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University of Southampton Research Repository University of Southampton Research Repository Copyright © and Moral Rights for this thesis and, where applicable, any accompanying data are retained by the author and/or other copyright owners. A copy can be downloaded for personal non- commercial research or study, without prior permission or charge. This thesis and the accompanying data cannot be reproduced or quoted extensively from without first obtaining permission in writing from the copyright holder/s. The content of the thesis and accompanying research data (where applicable) must not be changed in any way or sold commercially in any format or medium without the formal permission of the copyright holder/s. When referring to this thesis and any accompanying data, full bibliographic details must be given, e.g. Thesis: Author (Year of Submission) "Full thesis title", University of Southampton, name of the University Faculty or School or Department, PhD Thesis, pagination. Data: Author (Year) Title. URI [dataset] University of Southampton Faculty of Engineering and Physical Sciences School of Physics and Astronomy Three-dimensional materials made from engineered oligonucleotides and nanoparticles by Angela Federica De Fazio ORCID ID 0000-0002-9733-3981 Thesis for the degree of Doctor of Philosophy September 2019 University of Southampton Abstract Faculty of Engineering and Physical Sciences School of Physics and Astronomy Thesis for the degree of Doctor of Philosophy Three-dimensional materials made from engineered oligonucleotides and nanoparticles by Angela Federica De Fazio In the last decades, the ability to assemble nanoparticles into programmed 2D or 3D structures by means of synthetic oligonucleotides has resulted into the fabrication of novel nanomaterials with unique physical and chemical properties. Nuclei acids are an exceptional platform for the architecture of complex structures, allowing routes to flexible and precise placing of functional nanoparticles. The physicochemical properties of featured materials can be readily tuned by varying the constituent building blocks. In this thesis, the advanced programming of the assembly processes was combined with the use of innovative ligation techniques. DNA-functionalised nanoparticles of different composition, size and shape were prepared and used in DNA-guided assembling processes (Chapter 3). Furthermore, engineered synthetic DNA strands were designed and employed for the fabrication of nanoparticle assemblies with stability and resistance against DNA denaturing conditions (Chapter 4). DNA ligation was realised using a UV-sensitive molecule, the 3-cyanovinyl carbazole. Following light-stimulation, this compound allows the formation of an interstrand crosslink within a DNA duplex, providing a novel tool for the manipulation of three-dimensional nanoparticles assemblies. In contrast with other crosslinking techniques, the carbazole interstrand bond can be reversed, using a different wavelength as an external trigger. The efficient application of the 3-cyanovinyl carbazole in extended nanoparticle crystals is demonstrated for the first time. DNA-directed heterogeneous assemblies of plasmonic and fluorescent nanoparticles were also manufactured (Chapter 5). The interplay between gold and upconversion nanoparticles within the same aggregate structure and the effect on the linear and non-linear optical properties was studied. Table of Contents Table of Contents Table of Contents ............................................................................................................ i Table of Tables ................................................................................................................ v Table of Figures ............................................................................................................. vii Research Thesis: Declaration of Authorship ................................................................. xvii Acknowledgements ...................................................................................................... xix Definitions and Abbreviations .................................................................................... xxiii Chapter 1 Introduction ...............................................................................................27 1.1 Theoretical background ........................................................................................... 28 1.1.1 Colloidal nanoparticles ..................................................................................... 29 1.1.1.1 Synthesis of gold nanoparticles ............................................................. 29 1.1.1.2 Synthesis of silver nanoparticles ........................................................... 32 1.1.1.3 Optical properties of metallic nanoparticles ......................................... 32 1.1.1.4 Synthesis and optical properties of upconversion nanoparticles ......... 35 1.1.1.5 Optical properties .................................................................................. 36 1.1.2 DNA nanotechnology ....................................................................................... 39 1.1.2.1 Structure and properties of oligonucleotides ....................................... 39 1.1.2.2 DNA crosslinking .................................................................................... 43 1.1.2.3 Strategies for oligonucleotide attachment on colloidal nanoparticles . 45 1.1.3 Self-assembly of nanoparticles ........................................................................ 48 Chapter 2 Experimental Procedures ............................................................................53 2.1 Synthesis of Nanoparticles ....................................................................................... 53 2.1.1 Synthesis of 14 nm spherical gold nanoparticles ............................................. 53 2.1.2 Synthesis of large spherical gold nanoparticles ............................................... 53 2.1.3 Synthesis of spherical silver nanoparticles ...................................................... 54 2.1.4 Synthesis of lanthanide-doped NaYF4 upconversion nanoparticles ................ 54 2.1.5 Synthesis of lanthanide-doped NaY:GdF4 upconversion nanoparticles .......... 55 2.1.5.1 Wet annealing of upconversion nanoparticles ..................................... 56 2.1.6 Synthesis of iron oxide nanoparticles .............................................................. 56 i Table of Contents 2.2 Oligonucleotide Functionalisation of Nanoparticles ............................................... 56 2.2.1 Surface modification of spherical metallic nanoparticles with a dense shell of oligonucleotides ............................................................................................... 57 2.2.2 Surface modification of large metallic nanoparticles with a dense shell of oligonucleotides ............................................................................................... 58 2.2.3 Surface modification of UCNPs and IONPs with synthetic oligonucleotides .. 58 2.2.3.1 PAA ligand exchange ............................................................................. 58 2.2.3.2 Carboxylation via silanisation and amination ....................................... 59 2.2.4 Oligonucleotide attachment on UCNPs and IONPs ......................................... 59 2.3 DNA-Nanoparticles Assemblies ............................................................................... 60 2.3.1 Annealing at constant temperature ................................................................ 60 2.3.2 Slow cooling procedure ................................................................................... 60 2.3.3 Silica embedding for imaging ........................................................................... 60 2.4 Light-induced crosslinking and denaturation experiments ..................................... 61 2.5 Characterisation Techniques ................................................................................... 61 2.5.1 Spectroscopic techniques ................................................................................ 61 2.5.1.1 UV-Visible spectroscopy........................................................................ 61 2.5.1.2 Oligonucleotides melting curves ........................................................... 61 2.5.1.3 DNA density on gold nanoparticles ....................................................... 62 2.5.1.4 DNA density on silver nanoparticles ..................................................... 62 2.5.1.5 Fluorescence measurements of upconversion nanoparticles .............. 62 2.5.1.6 Fourier-transform infrared spectroscopy ............................................. 63 2.5.2 Gel electrophoresis .......................................................................................... 63 2.5.3 Thermogravimetric analysis ............................................................................. 63 2.5.4 Microscopy techniques .................................................................................... 64 2.5.4.1 Transmission electron microscopy ....................................................... 64 2.5.4.2 Scanning electron microscopy .............................................................. 64 2.5.4.3 Optical microscopy ................................................................................ 64 2.5.5 Scattering techniques ...................................................................................... 65 2.5.5.1 Zeta potential .......................................................................................
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