▼ A single molecule FRET study was performed to gather structural and dynamic information about a G-Quadruplex (GQ) in the presence of potassium ions (K+) and Replication Protein A (RPA), a predominant single strand DNA binding protein. A GQ is a non-canonical DNA structure that forms in guanosine (G) rich sequences. The structure is composed of stacked tetrads, each formed by four G residues, and loops of unstructured ssDNA. This study concentrates on characterization of a three-layer GQ with loops that are three nucleotides long each. The results confirm the formation of the GQ structure, while revealing nearly 100% folding at the physiological concentration of K+ (150 mM). It was also found that RPA-mediated unfolding dominates folding by K+ under physiological conditions, giving some insight into this structure's physiological viability. The timescales of transitioning from an unfolded single strand structure to a folded GQ, along with the transition from a folded GQ to an RPA-bound unfolded structure were also measured in this single molecule assay. The transition from unfolded to folded GQ structure was measured to be 0.35±0.10 seconds, while the transition from a folded GQ to an RPA-bound unfolded structure was 0.28±0.10 seconds. These results suggest that the folding and unfolding dynamics of this structure take place on a similar timescale. The rest of this study compares the results from this specific GQ structure to results gathered from the same assays on other GQ structures with varying number of layers and loop lengths to draw conclusions about these structures’ physiological relevance. Advisors/Committee Members: Balci, Hamza.

▼ A surface plasmon resonance spectrometer was constructed in a Kretschmann configuration. This was constructed atop a 2' by 3' optical breadboard. A HeNe laser was fixed to the breadboard and an N-BK7 right angle prism and a silicon detector were mounted on two independent motorized rotation stages. Software was developed in order to control the motion of the stages acquire voltage measurements from the detector via a data acquisition card. Software was also developed to begin to analyze the resulting data. Advisors/Committee Members: Gleeson, James.