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Synthesis of novel molecules for specific recognition of DNA G-quadruplex structures and rapid analysis of their binding to telomeric DNA on a gold surface.

Walsh, Killian (2014) Synthesis of novel molecules for specific recognition of DNA G-quadruplex structures and rapid analysis of their binding to telomeric DNA on a gold surface. Master of Science thesis, Dublin City University.

When confronted with nucleobase interactions, most people will think of the Watson-Crick base pairs. However, research from a variety of different disciplines has shown that the use of nucleobases as a scaffold to build larger functional assemblies through a variety of noncovalent interactions is much more versatile. Although all nucleobases have the ability to homodimerize, homo-oligomers of guanine derivatives are perhaps the most interesting. One of the most distinctive examples is the G-tetrad, a hydrogen-bonded macrocycle formed by cation-templated assembly of guanosine. In the late 1980s it was suggested that this motif, when formed in DNA, might be biologically relevant, which sparked enormous research interest in these naturally occuring architectures. The scope of the present work also relates to the G-quartet motif, and it fits particularly well with contemporary studies in molecular self-assembly and noncovalent synthesis. A series of 8-aryl-2'-deoxyguanosine (8ArdG) analogues was synthesised and their ability to induce G-quadruplex formation was investigated. Four lead compounds were selected to analyse the variation in G-quadruplex stability based on the position of functional groups. The detection method used was of novel design, based on quenching of immobilised fluorescently labelled DNA on a gold surface. The DNA undergoes structural changes upon binding to the 8ArdG, indicating the formation of G-quadruplex, which can be detected as a decrease in fluorescence signal. The formation of G-quadruplex was further validated by the use of Dual Polarisation Interferometry (DPI). A library of three novel compounds a one previously reported compound was successfully synthesised and fully characterised by NMR and IR spectroscopy. One of the novel compounds, 8-(4-pyrazole)-2`-deoxyguanosine, displayed novel characteristics as revealed by two dimensional NMR analysis. This novel compound displayed unusual chemical shifts attributed to a previously unreported molecular conformation. DPI analysis, using thiolated telomere DNA successfully bound to surface of amine coated chip, has revealed self-assembly in the presence of 8-(4-pyrazole)-2`-deoxyguanosine. As it is shown in this work, the noncovalent bond is a powerful synthetic tool in the preparation of complex molecular architectures. The G-quartet in particular serves as an excellent model to learn about the fundamentals and utility of noncovalent interactions in molecular self-assembly and drug discovery.
Item Type:Thesis (Master of Science)
Date of Award:November 2014
Supervisor(s):O'Kennedy, Richard, Gubala, Vladimir and Nolan, Kieran
Uncontrolled Keywords:DNA structures; Genetics
Subjects:Biological Sciences > Biotechnology
DCU Faculties and Centres:DCU Faculties and Schools > Faculty of Science and Health > School of Biotechnology
Use License:This item is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 3.0 License. View License
ID Code:20245
Deposited On:04 Dec 2014 15:26 by Richard O'Kennedy . Last Modified 27 Sep 2019 10:40

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