Histochemistry

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.

Basic green 4 (Malachite green) is a cationic dye that is widely used as a bactericide in aquaculture and is also commonly used in laboratories for the determination of phosphates. Basic green 4 exhibits high cytotoxicity and carcinogenicity to mammalian cells, specifically shown by its IC₅₀ values of 2.03 µM for HEp-2 human laryngeal cells and 13.8 µM for Caco-2 human colorectal adenocarcinoma cells, and it can promote the development of liver tumors. The maximum absorbance wavelength is 621 nm.

TMB dihydrochloride is the dihydrochloride form of TMB (HY-15930). TMB dihydrochloride 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 dihydrochloride 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 dihydrochloride can detect the singlet oxygen produced by the outer membrane of Escherichia coli ATCC 25922.

Phenol red (Phenolsulfonephthalein) sodium salt is a pH indicator dye. Phenol Red sodium salt is also an antagonist of rat P2X1R. Phenol Red sodium salt enhances the halogenating activity of myeloperoxidase. Phenol Red sodium salt shows a distinct color change from pink to yellow in a positive pH reaction.

Nile blue chloride is a highly fluorescent and photostable organic dye. Nile blue chloride and fluorescein isothiocyanate (FITC) can be used to construct a ratiometric pH sensitive probe for tracking the pH of the extracellular fluid between cancer cells in realtime. Nile Blue chloride has the potential for the research of nonlinear optics.

Phenolphthalein is an acid-base indicator that is colorless in an acidic environment and pink in an alkaline environment. Phenolphthalein is genotoxic and potentially carcinogenic to mice. In addition, phenolphthalein is also a blood indicator.

Fast Red Violet LB Zinc chloride is a stain that stains tartrate-resistant acid phosphatase (TRAP) and Fast Red Violet LB Zinc chloride can be used to stain alkaline phosphatase (ALP) activity.

Thionin acetate is a compound present in the seeds, stems, roots, and leaves of many plant species with antibacterial activity. Thionin acetate is a metachromatic cationic histological dye widely used in biological staining, such as Nissl staining.

Nile Blue A (Nile blue sulfate) is used to differentiate melanins and lipofuscins. It is also useful for staining fats and preparation of an amperometric glucose sensor.

Safranin (Safranin T) is an important and classical phenazinium dye. Safranin has been extensively used in the academic field as a spectroscopic probe and indicator. Safranin possesses a planar structure and cationic charge. Safranin can readily intercalate into biological macromolecules, including DNA and proteins. Safranin has antibacterial effects against gram-positive bacteria (S. aureus). Safranin can be used as a redox indicator in the determination of metal ion concentration.

Azure A chloride is a phenothiazine dye. Azure A chloride is an alternative DNA dye used for the separation of DNA and protein fragments in agarose gel electrophoresis and PAGE. Azure A chloride can be chemisorbed on the surface of mild steel according to the Langmuir adsorption isotherm to form a protective film. Azure A chloride binds to double-stranded DNA in a non-cooperative manner via weak intercalation, triggering molecular conformational disturbance, restricted rotational motion, and changes in optical activity.

Oxazine 170 perchlorate is a laser dye with a wide excitation spectrum range (300−550 nm), which strongly absorbs light with a wavelength greater than 550 nm, and it emits fluorescence with a wavelength of about 645 nm.

ANS ammonium is a potent antibacterial agent and a textile dye. ANS ammonium can be used as fluorescence probe. ANS ammonium blocks the binding of triiodothyronine to thyroxine binding globulin in radioimmunoassay of triiodothyronine.

Sudan III is a hydrophobic bisazo dye.

Solvent Blue 35 (Sudan Blue II) is a blue solvent dye that can be used to mark specific diesel fuels, among other things.

Fast red TR salt hemi zinc chloride is an aryl diazonium salt and chromogenic coupling reagent. Fast red TR salt hemi zinc chloride couples with α-Naphthol released by hydrolysis of α-naphthyl phosphate to form an azo dye complex with maximum absorption at 410 nm and 540 nm. Fast red TR salt hemi zinc chloride supports the chromogenic reaction in spectrophotometric detection of serum acid phosphatase activity.

Sudan IV is an agonist of the aryl hydrocarbon receptor (AhR) that activates downstream signaling pathways and induces CYP1A1 expression. Sudan IV promotes CYP1A1 gene transcription by activating AhR-ARNT heterodimers and binding to exogenous response elements (XREs) on DNA, thereby enhancing drug metabolizing enzyme activity. Sudan IV can be used to study the toxicity mechanisms of industrial dyes and the effects of interactions with serum proteins (such as bovine serum albumin (BSA)) on their distribution in vivo. Sudan IV is a fat-soluble diazo dye that can be used to stain lipids, triglycerides, and lipoproteins on frozen sections.

Pararosaniline hydrochloride (Basic red 9) is a pH-responsive basic dye, as a biological stain to track certain proteins. The pH of the acidified Pararosaniline hydrochloride reagent has a significant effect on the color and the maximum absorption wavelength (λmax) of the reaction system, with its optimum pH 0.48 and a λmax at 549 nm. Pararosaniline hydrochloride is also a strong modifier of RNA splicing. Pararosaniline hydrochloride has been used in the analysis of SO₂ and formaldehyde and staining of bacteria or other organisms. Pararosaniline hydrochloride is extensively used in industries like textile, printing, paper, cosmetic, and leather.

Nuclear Fast Red, an anthraquinone dye, is commonly used in conjunction with an excess of aluminum ions as a red nuclear counterstain. Nuclear fast red has been used as a histochemical and colorimetric reagent for calcium. Nuclear fast red as highly sensitive "off/on" fluorescent probe for detecting guanine.

Bromothymol Blue is a pH indicator.