The fabrication, functionalization, and application of amorphous carbon substrates for array fabrication and analysis

This dissertation describes the development and application of amorphous carbon substrates for the fabrication and analysis of biomolecule and small molecule arrays. Carbon-based substrates such as nano-crystalline diamond, glassy carbon and amorphous carbon thin films are desirable substrates for array fabrication as they show superior chemical stability over their silicon, glass, and gold analogs.;The stability of carbon substrates make them ideal candidates for high density biomolecule array fabrication and the in situ synthesis of both biomolecules and small organic molecules directly onto the substrate. Stable array substrates make the parallelization of surface assays requiring long incubations, repeated usage, and exposure to harsh chemical conditions a chemical reality. Carbon substrates, however, have not become widely used because they lack the variety of attachment chemistries available for silanized glass substrates and gold substrates modified with self-assembled monolayers. This dissertation describes multiple new attachment chemistries, allowing aldehyde-, carboxylic acid-, and acyl chloride-terminated amorphous carbon substrates to easily be fabricated. Hydroxyl-terminated amorphous carbon substrates are also used for the in situ synthesis of oligonucleotide arrays. A second approach is to attach molecules containing strong nucleophiles such as a Grignard reagent. While the chemistries discussed in this dissertation have been used predominantly on amorphous carbon substrates, they are also transferable to their glassy carbon and nano-crystalline diamond analogs.;An added benefit of using amorphous carbon substrates is that they offer a chemical stability comparable to nano-crystalline diamond substrates and are easily integrated with a wide variety of other materials, due to the room-temperature deposition process. Carbon-on-metal substrates were fabricated by applying a thin amorphous carbon films to surface plasmon conducting metal substrates. The carbon-on-metal substrates were used to fabricate in situ synthesized oligonucleotide arrays and to then monitor DNA-DNA and DNA-protein interactions with surface plasmon resonance imaging. The stability and compatibility of oligonucleotide arrays synthesized on the carbon-on-metal substrates with fluorescence-based analysis methods were compared with oligonucleotides synthesized on silanized glass substrates. The carbon-on-metal substrates exhibited a greater stability upon exposure to prolonged incubations at elevated temperatures as well as when subjected to serial hybridizations/dehybridizations.