Sequence-dependent photophysical properties of Cy3-labeled DNA

We have investigated the photophysical properties of Cy3-labeled DNA. Results show that the fluorescence efficiency of the dye changes dramatically upon covalent attachment, and that factors such as DNA sequence, or whether the dye is next to a single- or double-stranded region, also play a crucial role. Such dramatic dependence on the microscopic environment of the probe is due to the existence of an activated photoisomerization process that competes with fluorescence emission to deactivate the excited state. Cy3-DNA interactions, which depend on DNA sequence and the flexibility of the biopolymer, restrict the ability of the dye to photoisomerize and therefore increase the lifetime of the excited state. In this manuscript, we review the results of our most recent studies, and discuss the consequences of the photophysical behavior of Cy3 in biophysical research.

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