{"id":{"repo_id":"york","oai_identifier":"oai:yorkspace.library.yorku.ca:10315/40726"},"canonical_url":"https://search.dev.ndltd.org/etd/york/oai:yorkspace.library.yorku.ca:10315/40726","repository":{"repo_id":"york","name":"York University","base_url":"https://yorkspace.library.yorku.ca/oai/request"},"display":{"title":"Studying the Structural Dynamics and Aptamer-Ligand Interactions in the Cocaine-Binding Aptamer through Fluorescence Spectroscopy","abstract":"Since 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.","abstract_html":"Since 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.","abstract_has_math":false,"creators":["Shoara, Amin Aron"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Johnson, Philip E."],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-12-14","date_published":"2022-12-14","updated_at":"2026-07-24T06:33:45Z","subjects":["Biochemistry","Chemistry","Molecular biology"],"languages":["en"],"rights":["Author owns copyright, except where explicitly noted. Please contact the author directly with licensing requests."],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/10315/40726","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Johnson, Philip E."]},{"key":"dc:creator","label":"Author","values":["Shoara, Amin Aron"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2022-12-14T16:36:25Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2022-12-14T16:36:25Z"]},{"key":"dc:date.issued","label":"Date","values":["2022-12-14"]},{"key":"dc:type","label":"Dc Type","values":["Electronic Thesis or Dissertation"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Biochemistry","Chemistry","Molecular biology"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Author owns copyright, except where explicitly noted. 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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."]},{"key":"dc:title","label":"Title","values":["Studying the Structural Dynamics and Aptamer-Ligand Interactions in the Cocaine-Binding Aptamer through Fluorescence Spectroscopy"]}]}],"canonical_facts":{"dc:contributor.advisor":["Johnson, Philip E."],"dc:creator":["Shoara, Amin Aron"],"dc:date.accessioned":["2022-12-14T16:36:25Z"],"dc:date.available":["2022-12-14T16:36:25Z"],"dc:date.issued":["2022-12-14"],"dc:description.abstract":["Since 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.uri":["http://hdl.handle.net/10315/40726"],"dc:language":["en"],"dc:rights":["Author owns copyright, except where explicitly noted. Please contact the author directly with licensing requests."],"dc:subject":["Biochemistry","Chemistry","Molecular biology"],"dc:title":["Studying the Structural Dynamics and Aptamer-Ligand Interactions in the Cocaine-Binding Aptamer through Fluorescence Spectroscopy"],"dc:type":["Electronic Thesis or Dissertation"]},"updated_at":"2026-07-24T06:33:45Z"}