| Biomolecular interaction represents a field of study concerning DNA-DNA, DNA-RNA, DNA-small molecule, protein-DNA, and protein-small molecule interactions. The ability to characterize biomolecular interactions is critical to understanding the functions of these biomolecules. Due to the enormous complexity of the interaction networks, high-throughput methods are highly desired especially for large scale screening of biomolecular interactions. Surface-based technology is particularly amenable to this purpose as flat surfaces are readily multiplexed to bear up to hundreds of thousands of probe sites, making possible the parallel analysis of thousands of parameters in a single experiment. This dissertation describes the development of protein and DNA-modified surfaces for the study of biomolecular interactions.;Protein arrays were fabricated by spotting proteins on NHS-ester functionalized gold surfaces for the analysis of cell surface carbohydrate expression. A variety of biomolecules including DNA, proteins, and small molecules were patterned on amorphous carbon surfaces by photolithography and their biomolecular interactions were studied. Both glass and carbon surfaces modified with hydroxyl groups were used for the in situ synthesis of DNA arrays.;This dissertation also describes an approach for the control of oligonucleotide density in light-directed DNA array fabrication by varying the UV light exposure dose on surfaces. Similar results were obtained on different surfaces, suggesting that the approach is generally applicable. The ability to control surface oligonucleotide density could help realize the potential of DNA-modified surfaces as the performance of DNA-modified surfaces is strongly dependent on the surface oligonucleotide density.;Finally, this dissertation describes the use of DNA-modified surfaces to sequence-specifically capture protein-DNA complexes of interest followed by protein analysis using mass spectrometry. A transcription factor was captured on surfaces and identified and quantified using mass spectrometry. This approach, which combines DNA-modified surfaces with biological mass spectrometry, can be extended to more complex biomolecular interactions, advancing our understanding of their biological functions. |
