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Dyes

Bodipys:

http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Warning Vendor Response to follow - and TMI index extremely high (too much info).  But Sarah kindly asked. Short answer: Sarah Locknar was certainly correct that you need to know which BODIPY you are interested in (there are many) to understand their photophysical properties. But BODIPY Dyes are indeed dyes onto themselves, not merely linkers.  
Long Answer
The core structure of the non-polar BODIPY fluorophore (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) is indeed a fluor but when other additions are made it changes it Ex/Em properties.  Thus for a while they were named as the BODIPY equivalent of the most closely related dye.  BODIPY TR, has similar Ex/Em as Texas red and so on.  But eventually this strategy failed as additional BODIPY dyes were made, so we went to naming them after the Ex/Em maxima - thus BODIPY 581/591 etc.  BODIPY can be functionalized to serve many purposes (I counted 167 products that we offer.)  Great lipid probes, live cell probes, receptor probes and the like. In response to the initial query about Q.Y.s, the inventor, Dr. Hee Chol Kang, an 18 year veteran of the site, responded:
"After digging into my very old file, I can give you the following information. BODIPY R6G: Fluorescence Q.Y.= 0.9 (It was compared with Rhodamine R6G in methanol solution which has Q.Y of 0.9. They have same number)BODIPY 650/665: Fluorescence Q.Y.= 0.46 (It was compared with sulforhodamine 101 in pH7 buffer solution. The  fluorescence Q.Y. of sulforhodamine 101 was considered to be 0.9)."  For the extreme devotees of these dyes I have clipped even more info below.
BODIPY fluorophores have spectral characteristics that are often superior to those of fluorescein, tetramethylrhodamine, Texas Red and longer-wavelength dyes and may be substituted for these dyes in some applications. With derivatives that span the visible spectrum , BODIPY dyes are proving to be extremely versatile. We use them to generate fluorescent conjugates of proteins, nucleotides, oligonucleotides and dextrans, as well as to prepare fluorescent enzyme substrates, fatty acids, phospholipids, lipopolysaccharides, receptor ligands and polystyrene microspheres. BODIPY dyes are unusual in that they are relatively nonpolar and the chromophore is electrically neutral (Figure 1.42). These properties sometimes enhance the affinity of their ligand conjugates for receptors, as long as the overall conjugate is not too lipophilic. BODIPY dye conjugates of low molecular weight molecules also tend to be more permeant to live cells than are conjugates of charged fluorophores (Section 14.2). In addition, oligonucleotide conjugates of several of our BODIPY dyes have been reported to be useful for DNA sequencing  (Section 8.2, Table 8.1), in part because the dye exhibits minimal effect on the mobility of the fragment during electrophoresis. And with their high peak intensity, reactive BODIPY dyes are among the most detectable amine-derivatization reagents available for HPLC and capillary electrophoresis. The BODIPY dyes are more useful than most other long-wavelength dyes, including fluoresceins and carbocyanines, for assays that measure fluorescence polarization  (Technical Focus: Fluorescence Polarization (FP)). Furthermore, BODIPY dyes have exceptionally large cross-sections for excitation by multiphoton excitation sources. 
Solutions of the alkyl-substituted derivatives have a green, fluorescein-like fluorescence. However, when substituents that yield additional conjugation are added to the parent molecule, both the absorption and emission spectra of the resulting derivatives can shift to significantly longer wavelengths, with emission maxima of greater than 750 nm now possible with some BODIPY derivatives. Our goal has been to develop BODIPY dyes that are optimal for the major excitation sources and that match the common optical filter sets (Table 23.12). Accordingly, our best BODIPY substitutes for the fluorescein, rhodamine 6G, tetramethylrhodamine and Texas Red fluorophores are BODIPY FL, BODIPY R6G, BODIPY TMR and BODIPY TR, respectively (Figure 1.43). Because there are so many BODIPY dyes, we have had to develop a systematic strategy for naming them. Except for BODIPY FL, BODIPY R6G, BODIPY TMR and BODIPY TR, we now identify these dyes with the registered trademark BODIPY followed by the approximate absorption/emission maxima in nm (determined in methanol); for example, the BODIPY 581/591 dye. 
Mike Ignatius, PhD
Cell Biology and Imaging
Invitrogen/Molecular Probes
29851 Willow Creek Road
Eugene,  Oregon  97402
From: http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

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Last Updated: 2014-07-24