Adams, Carson Jeffery2017-10-102017-10-102017https://hdl.handle.net/1794/2281545 pages. A thesis presented to the Department of Biochemistry and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2017The fluorescent molecules cyanine-3 (Cy3) and cyanine-5 (Cy5) were inserted into opposing sides of both duplex and fork regions of the DNA backbone as probes for local conformation. The spectroscopic methods of absorbance and circular dichroism were used to observe the strength of exciton coupling within these dimers. Opposing Cy5 dyes in the duplex region of DNA showed strong exciton coupling, with the identification of H and J components in the spectra. The height and energies of the H and J component peaks are related to the conformation of these coupled dyes, suggesting that these results provide a useful basis for future conformational analysis of the duplex Cy5 dimer system. Cy3-Cy5 dimers showed similar signs of coupling, but H and J components were not identified. In the fork region of DNA, coupling of opposing Cy5 dyes was not apparent, suggesting that the dyes in the fork show weaker coupling and require more sensitive methods for conformational analysis.en-USCreative Commons BY-NC-ND 4.0-USDNASpectroscopyCyanineAbsorbanceCircular DichroismConformationThesis/Dissertation