Labelling

JOE is a fluorescein-derived xanthene dye containing methoxy groups and chlorine atoms. Its absorption and emission spectra are between FAM and TAMRA/ROX channels. For this reason, this fluorophore is often used for multiplex detection, including DNA sequencing. This derivative is an activated N-hydroxysuccinimide ester used to label proteins, peptides, amino-modified oligonucleotides, and other target molecules via conjugation with amines.

BP Fluor 488 is a fluorescent dye. BP Fluor 488 is a fluorophore pH-insensitive over a broad pH range (from 4 to 10). It has an absorption maximum at 495 nm and an emission maximum at 519 nm in the green spectrum region. The dye is hydrophilic and can be used to introduce the fluorescent label into various molecules, including proteins and antibodies. Conjugates of molecules with BP Fluor 488 have high brightness and photostability and are commonly used in flow cytometry and microscopy. This allows the detection of biological objects with high sensitivity at a longer imaging time. BP Fluor 488 Propyl azide interacts with alkynyl derivatives of biomolecules in Click Chemistry reactions either in the presence of copper (I) catalyst (with terminal alkynes) or without catalyst (with cyclooctynes), leading to the formation of stable adducts.

AMCA azide for сlick сhemistry conjugation with terminal alkynes via a copper-catalyzed click reaction or strained cyclooctynes via a copper-free click reaction. AMCA (aminomethylcoumarin acetate) is one of the brightest blue fluorescent dyes. This fluorophore has a relatively large Stoke’s shift, high resistance to photobleaching, and pH-independent fluorescence from pH 4 to 10. AMCA is a widely used fluorophore for multiple-color labeling due to its minimal fluorescence overlap with green- and longer wavelength-emitting fluorescent dyes.

Cyanine3B azide for click chemistry conjugation with terminal alkynes via a copper-catalyzed click reaction or strained cyclooctynes via a copper-free click reaction. Cyanine3B is a yellow-emitting cyanine dye that is an improved version of the Cyanine3 fluorophore with significantly higher fluorescence quantum yield and photostability. Due to the fixed conformation, Cyanine3B has the highest emission quantum yield compared to other dyes of this wavelength. This is a non-sulfonated dye that requires an organic co-solvent (DMF, DMSO, or other) for efficient labeling in water.

Phenylethynylpyrene (PEP) fluorophore is a polyaromatic hydrocarbon label with high sensitivity to microenvironment. Similarly to pyrene, PEP dye readily forms excimers. However, PEP fluorescence is more red-shifted. PEP can be used as microenvironment probe, and as a label for assays based on excimer formation. This reagent contains triethyleneglycol linker to facilitate dissolution of non-polar PEP dye in organo-aqueous labeling reaction mixtures. With this azide, and click chemistry, it is easy to turn any molecule bearing alkyne into PEP-labeled probe.

ROX azide is an alkyne-reactive derivative of ROX (Rhodamine X, Rhodamine 101) dye. ROX is a red-emitting fluorophore possessing high brightness and fluorescence quantum yield. This reagent is a pure 6-isomer. It is used for labeling alkyne and cycloalkyne-containing biomolecules via copper-catalyzed and copper-free click chemistry reactions. This reagent is presented as a solid form and as a 10 mM solution in DMSO.

SIMA (dichloro-diphenyl-fluorescein) is a dye with spectral properties similar to HEX but with a higher quantum yield. SIMA azide is used to produce fluorescently labeled primers and hybridization probes for quantitative PCR. Oligonucleotides with a SIMA label can be easily generated via azide-alkyne cycloaddition between SIMA azide and alkyne-containing oligonucleotide.

TET (tetrachlorofluorescein) is a green-fluorescent fluorescein derivate with absorption maximum at 519 nm and emission maximum at 535 nm. TET is spectrally similar to R6G, JOE, and VIC, widely used for labeling PCR probes. Oligonucleotides labeled with TET are often used in real-time PCR; the preparation of such oligonucleotides can be performed using click chemistry. This derivative is an azide, a pure 6-isomer, for conjugating TET to other molecules by copper-catalyzed and copper-free click reactions.

Azide derivative of red fluorescent dye TR (Texas Red, sulforhodamine 101 acid chloride) for click chemistry conjugation with terminal alkynes via a copper-catalyzed click reaction or strained cyclooctynes via a copper-free click reaction. TR is a red-fluorescent dye used for cell staining, fluorescence microscopy applications, and cell sorting with fluorescent-activated cell sorting machines. Texas Red is also commonly used in molecular biology, mainly quantitative RT-PCR and cellular assays.