Fluorescent dyes

Coumarin () or '2H-chromen-2-one' is an aromatic organic chemical compound with formula . Its molecule can be described as a benzene molecule with two adjacent hydrogen atoms replaced by an unsaturated lactone ring , forming a second six-membered heterocycle that shares two carbons with the benzene ring. It belongs to the benzopyrone chemical class and is considered a lactone.

thumb|Phycocyanobilin, a common phycobilin found in cyanobacteria and some algae Phycobilins (from Greek: (phykos) meaning "alga", and from Latin: bilis meaning "bile") are light-capturing bilins found in cyanobacteria and in the chloroplasts of red algae, glaucophytes and some cryptomonads (though not in green algae and plants). Most of their molecules consist of a chromophore which makes them coloured. They are unique among the photosynthetic pigments in that they are bonded to certain water-soluble proteins, known as phycobiliproteins. Phycobiliproteins then pass the light energy to chlorop

color

DAPI (pronounced 'DAPPY', /ˈdæpiː/), or 4′,6-diamidino-2-phenylindole, is a fluorescent stain that binds strongly to adenine–thymine-rich regions in DNA. It is used extensively in fluorescence microscopy. As DAPI can pass through an intact cell membrane, it can be used to stain both live and fixed cells, though it passes through the membrane less efficiently in live cells and therefore provides a marker for membrane viability.

thumb|right|300px|Space-filling model of [[firefly luciferin(color coding: black=carbon, white=hydrogen, blue=nitrogen, red=oxygen, yellow=sulfur)]]

Umbelliferone, also known as 7-hydroxycoumarin, hydrangine, skimmetine, and '''beta-umbelliferone''', is a natural product of the coumarin family.

Perylene or perilene is a polycyclic aromatic hydrocarbon with the chemical formula C20H12, occurring as a brown solid. It or its derivatives may be carcinogenic, and it is considered to be a hazardous pollutant. In cell membrane cytochemistry, perylene is used as a fluorescent lipid probe. It is the parent compound of a class of rylene dyes.

chemical compound

group of fluorescent dyes for DNA staining

thumb|Rhodamine core structure thumb|Rhodamine in water Rhodamine is a family of related dyes, a subset of the triarylmethane dyes. They are derivatives of xanthene. Important members of the rhodamine family are rhodamine 6G, Rhodamin WT, Texas Red (Sulforhodamin 101), rhodamine 123, and rhodamine B. They are mainly used to dye paper and inks, but they lack the lightfastness for fabric dyeing.

Rubrene (5,6,11,12-tetraphenyltetracene) is the organic compound with the formula . It is a red colored polycyclic aromatic hydrocarbon. Because of its distinctive optical and electrical properties, rubrene has been extensively studied. It has been used as a sensitiser in chemoluminescence and as a yellow light source in lightsticks.

blue fluorescent dye used to enhance apparent brightness of white paper, fabric, and plastics

'(E)-Stilbene, commonly known as trans-stilbene', is an organic compound represented by the condensed structural formula CHCH=CHCH. Classified as a diarylethene, it features a central ethylene moiety with one phenyl group substituent on each end of the carbon–carbon double bond. It has an (E) stereochemistry, meaning that the phenyl groups are located on opposite sides of the double bond, the opposite of its geometric isomer, cis-stilbene. Trans-stilbene occurs as a white crystalline solid at room temperature and is highly soluble in organic solvents. It can be converted to cis-stilbene

Benzanthrone (BZA) is a polycyclic aromatic hydrocarbon. It is a yellow solid. Its derivatives are used as a dyestuff intermediate for anthraquinone-based dyes. Dehydrogenative coupling gives violanthrone. It is prepared by reduction of anthroquinone to anthrone followed by alkylation with a mixture of glycerol and sulfuric acid.

Pyranine is a hydrophilic, pH-sensitive fluorescent dye from the group of chemicals known as arylsulfonates. Pyranine is soluble in water and is used as a coloring agent, biological stain, optical detecting reagent, and pH indicator. Pyranine is also used in yellow highlighters to provide their characteristic fluorescence and bright yellow-green colour. It is also found in some types of soap.

Phycoerythrobilin is a red phycobilin, i.e. an open tetrapyrrole chromophore found in cyanobacteria and in the chloroplasts of red algae, glaucophytes and some cryptomonads. Phycoerythrobilin is present in the phycobiliprotein phycoerythrin, of which it is the terminal acceptor of energy. The amount of phycoerythrobilin in phycoerythrins varies, depending on the organism. In some Rhodophytes and oceanic cyanobacteria, phycoerythrobilin is also present in the phycocyanin, then termed R-phycocyanin. Like all phycobilins, phycoerythrobilin is covalently linked to these phycobiliproteins by a thio

'(Z)-Stilbene' is a diarylethene, that is, a hydrocarbon consisting of a cis ethene double bond substituted with a phenyl group on both carbon atoms of the double bond. The name stilbene was derived from the Greek word , which means shining.

chemical compound

Fura-2, an aminopolycarboxylic acid, is a ratiometric fluorescent dye which binds to free intracellular calcium. It was the first widely used dye for calcium imaging, and remains very popular. Fura-2 is excited at 340 nm and 380 nm of light, and the ratio of the emissions at those wavelengths is directly related to the amount of intracellular calcium. Regardless of the presence of calcium, Fura-2 emits at 510 nm of light. The use of the ratio automatically cancels out confounding variables, such as variable dye concentration and cell thickness, making Fura-2 one of the most appr

1,1,4,4-tetraphenylbutadiene (TPB) is an organic compound with the formula . Other isomers are possible, but the term usually refers to the derivative of butadiene with two phenyl group on each of the terminal carbon atoms It is a white solid that has attracted some attention as an electroluminescent dye.

chemical compound

5,12-Bis(phenylethynyl)naphthacene is a fluorescent dye used in lightsticks. It yields orange light.

thumb|Samples of halogenated BODIPY dyes in ambient lighting and fluorescing under UV

Diphenylhexatriene is a fluorescent hydrocarbon used in the study of cell membranes. It is almost non-fluorescent in water, but it exhibits strong fluorescence when it is intercalated into lipid membranes. It incorporates itself into the lipid bilayer and acts like a lipid.

9,10-Bis(phenylethynyl)anthracene (BPEA) is an aromatic hydrocarbon with the chemical formula is C30H18. It displays strong fluorescence and is used as a chemiluminescent fluorophore with high quantum efficiency.

1-Chloro-9,10-bis(phenylethynyl)anthracene is a fluorescent dye used in lightsticks. It emits yellow-green light, used in 30-minute high-intensity Cyalume sticks.

2-Chloro-9,10-bis(phenylethynyl)anthracene is a fluorescent dye used in lightsticks. It emits green light, used in 12-hour low-intensity Cyalume sticks.

chemical compound

chemical compound

Indo-1 is a popular dye that is used as a ratiometric calcium indicator similar to Fura-2. In contrast to Fura-2, Indo-1 has a dual emissions peak and a single excitation. The main emission peak in calcium-free solution is 475 nm while in the presence of calcium the emission is shifted to 400 nm. It is widely used in flow cytometry and laser scanning microscopy, due to its single excitation property. However, its use for confocal microscopy is limited due to its photo-instability caused by photobleaching. Indo-1 is also able to keep possession of its ratiometric emission, dissimilar

IAEDANS is an organic fluorophore (fluorescent molecule). It stands for 5-({2-[(iodoacetyl)amino]ethyl}amino)naphthalene-1-sulfonic acid. It is widely used as a marker in fluorescence spectroscopy.

Bisbenzimide (Hoechst 33342) is an organic compound used as a fluorescent stain for DNA in molecular biology applications. Several related chemical compounds are used for similar purposes and are collectively called Hoechst stains.

EDANS (5-((2-Aminoethyl)amino)naphthalene-1-sulfonic acid) is a donor for FRET-based nucleic acid probes and protease substrates. EDANS is often paired with DABCYL or DABSYL. The combination can be used in enzyme assays. When the two compounds are in close proximity, most of the energy emitted from EDANS will be quenched by DABCYL. However, if the compounds are separated (for example, by substrate cleavage) EDANS will fluoresce, giving an indication of enzyme presence.

chemical compound

chemical compound

histological technique

Violanthrone, also known as dibenzanthrone, is an organic compound that serves as a vat dye and a precursor to other vat dyes. X-ray crystallography confirms that the molecule is planar with C2v symmetry. Isomeric with violanthrone is isoviolanthrone, which has a centrosymmetric structure.

Bimane is a heterocyclic chemical compound. Bimane forms the core of a class of fluorescent dyes known as bimane dyes.

'6-Methoxy-(8-p-toluenesulfonamido)quinoline (TSQ') is one of the most efficient fluorescent stains for zinc(II). It was introduced by Soviet biochemists Toroptsev and Eshchenko in the early 1970s. The popularity of TSQ as physiological stain rose after seminal works by Christopher Frederickson two decades later. TSQ forms a 2:1 (ligand-metal) complex with zinc and emits blue light upon excitation at 365 nanometers. TSQ has been extensively applied for determination of extracellular or intracellular levels of Zn2+ in biological systems, also to study Zn2+ in mossy fibers of the hippocampus.

class of pigments

Laurdan is an organic compound which is used as a fluorescent dye when applied to fluorescence microscopy. It is used to investigate membrane qualities of the phospholipid bilayers of cell membranes. One of its most important characteristics is its sensitivity to membrane phase transitions as well as other alterations to membrane fluidity such as the penetration of water.

Fluorescent dyes with applications in molecular research

2-Chloro-9,10-diphenylanthracene is a fluorescent dye used in glow sticks for a blue-green glow. It is a chlorinated derivative of 9,10-diphenylanthracene.