Identification of Nonradiative Decay Pathways in Cy3

Abstract

Photoexcited fluorescent markers are extensively used in spectroscopy, imaging, and analysis of biological systems. The performance of fluorescent markers depends on high levels of emission, which are limited by competing non-radiative decay pathways. Smallmolecule fluorescent dyes have been increasingly used as markers due to their high and stable emission. Despite their prevalence, the non-radiative decay pathways of these dyes have not been determined. Here, we investigate these pathways for a widely-used indocarbocyanine dye, Cy3, using transient grating spectroscopy. We identify a nonradiative decay pathway via a previously unknown dark state formed within ∼ 1 ps of photoexcitation. Our experiments, in combination with electronic structure calculations, suggest that the generation of the dark state is mediated by picosecond vibrational mode coupling, likely via a conical intersection. We further identify the vibrational modes, and thus structural elements, responsible for the formation and dynamics of the dark state, providing insight into suppressing non-radiative decay pathways in fluorescent markers such as Cy3.

Engineering couplings for exciton transport using synthetic DNA scaffolds

“…In addition, homodyne transient grating measurements show coupling to approximately the same modes through the presence of a peak at the same frequency ( Figure S17A). 84 As illustrated in Figure S17B, the broad peak observed in Figure 3D is consistent with rapid dephasing of normal mode vibrations delocalized over Cy3 from 250-750 cm À1 . The free Cy3 in solution showed larger amplitude oscillations than the DNA-bound Cy3 (Section S2.5).…”

Binding of dsRNA byD. melanogasterDicer-2 is substrate-dependent and regulated by Loquacious-PD

“…When the local environment of indocarbocyanine dyes becomes more rigid, their excited state isomerization is hindered, which is reflected in an extension of their fluorescence lifetime and an increase in their brightness. (59–63) This effect has been observed in homogeneous bulk solutions in a viscosity- and temperature-dependent manner, and it is the basis of protein-induced fluorescence enhancement effects. (46) Beyond these excited state decay dynamics that reflect primarily an intramolecular process, collective processes can reflect important local environment properties – e.g., the three-dimensional reorientation of a group of chromophores can be observed in their time-resolved fluorescence anisotropy.…”

Designing excitonic circuits for the Deutsch–Jozsa algorithm: mitigating fidelity loss by merging gate operations

“…Moreover, the electronic coupling between Cy3 dye pairs has been demonstrated to be tunable when these dyes are scaffolded in DNA. 37 We expect that a similar analysis can be carried out in other exciton molecular systems, perhaps less prone to noise than the constructs we employ here.…”