BODIPY fluorophores properties

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]. 

BODIPY 530/550 C3 is 4,4-difluoro-5,7-diphenyl-4-bora-3a,4a-diaza-s-indacene-3-propionic acid (Molecular Probes). This derivative of the basic BODIPY structure contains two phenyl rings off the No. 5 and 7 carbon atoms and a propionic acid group on the No. 3 carbon atom. The carboxylate group may be used to attach the fluo-rophore to amine-containing molecules via a carbodiimide reaction to create an amide bond. The substituents on this BODIPY fluorophore result in alterations to its spectral properties, pushing its excitation and emission maximums up to higher wavelengths. 

Schmidt, E. Yu., B. A. Trofimov, A.I. Mikhaleva etal. 2009. Synthesis and optical properties of 2-(benzo[b]thiophene-3-yl)pyrroles and a new BODIPY fluorophore (BODIPY=4,4-... 

The number of new NIR fluorophores that can be used in biological systems has grown substantially in recent years as a consequence of extensive research efforts to improve the properties of available dyes. A brief overview of the various types of long-wavelength (above 600 nm) fluorophores including phycobiliproteins, BODIPY, and Alexa Fluor dyes (Life Technologies), Cy dyes (GE Healthcare),... 

BODIPY is a short for 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene, the basic structure of this type of fluorophore (see Fig. 6.5). Derivatives of this dye have been created by modification of positions 1, 3, 5, 7, and 8, generating an array of fluorophores with very distinct excitation and emission properties [38]. Molecular Probes has synthesized a wide number of BODIPY dyes whose excitation... 

The optical properties of organic dyes (Fig. ld-f, Table 1) are controlled by the nature of the electronic transition(s) involved [4], The emission occurs either from an electronic state delocalized over the whole chromophore (the corresponding fluorophores are termed here as resonant or mesomeric dyes) or from a charge transfer (CT) state formed via intramolecular charge transfer (ICT) from the initially excited electronic state (the corresponding fluorophores are referred to as CT dyes) [4], Bioanalytically relevant fluorophores like fluoresceins, rhodamines, most 4,4 -difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPY dyes), and cyanines (symmetric... 

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]. 

Given these problems with fluorescein, several alternatives with similar spectral properties are now commercially available. Molecular Probes, Incorporated, sells Oregon Green 488 and BODIPY FL as alternates to fluorescein with improved imaging properties (see Appendix, this chapter). Similarly, one of the cyanine-based fluorophores developed by Waggoner and co-workers (1989), Cy2, substitutes well for fluorescein in our hands and is available commercially (see Appendix, this chapter). 

---