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<p>The entrapment of biomolecules within TEOS-based sol-gel derived organic/inorganic nanocomposite materials has proven to be a viable platform for the development of biosensors and solid-phase biocatalysts. In this thesis, a series of organically modified silica materials were prepared by a two-step aqueous processing method that was suitable for biomolecule entrapment, and were formed as submicron thick films by dipcasting. Dispersed additives, such as polymers (Class I materials) and covalently bound additives, such as organically modified silanes (Class II materials), were used to modify the internal environment compared to the undoped matrices and to correlate the properties of entrapped enzymes.</p> <p>The morphology of organically modified silica materials could be modified through the use of either separate or co-hydrolysis of the silane precursors, with the later method generating optically transparent materials. Fluorescence microscopy revealed chemical heterogeneity in materials that appeared to be homogeneous by brightfield or SEM.</p> <p>Fluorescence emission studies of a solvatochromic dye entrapped within the film confirmed that the internal chemical environment of the films was strongly affected by doping with polymers and organosilanes. The films showed a rapid initial change in chemical properties owing to solvent evaporation, followed by a much slower evolution over several months owing to continued condensation reactions within the film.</p> <p>A reagentless biosensor was designed based on co-entrapment of an enzyme and a fluorescently labeled polymer. The enzymes urease and lipase were selected for this study as both catalyze reactions that alter the local pH. By co-entrapping pH sensitive fluorophores (SNARF-I and fluorescein) bound to a high molecular weight polymer, it was possible to detect the analytes urea and glyceryl tributyrate using changes in the fluorescence intensity (fluorescein) or emission ratio (SNARF-l). By tuning the polarity of the matrix it was possible to optimize the sensitivity of the sensing film for both the polar and non-polar analyte.</p> / Doctor of Philosophy (PhD)

Functional nucleic acids (FNAs), which include both DNA/RNA aptamers and DNA enzymes, have emerged as promising biological recognition elements for biosensors. These species typically require immobilization on or within a solid support, which is usually interfaced to some kind of signal transducer and readout system when use in biosensor. Our group has successfully immobilized several functional nucleic acids in the past, including fluorescence-signalling DNA enzymes, DNA aptamers and RNA aptamers by entrapping them into porous silica or organosilica materials prepared by the sol-gel method using percursors such as sodium silicate (SS), diglyceryl silane (DGS), tetrametylorthosilicate (TMOS) and trimethoxymethysilane (MTMS). While the earlier work established the ability of entrapped FNAs to retain binding and catalytic activity, only limited information was obtained on how different factors affect the performance of immobilized FNAs, and no information was obtained on the effects of aging and storage conditions on FNA performance. The initial objective of this thesis was to employ advanced fluorescence methods to better understand the nature of immobilized DNA and RNA aptamers, and in particular how entrapment in different sol-gel based materials affected FNA performance for detection of small molecule analytes. It was found that the ability of the entrapped aptamer reporters to remain fully hybridized was the most important factor in terms of signalling capability for both DNA and RNA aptamer reporters. It was also observed that more polar materials derived from SS were optimal for both types of aptamer reporters, since these allowed the entrapped aptamers to remain hydridized to their complementary strands and still retain the dynamic motion needed to undergo structure switching, while providing a minimum degree of leaching. The second objective of my research was to develop a paper-based biosensing device incorporating immobilized DNA and RNA aptamers that could be used in the fields of point-of-care diagnostics to further expand the utility of structure-switching aptamer reporters to real world application. A dual response (fluorescence / colorimetric) paper-based sensor utilized printed graphene oxide to immobilize both a RNA and a DNA aptamer in a recognition zone. Upon target addition, the aptamer desorbed and eluted to an amplification zone where rolling circle amplification was used to generate a colorimetric output. This sensor could function with clinical samples such as serum and stool, and allowed detection of key bacterial markers (ATP and glutamate dehydrogenase) at clinically relevant levels. / Thesis / Doctor of Philosophy (PhD)

This thesis describes the use of functional nucleic acid (FNA) superstructures entrapped within monolithic macroporous sol–gel-derived silica for solid-phase flow-based sensing of small molecules and macromolecular proteins. The work described herein overcomes a long-standing issue with entrapment of biomolecule into sol–gel-derived materials; the mesoporous pore morphology required to retain entrapped biomolecules prevents detection of large analytes as these can’t access the entrapped species. It is shown that large DNA superstructures can be produced through rolling circle amplification of a functional nucleic acid, resulting in concatemeric FNA species with dameters of several microns. Such species can be entrapped within macroporous sol-gel derived materials with micron-sized pores with minimal leaching, thus allowing for detection of a wide range of molecules, including biomolecules. Optimal materials for entrapment of FNA superstructures was achieved using a high-throughput material screening method, which minimized biomolecule leaching while maintaining FNA activity. Using an optimized material, concatemeric aptamer superstructures were entrapped within macroporous monolithic columns for flow-based detection of small molecules and proteins, extending the range of analytes that can be analyzed using biohybrid monolithic columns. Preliminary studies on the formation and properties of a DNAzyme superstructure for detection of E. coli detection were also performed, which provided valuable information on factors that must be controlled to allow reproducible fluorescence-based detection of E. coli using the crude intracellular matrix as the target. / Thesis / Master of Science (MSc)

Thesis (M.Sc. (Physics)) -- University of Limpopo, 2017 / The undoped ZnO nanoparticles, In or Co single doped ZnO nanoparticles and the In and Co combinational doped ZnO nanoparticles were synthesised through sol-gel technique. The samples were characterised using XRD, TEM, FTIR, Raman spectroscopy, UV-Vis, PL and also tested for the gas sensing applications. XRD patterns revealed that the synthesised samples were of ZnO hexagonal wurtzite structure. The lattice parameters and the bond length of all the undoped and doped ZnO samples were determined and found to be similar to that of the Bulk ZnO. The average particle size of the undoped and doped ZnO nanoparticles were calculated and found to reduce with an introduction of dopants while increasing with an increase in temperature. The strain of all the prepared samples were also determined and observed to be in an inverse relation to the particle size. TEM images showed that the synthesised samples were spherically shaped and that was in agreement with XRD results, while the EDS results showed that In and Co were successfully doped into the ZnO nanoparticles. Raman and FTIR spectroscopy indicated that the prepared samples were indeed ZnO nanoparticles which confirmed the XRD results. The UV-Vis results showed a red-shift in the energy band gap with an introduction of dopants and that was related to the reduction of the particle size, this results were consistent with the PL results. Gas sensing results showed that doping Co and In into the ZnO nanoparticles has an effect into ZnO properties. Combinational-doping of In and Co was found to increase the response to the gases CH4, CO, NH3 and H2 as compared to the undoped and singly doped ZnO nanoparticle sensors. The response\recovery time was found to be affected with introduction of In and Co. Improvements were also observed in the operating temperature and the selectivity of the single doped and co-doped ZnO nanoparticles towards different gases used in this study. / University of Limpopo IBSA National Research Foundation (NRF)

Stable suspensions of superparamagnetic cobalt nanoparticles have been prepared in poly(dimethysiloxane) (PDMS) carrier fluids in the presence of poly[dimethylsiloxane-b-(3-cyanopropyl)methylsiloxane-b-dimethylsiloxane] (PDMS-PCPMS-PDMS) triblock copolymers as steric stabilizers. A series of the polysiloxane triblock copolymers with systematically varied molecular weights were prepared via anionic polymerization using LiOH as an initiator. These copolymers formed micelles in toluene or poly(dimethylsiloxane) (PDMS) carrier fluids and served as "nanoreactors" for thermal decomposition of the CO₂(CO)8 precursor. The nitrile groups on the PCPMS central blocks are thought to coordinate onto the particle surface, while the PDMS endblocks protrude into the reaction medium to provide steric stability. The particle size can be controlled by adjusting the cobalt to copolymer ratio. Ordered self-assemblies of these cobalt nanoparticles are observed when the dispersions are cast from toluene. Electron diffraction spectroscopy reveals that the cobalt nanoparticles have fcc crystal structures. TEM shows non-aggregated cobalt nanoparticles with narrow size distributions, which are evenly surrounded with copolymer sheaths. However, some degree of surface oxidation was observed over time, resulting in a decrease in magnetic susceptibility. Novel poly[dimethylsiloxane-b-methyltriethoxysilylsiloxane-b-(3-cyanopropyl) methylsiloxane-b-methyltriethoxysilylsiloxane-b-dimethylsiloxane] (PDMS-PMTEOS-PCPMS-PMTEOS-PDMS) pentablock terpolymers were prepared. These terpolymers could fill the dual role both as steric stabilizers for preparing stable cobalt nanoparticle dispersions and precursors for the particle coating process. Silica films coated on the particles surfaces were employed to prevent the surface oxidation of the nanoparticles. Specific saturation magnetic measurement indicates that coating the nanoparticles with silica thin films can effectively inhibit the oxidation process. / Ph. D.

Conventional fibers are comprised of a solid glass core and solid glass cladding often protected by a thin polymer sheath. The finely tuned difference in refractive indices, for step index-fibers, is achieved by doping the core with germanium or elements with similar effects. Holey fibers (including photonic crystal fibers) comprise of a pure silica core, and a pure but porous silica cladding of air holes [1]. This provides a huge difference in the refractive indices on the cladding and core without doping. This translates into radiation resistant fibers with very low losses and very robust to high temperatures to mention a few [2]. Several successful attempts have been made for ordered holey optical fibers since the initial publication by Knight et al; random holey optical fibers, which can be just as effective, have yet to be fabricated [3]. Sol-gel processing of silicon alkoxides can be used to fabricate silica monoliths of tailored pore densities and sizes [4]; this makes the process attractive for random holey fiber preform manufacturing. Similar attempts have been made by Okazaki et al [5] to make conventional optical fibers. This paper chronicles efforts to make random holey fiber optical preforms from silica sol-gel monoliths, characterized for some structural properties. Silica monoliths can be made by hydrolysis and condensation of TEOS (tetraethylorthosilicate) or TMOS (tetramethylorthosilicate). These can be catalyzed in a single step or two-step process, aged and dried at ambient pressures and temperatures, as well as by supercritical fluid extraction of CO2. Mechanical strengthening techniques as described by Okazaki [5] have also been employed. The silica gel monoliths are characterized by helium pycnometry and scanning electron microscopy. Various shapes and densities of silica monoliths have been prepared and characterized. Some of these have also drawn into fibers to demonstrate their viability. / Master of Science