| Summary: | The aim of the work described in this thesis was to investigate and exploit the properties of hydrogen bonded supramolecular self-assembled networks (SANs) through use as a template to pattern substrate surfaces at the sub 10 nm length scale. This would potentially allow control over the spatial distribution of molecules, and thus the chemical and biofunctionality of a surface at this length scale. Complementary surface analysis techniques were used throughout the project to characterise substrates functionalised with SANs and subsequent biomolecule adsorption including: atomic force microscopy (AFM), scanning tunnelling microscopy (STM), PeakForce QNM (PF-QNM), time of flight secondary ion mass spectrometry (ToF-SIMS), and X-ray photoelectron spectroscopy (XPS). A hydrogen bonded PTCDI-melamine SAN, previously investigated with UHV STM, was selected for these studies as a suitable candidate system to explore the biofunctionality of SANs. As AFM is the preferred SPM technique to obtain images of biomolecules the resolution capabilities of our AFM system were fIrst tested through the use of different imaging modes and tips, as well as two model systems. The fIrst model system used ferritin, a spherical protein with a diameter of ~ 12 nm, subsequently deposited onto a HOPG substrate. The AFM was able to successfully achieve resolution of individual ferritin molecules. The second model system used C60 fullerenes with a diameter of ~ 1 nm deposited onto a Si (100) substrate; the obtained AFM images showed features attributable to individual fullerene molecules. While STM regularly resolved the molecular structure of SANs formed from solution deposition methods, no unit cell structure of the SAN was observed in AFM images of samples prepared in a similar manner. Instead multi layers and aggregates of material were observed across the sample surface. Therefore, optimisation of the PTCDImelamine SAN solution deposition protocol was undertaken in order to allow reproducible formation of organised domains of the PTCDI-melamine SAN across an extended surface area. Surface chemical characterisation was undeltaken with ToF-SIMS and XPS of different Au substrate preparation methods and PTCDI-melamine SAN solution deposition protocols. In conjunction with STM images the results suggested that Korolkov's PTCDImelamine SAN solution deposition protocol and UV cleaned Au (111) substrates were the preferred sample preparation methods. SPM confrrmation of the presence of multilayers Abstract when the PTCDI-melamine SAN is deposited from solution onto Au substrates was also obtained. In order to explore the biofunctionality of the PTCDI-melamine SAN its potential bioapplication in a DNA based sensor was investigated. 12mer ssDNA oligonucleotides were selected as suitable candidate molecules. Through combination of results obtained from ToF-SIMS, XPS, AFM, STM and PF-QNM there is a suggestion that DNA hybridisation efficiency is increased when the ssDNA oligonucleotides are adsorbed onto PTCDI-melamine patterned Au (111) substrates, as opposed to when adsorbed onto bare Au (111) substrates. This is possibly due to the PTCDI-melamine SAN controlling the spatial distribution of the adsorbed ssDNA oligonucleotides, thereby reducing steric hindrance. The results described in the thesis provide proof-of-concept that the use of SANs can provide some improvements for surface biomolecule functionalisation strategies. However, further work is required to quantify several factors such as overall surface coverage of organised domains of the PTCDI-melamine SAN, and the potential improvements to surface bound DNA hybridisation efficiency. ii
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