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Protein Detection Using Dynamic DNA Assembly Open Access


Other title
Protein Detection
DNA Assembly
DNA Nanotechnology
Type of item
Degree grantor
University of Alberta
Author or creator
Li, Feng
Supervisor and department
Le, X. Chris (Chemistry)
Examining committee member and department
Gibbs-Davis, Julianne M. (Chemistry)
Campbell, Robert E. (Chemistry)
McDermott, Mark T. (Chemistry)
Sweedler, Jonathan V. (Chemistry)
Department of Chemistry

Date accepted
Graduation date
Doctor of Philosophy
Degree level
Dynamic DNA assemblies are useful to generate or amplify signals for detection of nucleic acids. However, application of DNA assemblies to proteins is more challenging. The major research goal of my thesis is to expand the scope of dynamic DNA assemblies to proteins. I developed a fluorescence turn-on assay and studied thermal stability of DNA functionalized gold nanoparticles (DNA-AuNPs) as a function of organosulfur anchor groups and DNA surface densities. An attempt to use DNA-AuNPs as detection probes in western blot protein analyses revealed nonspecific protein adsorptions. By applying dynamic DNA assembly to Aptamer-functionalized gold nanoparticles (Apt-AuNPs), I designed a competitive protection strategy that was able to effectively eliminate nonspecific protein adsorptions on Apt-AuNPs, enabling specific and sensitive detection of target proteins from human serum samples. To broaden the use of dynamic DNA assembly as tools for protein detection, I developed a binding-induced DNA strand-displacement strategy that could convert protein bindings to the release of pre-designed output DNA molecules. The output DNA molecules were used to trigger various DNA assemblies. Using this strategy, I developed a binding-induced strand-displacement beacon and a binding-induced catalytic DNA circuit, both of which could be used as isothermal and enzyme-free signal amplification strategies for protein detection. I have further developed a molecular translator that acted by binding-induced dynamic DNA assemblies on AuNPs, enabling highly sensitive and specific detection of different protein targets in homogeneous solutions. The techniques and strategies described in this thesis can be potentially used to construct a variety of protein-mediated DNA assemblies and nanostructures. A promising application is in the area of point-of-care diagnostics, taking advantage of binding-induced DNA assembly, molecular and/or signal amplification, and nanoparticle-based visualization.
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
Citation for previous publication
Zhang, H.; Li, F.; Dever, B.; Li, X-F.; Le, X. C. Homogeneous Binding Assays for Nucleic Acids and Proteins. Chemical Reviews, Published online Dec. 11, 2012. DOI: 10/1021/300340p.Li, F.; Li, J.; Wang, C.; Zhang, J.; Li, X.-F.; Le, X. C. Competitive protection of aptamer-functionalized gold nanoparticles by controlling DNA assembly. Analytical Chemistry, 2011, 83, 6464-6467.Li, F.; Zhang, H.; Wang, Z.; Li, X.; Li, X.-F.; Le, X. C. Dynamic DNA assemblies mediated by binding-induced DNA strand displacement. Journal of the American Chemical Society, 2013, 135, 2443-2446.Li, F.; Zhang, H.; Lai C.; Li, X-F.; Le, X. C. A Molecular Translator that Acts by Binding-Induced DNA Strand Displacement for a Homogeneous Protein Assay. Angewante Chemie International Edition, 2012, 51, 9317-9320.10. Li, F.; Zhao, Q.; Wang, C.; Lu, X.; Li, X.-F.; Le, X. C. Detection of E. coli O157: H7 using gold nanoparticle labeling and inductively coupled plasma-mass spectrometry. Analytical Chemistry, 2010, 82, 3399-3403.

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