Spectral fine tuning of cyanine dyes: electron donor—acceptor substituted analogues of thiazole orange

Abstract

The introduction of electron donor and acceptor groups at strategic locations on a fluorogenic cyanine dye allows fine-tuning of the absorption and emission spectra while preserving the ability of the dye to bind to biomolecular hosts such as double-stranded DNA and a single-chain antibody fragment originally selected for binding to the parent unsubstituted dye, thiazole orange (TO). The observed spectral shifts are consistent with calculated HOMO-LUMO energy gaps and reflect electron density localization on the quinoline half of TO in the LUMO. A dye bearing donating methoxy and withdrawing trifluoromethyl groups on the benzothiazole and quinoline rings, respectively, shifts the absorption spectrum to sufficiently longer wavelengths to allow excitation at green wavelengths as opposed to the parent dye, which is optimally excited in the blue.

A new structure–activity relationship for cyanine dyes to improve photostability and fluorescence properties for live cell imaging

“…In fact, Armitage et al could show for thiazole orange-derived dyes that electron-withdrawing substituents in particular at the benzothiazole core (structural counterpart of the indole in our dyes) lower the energy of the HOMO (and LUMO equally), while those substituents at the quinolinium part leave the HOMO energy rather unaffected (and reduce mainly the LUMO energy). 3 , 28 This can also be assumed for our cyanine-indole-quinolinium dyes because it agrees with the thermal reactivity described above.…”

Photo‐isomerization of the Cyanine Dye Alexa‐Fluor 647 (AF‐647) in the Context of dSTORM Super‐Resolution Microscopy

“…In support of this assignment, we note that the computed opticala bsorption transitionsa re in line with experimental results. Using ZINDO-S methods, [97] the absorption maximum calculated for the energy-minimized NN ADJ geometry lies at 648.1 nm, with an oscillator strength of 1.513,i nawater reservoir (Table S6). This transition is primarily from the HOMO to the LUMO (coefficient 0.6811) with as mall contribution from HOMOÀ1t oL UMO + 1( coefficient 0.1134).…”

LUCS (Light-Up Cell System), a universal high throughput assay for homeostasis evaluation in live cells

“…If TO photophysical properties have been extensively studied with respect to applications in DNA/RNA quantification, far less is known about its behavior in live cells, apart from topological information 22 , 23 (Fig. S2 ).…”