Diseases such as Alzheimer’s and Parkinson’s are classified as B-amyloid diseases due to the presence of plaques composed of B-amyloid fibrils, aggregations of misfolded proteins, in the affected tissues. Poorly functioning bioenergetics reactions such as those in cytochrome oxidase are linked to cardiomyopathies. Very early reaction intermediates such as misfolding in proteins that arise in less than a millisecond can lead to a cascade that results in diseases. Reaction mechanisms and kinetics of such sub-millisecond events are especially difficult to investigate experimentally due to (i) the lack of suitable methods to rapidly mix reactants, and/or (ii) lack of facile detection methods that are sensitive to molecular structure. Current techniques for such investigations are impractical in many cases or have serious limitations. The most promising method to investigate fast reactions integrates microfluidic continuous-flow reactors (MCFMs) with Fourier Transform infrared (FTIR) imaging to obtain sub-millisecond temporal resolution and molecular-bond structural resolution.
My thesis primarily focuses on developing polymeric MCFMs compatible with FTIR imaging and developing robust methods for high-fidelity FTIR imaging and data analysis of sub-millisecond biomolecular reactions. We developed polymeric MCFMs using a low-cost cyclic olefin copolymer (COC) that is physically and spectrally biocompatible, and well suited for microfabrication. We used strong covalent bonding between device layers to enable the high flow rates needed to probe sub-millisecond reactions and developed robust FTIR imaging and analysis algorithms to extract high-quality FTIR spectral data. After validating the ability of the platform to provide both change in structural details of biomolecules and associated kinetics, we applied the platform and showed the ability of dodine as a chemical denaturant to enable FTIR protein dynamic studies by tracing the conformational change of apomyoglobin, and its unfolding kinetics. We successfully showed that the secondary structures of apomyoglobin behave differently during unfolding, and the unfolding kinetics changed depending on the dodine concentration
