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Open Access
Spectroscopic Analysis of Coupled Cyanine Dyes in DNA using Absorbance and Circular Dichroism
(University of Oregon, 2017) Adams, Carson Jeffery
The 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.