Quantum yield BODIPY fluorophores

Fluorophores containing 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene as a core skeleton are commonly designated as BODIPY fluorophores. Due to their useful photophysical properties including high fluorescence quantum yields, high molar absorption coefficient, narrow absorption and emission band width, and their high photostability [50], BODIPY dyes are proven to be extremely versatile and useful in many biological applications Fig. 11 [68]. 

Direct labeling of a biomolecule involves the introduction of a covalently linked fluorophore in the nucleic acid sequence or in the amino acid sequence of a protein or antibody. Fluorescein, rhodamine derivatives, the Alexa, and BODIPY dyes (Molecular Probes [92]) as well as the cyanine dyes (Amersham Biosciences [134]) are widely used labels. These probe families show different absorption and emission wavelengths and span the whole visible spectrum (e.g., Alexa Fluor dyes show UV excitation at 350 nm to far red excitation at 633 nm). Furthermore, for differential expression analysis, probe families with similar chemical structures but different spectroscopic properties are desirable, for example the cyanine dyes Cy3 and Cy5 (excitation at 548 and 646 nm, respectively). The design of fluorescent labels is still an active area of research, and various new dyes have been reported that differ in terms of decay times, wavelength, conjugatibility, and quantum yields before and after conjugation [135]. New ruthenium markers have been reported as well [136]. 

The BODIPY fluorophore displayed an intense red-shifted fluorescence emission in CH2Q2 (625 nm, 0.84 fluorescence quantum yield), fully preserved in the solid state. 

NIR fluorophores are generally considered as substances that emit fluorescence in the NIR region (650-900 nm). Particularly, the fluorescence quantum yield (QY) of NIR fluorophores is always lower than that of short wavelength emission ones. Over the past few decades, enormous progress has been made in the field of NIR fluorescent dyes. There are several major NIR organic fluorescent chromophores, such as bay-substituted perylene or naphthalene bisimides, cyanine dyes, BODIPYs, DPPs, and porphyrins. 

Another series of earlier inaccessible BODIPY fluorophores (Table 2.18), which intensively fluoresce at 601-606 nm (quantum yield is up to 0.95) [227], has been synthesized from pyrroles bearing polycondensed aromatic substituents in position 2 of the pyrrole ring and mesitylaldehyde (Scheme 2.186). 

A key feature and important advantage of this method is a possibility to synthesize the asymmetric representatives of BODIPY (hitherto almost unknown) due to the involvement of a-unsubstituted pyrroles (having other substituents in other positions of the pyrrole ring) in condensation with 2,2,2-trifluoro-l-(pyrrol-2-yl)-l-ethanols. Absorption and emission bands of such fluorophores are red shifted (600-670 nm), the fluorescence quantum yield being close to 1.0 [642],... 

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