Histochemistry Dyes

Thioflavin T is a cationic Benzothiazole dye that shows enhanced fluorescence upon binding to amyloid in tissue sections. Excitation max.: ~385 nm (free); ~450 nm (bound); Emission max.: ~445 nm (free); ~485 nm (bound).

Thioflavine S is a fluorescent histochemical marker of dense core senile plaques. Thioflavine S can be used for Alzheimer's research.

Ruthenium red (Ammoniated ruthenium oxychloride) is a polycationic dye widely used for electron microscopy (EM) of cells, tissues and vegetative bacteria. Ruthenium red strongly reacts with phospholipids and fatty acids and binds to acidic mucopolysaccharides. Ruthenium red is a L-type calcium current (I_Ca) blocker.

TMB is a non-toxic, non-mutagenic, colorless dye that is also used as a chromogenic agent in enzyme detection systems based on horseradish peroxidase (HRP). TMB can function as a photoacoustic probe for reactive oxygen and nitrogen species (ROS/RNS), reacting with hypochlorite, hydrogen peroxide, singlet oxygen, and nitrogen dioxide to produce blue oxidation products. TMB can detect the singlet oxygen produced by the outer membrane of Escherichia coli ATCC 25922.

Brilliant Blue FCF is an aromatic hydrocarbon, a synthetic dye produced from petroleum and used as a colorant for food and other substances. The solution has a maximum absorption at 628 nm.

Alcian Blue 8GX is a commonly used phthalocyanine dye that binds to glycoproteins and glycosaminoglycans. Alcian Blue 8GX has a wide range of applications in biological staining, including proteins in brain tumors and DNA in cells and tissues.

Acriflavine (Acriflavinium chloride) is a fluorescent acridine dye that can be used to label nucleic acid. Acriflavine is an antiseptic agent. Acriflavine is a potent HIF-1 inhibitor that prevents the dimerization of HIF-1α and HIF-1β subunits. Acriflavine inhibits the interaction between monocarboxylate transporter 4 (MCT4) and Basigin. Acriflavine is used in cancer research, such as breast cancer, brain tumor and chronic myeloid leukemia. Acriflavine is a potent papain-like protease (PLpro) inhibitor, which inhibits SARS-CoV-2.

Eosin Y (Acid Red 87 free base) is a soluble acid red dye molecule. Eosin Y has a wide application in organic synthesis as a photoredox catalyst.

Congo Red is an azo dye. Congo Red (CR) binding been used as a diagnostic test for the presence of amyloid in tissue sections.

Bromophenol blue is an acid phthalein dye, and it is used as a tracking dye for electrophoresis. Bromophenol blue is also used as a pH indicator, with a transition range of pH 3 to 4.6. Bromophenol blue is used as a sensor for the determination of several compounds including ammonia, drugs, proteins and amino acids. The binding of Bromophenol blue to proteins is accompanied by the appearance of a strong absorbance at 610 nm.

Direct Blue 1 (Chicago Sky Blue 6B) is a complex dye for background autofluorescence in immunofluorescence histochemistry. Direct Blue 1 is a potent and competitive VGLUT inhibitor. Direct Blue 1 can inhibit the Aβ-binding small molecule PrP ligand. Direct Blue 1 has anti-inflammatory activity.

Hematoxylin (Natural Black 1), a naturally occurring flavonoid compound derived from Caesalpinia sappan Linn.. Hematoxylin is a nuclear stain in histology and is also a potent Aβ42 fibrillogenesis inhibitor with an IC₅₀ of 1.6 μM.

Brilliant blue R250 (Brilliant Blue R), an anionic dye, is the most popular stain to detect proteins resolved in SDS-PAGE gels.

Bathophenanthroline is a nitrogen-containing organic ligand that can form stable complexes with transition metal ions such as Ru²⁺. In proteomics, Bathophenanthroline is often used for in-gel protein staining. The negatively charged sulfonic acid groups of Bathophenanthroline interact electrostatically with the positively charged amino acid residues of proteins, thereby achieving specific binding to proteins and enhancing the fluorescent signal of detection. Bathophenanthroline can be used for protein separation and detection in SDS-PAGE gels in the field of proteomics, as well as other fluorescence studies[1]. Ex/Em=532 nm/610 nm[1].

Stains-All, a cationic carbocyanine dye, is a convenient probe to study the structural features of the individual calcium-binding sites of calmodulin (CaM) and related calcium-binding proteins (CaBP).

Toluidine Blue (Toluidine Blue O) is an alkaline quinonimine dye (vivo dye) with high affinity for acidic tissue components, staining nuclei blue and polysaccharides purple. Toluidine Blue shows heterostaining properties for mast cells, mucins and chondrocytes. Toluidine Blue can stain different components of plant tissues and cells in different colours. Toluidine Blue is also used as a diagnostic aid to identify malignant lesions, such as cancer.

Janus green B is a supravital stain. Janus green B staining reaction is oxygen dependent, and is reversibly inhibited by cyanide. Janus green B has been used for staining peripheral nerves in live insects, lymphatic vessels of rabbits and mitochondria.

Direct Black 38 (Chlorazol Black E) is a benzidine-based azo dye, a substrate of Enterococcus gallinarum, and is mainly used for textile dyeing. Direct Black 38 is biodegradable after being reduced by microbial enzymes (such as Enterococcus gallinarum azoreductase), breaking the azo bonds and releasing benzidine and 4-aminobiphenyl. Direct Black 38 can be used in environmental toxicology, wastewater treatment and carcinogenicity studies, but its metabolite benzidine is listed as a human carcinogen.

Merbromin is a mixed inhibitor of the 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2, with an IC₅₀ of 2.7 μM. Merbromin effectively inhibits the replication of the Zika virus (ZIKV) and shows anti-ZIKV activity by inhibiting ZIKVpro. Merbromin can also be used as a topical disinfectant for cuts and scrapes, and it serves as a biological dye.