Dyes, Stains and Tinctures

2',6'-Dimethylcarbonylphenyl-10-sulfopropylacridinium-9-carboxylate 4'-NHS ester is a chemiluminescent acridinium ester label used widely in clinical diagnostics, particularly in automated immunochemistry analysers. Acridinium ester labels are also useful research tools for the investigation of protein-carbohydrate interactions to characterise the binding affinity between specific carbohydrate and its binding protein. An example of those are lectin-acridinium ester conjugates used as chemiluminescent probes.

Cell permeable reagent for use in detection of peroxidase activity

Reagent for quantification of amino acids and peptides

Tetrazolium violet  is a monotetrazolium salt which forms water-insoluble formazans forming a purple colour. These salts are mainly used as indicators of extracellular redox activity and cell redox potential. Tetrazolium violet is positively charged and cell-permeable. Tetrazolium Violet has been used to stain agar layers in bacteriophage plaque formation assays.

5-Carboxyfluorescein (5-FAM) is a self-quenching dye and one of the most common labelling agents for biomolecules, cell staining and localisation studies. The fluorescence is pH dependent, therefore it has been used to measure the internal pH of cells. As it is only membrane permeable to dead cells, it can be used as a staining agent to distinguish viable and non-viable cells. It is also used in PCR to label the 5’ end of oligonucleotides in the presence of a quencher at the 3’ end (dual labelled probe). During the amplification process, the dye is cleaved and the fluorescence increases proportionally with the amount of the specific sequence amplified during the PCR process. The development of the fluorescence signal is therefore specifically related to the amplification of the target sequence. The carboxylic acid can be activated to react with a primary amine.

Amylose azure is a dye commonly used to detect and measure α-amylase activity in various applications. This dye is particularly useful in assessing the hydrolysis of starch by α-amylase. Amylose azure reacts with the enzyme and produces a blue color that can be quantified using spectrophotometry. In addition to its analytical applications, amylose azure is also used as a visual indicator of the presence of aluminum. The dye forms a complex with aluminum ions, resulting in a distinct color change that can be easily observed.

Phthalein dye used as a acid–base indicator in pH range of 9.3–10.5

Fluorogenic substrate for esterase; cell-permeable

Alizarin complexone dihydrate reacts with Lanthanum or Cesium(III) ions to form a red chelate, which, in turn, reacts with fluoride ions to give a blue ternary complex (Alizarin Fluorine Blue); to detect fluoride.

Fluorophore used to study molecular assemblies of surfactants and amphiphiles

The substructure resorufin is a fluorescent dye that changes color from orange to bright pink;  excitation/emission maxima = 563/587 nm.

pH indicator

WST-8 is a key substrate that serves as a sensitive chromogenic indicator for NADH. WST-like substrates have been applied to measure activity of dehydrogenase enzyme activity and the oxidation of NADH using NADH oxidase.

Brominated analog of carboxyfluorescein; singlet oxygen generator

5-(6)-Carboxytetramethylrhodamine (TAMRA) is a fluorescent dye that is used as a probe for DNA-based analysis. It binds to the 5' end of dsDNA, forming an intrastrand duplex. The fluorescence of TAMRA increases when it binds to dsDNA and can be used as a measure of the amount of DNA in a sample. TAMRA has been shown to be useful in the diagnosis of bowel disease and in the investigation of gene expression during body formation. This dye is also used as a marker for covalent linkages and high molecular weight proteins such as cyclin D2.

Chemiluminescence detection of biological residues

5-Carboxytetramethylrhodamine - (TAMRA) is a widely employed fluorescent dye (orange/red) that is suitable for different uses. In PCR applications, it has been used as both a reporter at the 5’ or as a quencher at the 3’ end. TAMRA-labelled oligonucleotides have been used to study interactions with DNA or DNA/protein interactions. It is an excellent fluorescent acceptor for FRET applications with a suitable dye pair. It is used as a protein/antibody labelling agent for structural studies, immunochemistry and flow cytometry. Bioconjugation is generally performed through coupling of the carboxylic acid to a primary amine at the N-terminus of a protein, on lysine side chains or amino-modified oligonucleotide.

Nucleic Acid Dye Green I is a DNA-staining dye that has found application in various high resolution assays for the detection of microbial or viral contaminant DNA.