using biophysical techniques including fluorometry methods. The results discussed in this study demonstrate how intrinsic fluorescence of ligands was exploited for aptamer-ligand binding and thermal stability analyses. Furthermore, photoisomerization of stilbene coupled with ligand-induced binding mechanism of the cocaine-binding aptamer were employed for the development of the Photochrome Aptamer Switch Assay. This research aims to gain insight into how aptamers interact with their ligands by utilizing the fluorescence properties of the ligands. Investigating the binding mechanisms of aptamers is essential in sensing technology since biosensors yield greater analytical sensitivity upon ligand-induced structural changes.
dc.identifier.urihttp://hdl.handle.net/10315/40726
dc.languageen
dc.rightsAuthor owns copyright, except where explicitly noted. Please contact the author directly with licensing requests.
dc.subjectBiochemistry
dc.subjectChemistry
dc.subjectMolecular biology
dc.subject.keywordsAptamer
dc.subject.keywordsDNA
dc.subject.keywordsRNA
dc.subject.keywordsProtein
dc.subject.keywordsFluorescence
dc.subject.keywordsSpectroscopy
dc.subject.keywordsLigand
dc.subject.keywordsStructure
dc.subject.keywordsDynamics
dc.subject.keywordsIntrinsic
dc.subject.keywordsMethod
dc.subject.keywordsAnalysis
dc.subject.keywordsBiophysical
dc.subject.keywordsX-ray crystallography
dc.subject.keywordsIsothermal titration calorimetry
dc.subject.keywordsNuclear magnetic resonance
dc.subject.keywordsDifferential scanning calorimetry
dc.subject.keywordsCocaine
dc.subject.keywordsQuinine
dc.subject.keywordsAntimalaria
dc.subject.keywordsAntimalarial
dc.subject.keywordsArtemisinin
dc.subject.keywordsElectrochemical
dc.subject.keywordsSensor
dc.subject.keywordsBiosensor
dc.subject.keywordsDetection
dc.subject.keywordsLevamisole
dc.subject.keywordsStilbene
dc.subject.keywordsSITS
dc.subject.keywordsPhotoisomerization
dc.subject.keywordsPhotochrome aptamer switch assay
dc.subject.keywordsPHASA
dc.subject.keywordsCocaine binding
dc.subject.keywordsOchratoxin A
dc.subject.keywordsOTA
dc.subject.keywordsOTX
dc.subject.keywordsQuenching
dc.subject.keywordsEnhancement
dc.subject.keywordsDifferential scanning fluorimetry
dc.subject.keywordsFluorometry
dc.subject.keywordsUltraviolet
dc.subject.keywordsVisible
dc.subject.keywordsLight
dc.subject.keywordsThermal stability
dc.subject.keywordsThermal melt denaturation
dc.subject.keywordsIsotherm
dc.subject.keywordsFunction
dc.subject.keywordsMN4
dc.subject.keywordsMN19
dc.subject.keywordsLigand induced binding folding mechanism
dc.subject.keywordsDopamine
dc.subject.keywordsSerotonin
dc.subject.keywordsStructure modeling
dc.subject.keywordsAptachain
dc.subject.keywordsAptamesh
dc.subject.keywordsFluorescence polarization
dc.subject.keywordsProtocol
dc.subject.keywordsPhotomultiplier
dc.subject.keywordsCLOD
dc.subject.keywordsCLOQ
dc.subject.keywordsThreshold
dc.subject.keywordsOptimization
dc.subject.keywordsQuantum yield
dc.subject.keywordsAffinity
dc.subject.keywordsKa
dc.subject.keywordsKd
dc.subject.keywordsDissociation constant
dc.subject.keywordsMerocyanine
dc.subject.keywordsFPhOBtz
dc.subject.keywordsDye
dc.subject.keywordsThree way junction
dc.subject.keywords3WJ
dc.subject.keywordsTWJ
dc.subject.keywordsThermal shift assay
dc.subject.keywordsConjugation
dc.subject.keywordsFluorescence decay kinetics
dc.subject.keywordsFluorescence anisotropy
dc.subject.keywordsMethod validation
dc.subject.keywordsDrug
dc.subject.keywordsSensitivity
dc.subject.keywordsCalibration
dc.subject.keywordsCurve
dc.subject.keywordsPlot
dc.subject.keywordsNon linear regression
dc.subject.keywordsSpike-recovery
dc.subject.keywordsAccuracy
dc.subject.keywordsCircular dichroism
dc.subject.keywordsExcitation
dc.subject.keywordsEmission
dc.subject.keywordsin vitro
dc.subject.keywordsStern Volmer constant
dc.subject.keywordsStokes shift
dc.subject.keywordsSELEX
dc.subject.keywordsEnthalpy
dc.subject.keywordsGibbs free energy
dc.subject.keywordsEntropy
dc.subject.keywordsWavelength
dc.subject.keywordsRefractive index
dc.subject.keywordsExtinction coefficient
dc.subject.keywordsFluorescence lifetime
dc.titleStudying the Structural Dynamics and Aptamer-Ligand Interactions in the Cocaine-Binding Aptamer through Fluorescence Spectroscopy
dc.typeElectronic Thesis or Dissertation

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