Date of Award


Degree Type


Degree Name

Doctor of Philosophy in Pharmaceutical Sciences


Biomedical and Pharmaceutical Sciences

First Advisor

Bongsup Cho


Chapter 1

Chemical contaminants in our environment may interact with macromolecules such as proteins and DNA in our bodies and have the potential to disrupt normal biological processes, leading to diseases such as cancer and metabolic conditions. Elucidation of these mechanisms, particularly the relationship between their structure and subsequent biological outcomes, is paramount to mitigating the harm associated with human exposure to such contaminants. It is also an important tool in the drug design/discovery process. This introductory chapter shall serve as background knowledge for readers unversed in the field, outlining several families of persistent chemical contaminants known to cause cancer and other disorders via interaction with proteins and DNA, some techniques for characterizing those interactions, and the significance of the findings reported in the technical chapters that follow.

Chapter 2

Despite an exponential increase in PFAS research over the past two decades, the mechanisms behind how PFAS cause adverse health effects are still poorly understood. Protein interactions are considered a significant driver of bioaccumulation and subsequent toxicity from re-exposure, however most of the available literature is limited to legacy PFAS. We utilized microcalorimetric and spectroscopic methods to systematically investigate the binding between human serum albumin (HSA) and perfluorocarboxylic acids (PFCAs) of varying chain lengths and their non-fluorinated fatty acid (FA) counterparts. The results reveal the optimal chain length for significant PFCA-HSA binding as well as some fundamental interactions, i.e., the polar carboxylic head of PFCA is countered by ionizable amino acids such as arginine, and the fluorocarbon tails stabilized by hydrophobic residues like leucine and valine. Additionally, fluorine's unique polarizability contributes to PFCA's stronger binding affinities relative to the corresponding fatty acids. Based on these observations, we posit that PFCAs likely bind to HSA in a 'cavity-filling' manner provided they have an appropriate size and shape to accommodate the electrostatic interactions. The results reported herein serve to widen the pool of structural information to explain PFAS bioaccumulation patterns and toxicity, as well as support the development of more accurate computational modeling of protein-PFAS interactions.

Chapter 3

Sequence context is well known to influence the structural characteristics and repair outcomes of DNA adducts, but there is limited information available on how the epigenetic modulator 5-methylcytosine (5-mC) affects conformational heterogeneity and mutagenicity of DNA lesions. Lesions derived from 2-aminofluorene (AF) have been extensively studied as models of chemical carcinogenesis and adopt a sequence-dependent mix of two major conformers: major-groove binding (B) and base-displaced stacked (S). In this study, we report a novel conformation-dependent bypass of the dG-AF lesion in epigenetically relevant sequence contexts (d[5′-CTTCTC#G*NCCTCATTC-3′], where C# is C or 5-mC, C* is G or G-FAF, and N is A, T, C, or G). Sequences with a 3′ flanking pyrimidine (-CGT- and -CGC-) were more efficiently bypassed when the 5′ flanking base was 5-mC, whereas sequences with a 3′ flanking purine (-CGA- and -CG1G-) exhibited the opposite effect. Moreover, the conformational basis behind these variations appeared to be different between the two groups; for -CGT- and -CGC-, bypass appeared to be inversely correlated with the population of the duplex-destabilizing S conformer with 5-mC. In contrast, the decrease in bypass for flanking purines in the 5-mC sequences relative to C seemed to be related to non-standard duplex formation. The present study widens the body of available information on the effects of common epigenetic modifications on chemical carcinogenesis. It provides a delicate conformational insight into how 5-mC influences bypass and mutagenesis in the sequence context of a lesion.



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