Density functional theory studies of Cy5 Dye interactions with DNA

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Student Presentation

Presentation Date


Faculty Sponsor

Lan Li


DNA nanotechnology provides the most viable means to self-assemble optically active molecules, such as organic dyes, with nearest neighbor distances of less than 10 nm. The ability to organize organic dyes due to the accuracy and simplicity that comes from using DNA self-assembly has driven potential applications ranging from medical diagnostics to quantum computing. The planar Cy5 dye (DiSC2(5)) can be configured in pairs, or dimers, with nearest neighbor distances of 2nm or less when covalently bound to DNA. At certain buffer concentrations, the dimers form an H-aggregate configuration (i.e., face-to-face) which results in a blue-shift in the absorption spectrum relative to the monomer spectrum. Density functional theory-based (DFT) total energy and electronic structure calculations can provide insight into the dye and dimer-DNA positions and orientations leading to a more understanding of experimental observations. Initial dye-dye structural calculations using the Vienna ab-initio simulation package (VASP) show the H-aggregate as being the most stable configuration. Different exchange-correlation functionals will be used to optimize the H-aggregate interactions with DNA. Resultant structures will provide an improved understanding of the quantum coherence signatures observed in DNA-assembled aggregate interactions.

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