BODIPY® fluorescent dye

Makrigiorgos, G. M. (1997) Detection of lipid peroxidation on erythrocytes using the excimer- forming property of a lipophilic BODIPY fluorescent dye. J. Biochem. Biophys. Methods 35(1), 23-35. 

Kainz, Q. M., A. Schatz, A. Zbpfl, W. 1. Stark, and O. Reiser. Combined covalent and noncovalent functionalization of nanomagnetic carbon surfaces with dendrimers and BODIPY fluorescent dye. Chem. Mater. 23, 2011 3606-3613. 

For all the cell internalization assays, PRPs have to be labeled with a fluorescent dye as a tracer. One such dye, BODIPY, functionalized with the... 

Recently, 2-phenylpyrrole needed for a fluorescent dye (BODIPY) assembly was successfully synthesized from acetophenone and acetylene (07CRV4891). 

Other lipid compositions with synthetic lipids, hydrogenated SPC (HSPC) and PEG-modified phospholipids are often used, especially for liposome formulations intended for parenteral applications use (long circulating or stealth liposomes) (41). Several analytical methods to follow loss of lipids during the preparation steps are available. Radioactively labeled lipids ( H-DPPC, C-DPPC) or cholesterol ( H-cholesterol) or H-cholesteryl hexadecyl ether (NEN Life Science Products, Boston, MA, USA) or lipophilic fluorescence dyes (e.g. lipophilic BODIPy derivatives. Molecular Probes) are added at appropriate amounts to the initial lipid mixtures. 

FIGURE50.9 Electrokinetic stacking injection on a microchip. Sample 67 nM BODIPY (a neutral fluorescent dye) in 150 mM NaCl. Run bnffer 80 mM sodium cholate, 10% ethanol, 5 mM tetraborate, pH 9. Sample was first injected by applying an electric field of 183 V/cm between the sample reservoir (S) and the outlet (O) for various periods of time as indicated in the figure. Separation was then carried out by applying 366 V/cm between the inlet (I) and outlet (O). An 80-s injection of 134 nM BODIPY in run buffer is included to show nonstacking injection. (From Palmer et al., Anal. Chem., 73, 725, 2001. With permission.)... 

FIGURE 50.13 Comparison of ITP/CE and CE separations of two fluorescent dyes Alexa Fluor 488 (first peak) and BODIPY (second peak). Inset electropherogram shows separation (with no stacking) of 100 nM initial concentrations of Alexa Fluor 488 and BODIPY. 5 mM HEPES was used as a background electrolyte and the applied electric field was 280 V/cm. For ITP/CE mode (main plot), initial concentrations of Alexa Fluor 488 and BODIPY were both 1 pM in 5 mM HEPES (i.e., diluted by a factor of 1 x 10 ). Here, LE was 1 M NaCl and the nominal applied fleld was 220 V/cm. The concentration increase and signal increase for Alexa Eluor 488 (first peak) are 6.4 x 10 and 4.5 x 10, respectively. (Reprinted from Jung et al.. Anal. Chem., 78, 2319, 2006. With permission.)... 

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. 

A second area of optoelectronic materials are the BODIPY (boron-dipyrromethene) fluorescent dyes. These materials are prepared by condensation of pyrroles with aldehydes, followed by complexation of boron. Attempts to prepare the mesityl-substituted pyrroles via the hindered mesitylketoximine 67 were unsuccessful due to difficulty in generating 67 under standard conditions (NH2OH HCI, heat). However, reaction of the mesityl Grignard reagent with proprionitrile followed by reaction with NH2OH HCI provided ketoximine 67, which was successfully converted to the corresponding pyrrole in 23% yield. The cesium salt of ketoximine 67 was also converted to the same pyrrole in 41%. ... 

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]. 

On the other hand, the introduction of halide substituents at the C-2 and C-6 position decreases fluorescence quantum yields and gives a bathochromic shift of emission maxima. For example, bromine at the C-2 and C-6 position in compound 14b deteriorates fluorescence quantum yields from 0.95 (14a) to 0.45 and the emission maximum is red-shifted by 42 nm. Moreover, iodine at the C-2,6 position in compound 14d gives the similar bathochromic shift to bromine (14b, 44 nm) and more dramatic reduction in quantum yields (almost nonfluorescent, photophysical properties were interpreted as the heavy atom effect of halides on a BODIPY core skeleton. The bathochromic shift of BODIPY dyes without dramatic decrease in quantum yield was observed by the introduction of vinyl substituents at the C-2 and C-6 position. The extension of conjugation... 

Rohand, T, Baruah, M, Qin, W. W, Boens, N. and Dehaen, W. (2006). Functionalisation of fluorescent BODIPY dyes by nucleophilic substitution. Chem. Commun. 266-268. 

The emission spectra of BODIPY derivatives normally display narrow bandwidths, providing intensely fluorescent labels for biomolecules. Unfortunately, they also have very small Stoke s shifts, typically on the order of only 10-20 nm. Excitation at the optimal wavelength may cause some interference in measurements at the emission wavelength due to light scattering or cross-over from the wide bandwidth of the excitation source. The dyes usually require excitation at sub-optimal wavelengths to prevent this problem. 

Recent literature contains many examples of the construction of cascades [56], Usually they are made by the covalent linking of monomer dyes, which allows strict control of their stoichiometry. The pyrene-Bodipy molecular dyads and triads are examples [57]. Efficient energy flow was reported in a purpose-built cascade molecule bearing three distinct chromophores attached to the terminal acceptor [58]. A combinatorial approach with the selection of the best hits can be applied using the assembly of fluorescent oligonucleotide analogs [59]. 

Jones LJ, Upson RH, Haugland RP, Panchuk-Voloshina N, Zhou M, Haugland RP. Quenched BODIPY dye-labeled casein substrates for the assay of protease activity by direct fluorescence measurement. Anal Biochem 1997 251(2) 144-152. 

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