{"id":{"repo_id":"maynooth","oai_identifier":"oai:mural.maynoothuniversity.ie:6714"},"canonical_url":"https://search.dev.ndltd.org/etd/maynooth/oai:mural.maynoothuniversity.ie:6714","repository":{"repo_id":"maynooth","name":"National University of Ireland - Maynooth","base_url":"http://mural.maynoothuniversity.ie/cgi/oai2"},"display":{"title":"Site-Specific Labelling of Nucleic Acids by Catalyst-Free 1,3-Dipolar Cycloadditions","abstract":"The focus of the novel research reported in this thesis is the labelling of nucleic acids by catalyst-free 1,3-dipolar cycloaddition reactions. Both nitrile oxide-alkyne cycloadditions (NOAC) and strain-promoted azide-alkyne cycloadditions (SPAAC) were explored. The possiblitity for ‘pre-synthetic’ functionalisation was demonstrated using non-nucleosidic phorphoramidite building blocks generated by NOAC. Three isoxazole phosphoramidites were prepared. Following in situ generation of the nitrile oxides from 1,2-, 1,3- or 1,4-disubstituted hydroxyethoxybenzaldehyde oximes and highly regioselective cycloadditions to a simple alkyne, the isomeric isoxazoles were obtained in excellent yields. Functional group interchange of the pendant hydroxy group to a phosphoramidite functionality facilitated coupling to DNA both by manual and instrument controlled solid phase DNA synthesis. Photoresponsive DNA, incorporating isomeric isoxazole-linked azobenzene moieties, was prepared by ‘post-synthetic’ modification of alkyne-functionalised oligonucleotides by NOAC. The compatibility of the azobenzene functionality with NOAC protocols was first confirmed with small molecule examples; the resulting cycloadducts were characterised by NMR spectroscopy and mass spectrometry (MS). Oligonucleotides incorporating azobenzene moieties at either the 5’- or the 3’- termini, or at an internal position, were subsequently synthesised and the photochemical and kinetic properties of selected examples were determined. A relationship was found between the thermodynamic and photochemical properties of the modified oligonucleotides and the substitution pattern on the aryl rings of the azobenzene moiety. DNA and 2’-OMe RNA sequences conjugated to a variety of chemically and biologically significant ligands were prepared by solid-phase SPAAC. A strained-cyclooctyne phosphoramidite was first conjugated to the 5’-terminus of oligonucleotides. Several azide labels were prepared, including benzyl, cinnamyl, biotinyl, cholesteryl and fluoresceinyl. Conjugation was clean and efficient in all cases. Oligonucleotides were characterised by HPLC and MALDI-TOF MS.","abstract_html":"The focus of the novel research reported in this thesis is the labelling of nucleic acids by catalyst-free 1,3-dipolar cycloaddition reactions. Both nitrile oxide-alkyne cycloadditions (NOAC) and strain-promoted azide-alkyne cycloadditions (SPAAC) were explored. The possiblitity for ‘pre-synthetic’ functionalisation was demonstrated using non-nucleosidic phorphoramidite building blocks generated by NOAC. Three isoxazole phosphoramidites were prepared. Following in situ generation of the nitrile oxides from 1,2-, 1,3- or 1,4-disubstituted hydroxyethoxybenzaldehyde oximes and highly regioselective cycloadditions to a simple alkyne, the isomeric isoxazoles were obtained in excellent yields. Functional group interchange of the pendant hydroxy group to a phosphoramidite functionality facilitated coupling to DNA both by manual and instrument controlled solid phase DNA synthesis. Photoresponsive DNA, incorporating isomeric isoxazole-linked azobenzene moieties, was prepared by ‘post-synthetic’ modification of alkyne-functionalised oligonucleotides by NOAC. The compatibility of the azobenzene functionality with NOAC protocols was first confirmed with small molecule examples; the resulting cycloadducts were characterised by NMR spectroscopy and mass spectrometry (MS). Oligonucleotides incorporating azobenzene moieties at either the 5’- or the 3’- termini, or at an internal position, were subsequently synthesised and the photochemical and kinetic properties of selected examples were determined. A relationship was found between the thermodynamic and photochemical properties of the modified oligonucleotides and the substitution pattern on the aryl rings of the azobenzene moiety. DNA and 2’-OMe RNA sequences conjugated to a variety of chemically and biologically significant ligands were prepared by solid-phase SPAAC. A strained-cyclooctyne phosphoramidite was first conjugated to the 5’-terminus of oligonucleotides. Several azide labels were prepared, including benzyl, cinnamyl, biotinyl, cholesteryl and fluoresceinyl. Conjugation was clean and efficient in all cases. Oligonucleotides were characterised by HPLC and MALDI-TOF MS.","abstract_has_math":false,"creators":["Freeman, Colin"],"institution":"National University of Ireland Maynooth","degree_name":"phd","degree_level":"doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2012,"date_issued":"2012","date_published":"2012","updated_at":"2026-07-24T03:02:52Z","subjects":[],"languages":["en"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":null,"outbound_label":null,"outbound_source":null},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["Freeman, Colin"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2012"]},{"key":"dc:date.issued","label":"Date","values":["2012"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["National University of Ireland Maynooth"]},{"key":"dc:relation.isreferencedby","label":"Dc Relation Isreferencedby","values":["https://mural.maynoothuniversity.ie/id/eprint/6714/"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["phd"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://mural.maynoothuniversity.ie/id/eprint/6714/1/Colin%20Freeman%20-%20PhD%20Thesis.pdf"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The focus of the novel research reported in this thesis is the labelling of nucleic acids by catalyst-free 1,3-dipolar cycloaddition reactions. Both nitrile oxide-alkyne cycloadditions (NOAC) and strain-promoted azide-alkyne cycloadditions (SPAAC) were explored. The possiblitity for ‘pre-synthetic’ functionalisation was demonstrated using non-nucleosidic phorphoramidite building blocks generated by NOAC. Three isoxazole phosphoramidites were prepared. Following in situ generation of the nitrile oxides from 1,2-, 1,3- or 1,4-disubstituted hydroxyethoxybenzaldehyde oximes and highly regioselective cycloadditions to a simple alkyne, the isomeric isoxazoles were obtained in excellent yields. Functional group interchange of the pendant hydroxy group to a phosphoramidite functionality facilitated coupling to DNA both by manual and instrument controlled solid phase DNA synthesis. Photoresponsive DNA, incorporating isomeric isoxazole-linked azobenzene moieties, was prepared by ‘post-synthetic’ modification of alkyne-functionalised oligonucleotides by NOAC. The compatibility of the azobenzene functionality with NOAC protocols was first confirmed with small molecule examples; the resulting cycloadducts were characterised by NMR spectroscopy and mass spectrometry (MS). Oligonucleotides incorporating azobenzene moieties at either the 5’- or the 3’- termini, or at an internal position, were subsequently synthesised and the photochemical and kinetic properties of selected examples were determined. A relationship was found between the thermodynamic and photochemical properties of the modified oligonucleotides and the substitution pattern on the aryl rings of the azobenzene moiety. DNA and 2’-OMe RNA sequences conjugated to a variety of chemically and biologically significant ligands were prepared by solid-phase SPAAC. A strained-cyclooctyne phosphoramidite was first conjugated to the 5’-terminus of oligonucleotides. Several azide labels were prepared, including benzyl, cinnamyl, biotinyl, cholesteryl and fluoresceinyl. Conjugation was clean and efficient in all cases. Oligonucleotides were characterised by HPLC and MALDI-TOF MS."]},{"key":"dc:format","label":"Dc Format","values":["text"]},{"key":"dc:title","label":"Title","values":["Site-Specific Labelling of Nucleic Acids by Catalyst-Free 1,3-Dipolar Cycloadditions"]}]}],"canonical_facts":{"dc:creator":["Freeman, Colin"],"dc:date":["2012"],"dc:date.issued":["2012"],"dc:description.abstract":["The focus of the novel research reported in this thesis is the labelling of nucleic acids by catalyst-free 1,3-dipolar cycloaddition reactions. Both nitrile oxide-alkyne cycloadditions (NOAC) and strain-promoted azide-alkyne cycloadditions (SPAAC) were explored. The possiblitity for ‘pre-synthetic’ functionalisation was demonstrated using non-nucleosidic phorphoramidite building blocks generated by NOAC. Three isoxazole phosphoramidites were prepared. Following in situ generation of the nitrile oxides from 1,2-, 1,3- or 1,4-disubstituted hydroxyethoxybenzaldehyde oximes and highly regioselective cycloadditions to a simple alkyne, the isomeric isoxazoles were obtained in excellent yields. Functional group interchange of the pendant hydroxy group to a phosphoramidite functionality facilitated coupling to DNA both by manual and instrument controlled solid phase DNA synthesis. Photoresponsive DNA, incorporating isomeric isoxazole-linked azobenzene moieties, was prepared by ‘post-synthetic’ modification of alkyne-functionalised oligonucleotides by NOAC. The compatibility of the azobenzene functionality with NOAC protocols was first confirmed with small molecule examples; the resulting cycloadducts were characterised by NMR spectroscopy and mass spectrometry (MS). Oligonucleotides incorporating azobenzene moieties at either the 5’- or the 3’- termini, or at an internal position, were subsequently synthesised and the photochemical and kinetic properties of selected examples were determined. A relationship was found between the thermodynamic and photochemical properties of the modified oligonucleotides and the substitution pattern on the aryl rings of the azobenzene moiety. DNA and 2’-OMe RNA sequences conjugated to a variety of chemically and biologically significant ligands were prepared by solid-phase SPAAC. A strained-cyclooctyne phosphoramidite was first conjugated to the 5’-terminus of oligonucleotides. Several azide labels were prepared, including benzyl, cinnamyl, biotinyl, cholesteryl and fluoresceinyl. Conjugation was clean and efficient in all cases. Oligonucleotides were characterised by HPLC and MALDI-TOF MS."],"dc:format":["text"],"dc:identifier.uri":["https://mural.maynoothuniversity.ie/id/eprint/6714/1/Colin%20Freeman%20-%20PhD%20Thesis.pdf"],"dc:language":["en"],"dc:publisher.institution":["National University of Ireland Maynooth"],"dc:relation.isreferencedby":["https://mural.maynoothuniversity.ie/id/eprint/6714/"],"dc:title":["Site-Specific Labelling of Nucleic Acids by Catalyst-Free 1,3-Dipolar Cycloadditions"],"dc:type":["Thesis"],"dc:type.qualificationlevel":["doctoral"],"dc:type.qualificationname":["phd"]},"updated_at":"2026-07-24T03:02:52Z"}