Date of Award
Doctor of Philosophy
The functional and pathogenic roles of biomolecules are often coupled to the self-association of their basic units into oligomers and aggregates whose structural details are difficult to distinguish because of their insoluble and heterogenous nature. This work focuses on DNA G-quadruplex motifs and amyloid peptides whose oligomers and aggregates are associated with numerous biological roles and human diseases. Infrared (IR) spectroscopy is a powerful tool which probes vibrational transitions whose signatures report on their arrangement within molecules. Advances in two-dimensional infrared (2D IR) spectroscopy have allowed structural characterization in increasingly complex biomolecules that are not amenable to traditional high-resolution techniques. However, careful consideration of the physical phenomena that lead to IR spectra are necessary to make accurate assignments. In the first portion of this work, using FTIR and 2D IR, we determine spectral markers that can differentiate size, metal ion coordination, and topology in DNA G-quadruplex motifs. IR studies aided by isotope labeling define the physical origin of these markers and allow for the construction of a structural landscape in parallel DNA G-quadruplex motifs. It is also shown that 2D IR and isotope editing probes site-specific structural changes in G-quadruplex motifs that can differentiate ion identity and location based on spectral shifts. In the latter portion of this work, we use a combination of spectroscopy and imaging techniques to show that a peptide derived from the human pro-apoptotic protein BAX forms amyloid aggregates whose structure is dependent on the presence of model membranes. Combined, the work in this thesis allows for the formulation of multiple hypotheses based on IR structural assignments regarding disease states and functional mechanisms of these systems.
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