| Biological macromolecules serve very distinct roles in the overall function of an organism and are responsible for critical biochemical processes. An understanding of the fundamental biophysical rules governing the interactions of biological macromolecules is therefore a critical first step towards understanding their biological function. Furthermore, this enables the development of new sensors, diagnostics and therapies. This thesis describes efforts to develop new molecules capable of selective recognition of diagnostic bacterial cell-surface markers, and the development of two new label-free sensor technologies.;Through the use of molecular modeling, a synthetic ligand specific to a unique bacterial component was synthesized in gram quantities. The molecule is based on the maltose binding protein active site, and contains a series of aromatic tryptophan residues attached to a stereoregular ter-cyclopentane scaffold (referred to as TWTCP). TWTCP demonstrates high specificity for the polar disaccharide head group of Lipopolysaccharide A, the primary constituent of the Gram-(−) bacterial cell membrane, and binds with a KD of ∼0.6 micromolar.;Given the properties of TWTCP, we set out to develop a device capable of distinguishing between Gram-(+) and Gram-(−) bacteria, relying on the absence of Lipid A in the Gram-(+) bacterial cell membrane. Incorporation of TWTCP into a porous silicon microcavity yielded a functional device that demonstrated a significant shift in the photoluminescence spectrum when incubated with a solution containing Lipid A. Given these data, we attempted to take the capabilities of this technology further and were able to detect a photoluminescence shift in the presence on Gram-(−) bacteria. In contrast, we observed no such shift in the presence of Gram-(+) bacteria. This was the first biosensing device of its kind in that all the components of this sensor (both the probe and substrate) were entirely man made.;As a complimentary technique to our porous silicon detector, we developed an additional biosensor that utilizes a regular crystalline silicon substrate and reflective interferometry to generate the signal. Employing a chip functionalized with the extracellular (7 kD) fragment of the enteropathogenic E. coli protein Tir, we demonstrated the ability to detect the presence of a unique cellular marker. The detected molecule was the extracellular fragment of the bacterial membrane protein Intimin (32 kD fragment). The E. coli Intimin protein fragment could be detected selectively with our biosensor to a concentration of approximately 350 nM, and exhibited no detectable levels of non-specific adsorption to the silicon surface. Additionally, we were able to detect the presence of this moiety in the context of a crude cellular lysate, demonstrating both the selectivity and sensitivity of our device towards our intended target even in the presence of complex biological mixtures.;Finally, we set out to develop synthetic compounds designed to target and bind to the aforementioned enteropathogenic E. coli marker protein, Intimin. An exhaustive computational effort yielded model structures with high degrees of structural similarity to the Intimin binding surface of Tir. A solid phase synthetic strategy was developed that allows for the production of these novel compounds in milligram quantities. |
