Handbook of Biological Dyes and Stains
| Name | CAS Registry Number | Merck Index Number | Chemical/Dye Class | Molecular Formula |
|---|---|---|---|---|
| Acid Funchsin | 3244-88-0 | 107 | Triphenylmethane | C20H17N3Na2O9S3 |
| Acridine Homodimer | 57576-49-5 | — | Acridine | C38H42Cl2N6O2 |
| Acridine Orange | 65-61-2 | — | Acridine | C17H20ClN3 |
| Alcian Blue 8GX | 33864-99-2 | 218 | Copper phthalocyanine | C56H68Cl4CuN16S4 |
| Alizarin | 72-48-0 | 251 | Anthraquinone | C14H8O4 |
| Alizarin Red S | 130-22-3 | 8573 | Anthraquinone | C14H7NaO7S |
| Allura Red | 25956-17-6 | 284 | Azo | C18H14N2Na2O8S2 |
| Amaranth | 915-67-3 | 375 | Azo | C20H11N2Na3O10S3 |
| 9-Amino-6-chloro-2-methoxyacridine (ACMA) | 3548-09-2 | — | Acridine | C14H11ClN2O |
| Aniline Blue (Methyl Blue) | 28983-56-4 | 6028 | Triphenylmethane | C37H27N3Na2O9S3 |
| Auramine O | 2465-27-2 | — | Diphenylmethane | C17H22ClN |
| Azure A | 531-53-3 | 927 | Phenothiazine | C14H14ClN3S |
| Azure B | 531-55-5 | 928 | Phenothiazine | C15H16ClN3S |
| BAPTA | 85233-19-8 | 957 | Aromatic | C22H24N2O10 |
| BAPTA M | 126150-97-8 | — | Aromatic | C34H40N2O18 |
| Basic Fuchsin | 632-99-5 | 5652 | Triphenylmethane | C20H20ClN3 |
| Bismark Brown Y | 10114-58-6 | 1253 | Azo | C18H20Cl2N8 |
| Blue Tetrazolium (BT) | 1871-22-3 | 9244 | Tetrazolium salt | C40H32Cl2N8O2 |
| BOBO 1 | 169454-13-1 | — | Cyanine | C41H54I4N6S2 |
| BOBO 3 | 169454-17-5 | — | Cyanine | C45H58I4N6S2 |
| Bodipy FL C5-Ceramide | 133867-53-5 | — | Organometallic, boron based | C34H54BF2N3O3 |
| Brilliant Blue FCF | 3844-45-9 | 1373 | Triphenylmethane | C37H34N2Na2O9S3 |
| Brilliant Cresyl Blue | 81029-05-2 | — | Phenoxazine | C17H20ClN3O×0.5 ZnCl2 |
| Brilliant Geen | 633-03-4 | 1374 | Triphenylmethane | C27H34N2O4S |
| BSPT | 38116-89-1 | — | Tetrazolium salt | C24H16ClN7O2S |
| BTC | 154324-80-8 | — | Benzothiazolylcoumarin | C33H29N3O12S |
| BTC AM | 176767-94-5 | — | Benzothiazolylcoumarin | C45H45N3O20S |
| Calcein | 1461-15-0 | — | Xanthene | C30H26N2O13 |
| Calcein AM | 148504-34-1 | — | Xanthene | C46H46N2O23 |
| Calcein Blue | 54375-47-2 | — | Coumarin | C15H15NO7 |
| Calcein Blue AM | 168482-84-6 | — | Coumarin | C21H23NO11 |
| Calcium Green 1 | 154719-40-1 | — | Xanthene | C43H27Cl2K6N3O16 |
| Calcium Green 2 | 170516-40-2 | — | Xanthene | C64H34Cl4K8N4O22 |
| Calcium Green 5N | 153130-66-6 | — | Xanthene | C43H26Cl2K6N4O18 |
| Carmine | 1390-65-4 | — | Anthraquinone | C44H43AlCaO32 |
| Coelenterazine | 55779-48-1 | — | Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-one | C26H21N3O3 |
| Coelenterazine cp | 123437-25-2 | — | Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-one | C25H25N3O3 |
| Coelenterazine f | 123437-16-1 | — | Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-one | C26H20FN3O2 |
| Coelenterazine h | 50909-86-9 | — | Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-one | C26H21N3O2 |
| Coelenterazine hcp | 123437-32-1 | — | Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-one | C25H25N3O2 |
| Coelenterazine n | 123437-22-9 | — | Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-one | C30H23N3O2 |
| Congo Red | 573-58-0 | 2498 | Azo | C32H22N6Na2O6S2 |
| CoroNa Green | 690993-66-9 | — | Xanthene | C30H29F2NO9 |
| CoroNa Green AM | 690993-67-0 | — | Xanthene | C33H33F2NO11 |
| CoroNa Red | 481667-01-0 | — | Xanthene | C42H49ClN4O8 |
| Cresyl Violet Acetate | 10510-54-0 | — | Phenoxazine | C18H15N3O3 |
| Crystal Violet | 548-62-9 | 4395 | Triphenylmethane | C25H30ClN3 |
| Cyanotolyl Tetrazolium Chloride (CTC) | 90217-02-0 | — | Tetrazolium salt | C16H14ClN5 |
| DAF FM | 254109-20-1 | — | Xanthene | C21H14F2N2O5 |
| Dansyl Cadaverine | 10121-91-2 | — | Naphthalene | C17H25N3O2S |
| DAPI | 28718-90-3 | — | Indole | C16H17Cl2N5 |
| Darrow Red | 15391-59-0 | — | Phenoxazine | C18H14ClN3O2 |
| DASPEI | 3785-01-1 | — | Styryl | C17H21IN2 |
| DASPMI | 959-81-9 | — | Styryl | C16H19IN2 |
| Di-2-ANEPEQ | 160605-94-7 | — | Styryl | C26H35Br2N3 |
| Di-4-ANEPPS | 90134-00-2 | — | Styryl | C28H36N2O3S |
| Di-8-ANEPPS | 157134-53-7 | — | Styryl | C36H52N2O3S |
| DiBAC4(3) | 70363-83-6 | — | Oxonol | C27H40N4O6 |
| DiBAC4(5) | 63560-89-4 | — | Oxonol | C29H42N4O6 |
| DiD | 127274-91-3 | — | Cyanine | C61H99ClN2O4 |
| Dihydroethidium | 104821-25-2 | — | Phenanthridine | C21H21N3 |
| Dihydrorhodamine 6G | 217176-83-5 | — | Xanthene | C28H32N2O3 |
| Dihydrorhodamine 123 | 109244-58-8 | — | Xanthene | C21H18N2O3 |
| DiI | 41085-99-8 | — | Cyanine | C59H97ClN2O4 |
| DiIC1(5) | 36536-22-8 | — | Cyanine | C27H31IN2 |
| DiOC2(3) | 905-96-4 | — | Cyanine | C21H21IN2O2 |
| DiOC5(3) | 53213-81-3 | — | Cyanine | C27H33IN2O2 |
| DiOC6(3) | 53213-82-4 | — | Cyanine | C29H37IN2O2 |
| DiOC7(3) | 53213-83-5 | — | Cyanine | C31H41IN2O2 |
| DiSBAC2(3) | 47623-98-3 | — | Oxonol | C19H24N4O4S2 |
| DiSC3(5) | 53213-94-8 | — | Cyanine | C25H27IN2S2 |
| Eosin B | 548-24-3 | 3602 | Xanthene | C20H6Br2N2Na2O9 |
| Eosin Y | 17372-87-1 | 3603 | Xanthene | C20H6Br4Na2O5 |
| Erythrosin | 16423-68-0 | 3693 | Xanthene | C20H6I4Na2O5 |
| Ethidium Bromide | 1239-45-8 | 4731 | Phenanthridine | C21H20BrN3 |
| Ethidium Homodimer-1 (EthD-1) | 61926-22-5 | — | Phenanthridine | C46H50Cl4N8 |
| Ethidium Homodimer-2 (EthD-2) | 180389-01-9 | — | Phenanthridine | C51H60I4N8 |
| Ethidium Monoazide (EMA) | 58880-05-0 | — | Phenanthridine | C21H18BrN5 |
| Ethyl Eosin | 6359-05-3 | — | Xanthene | C22H11Br4KO5 |
| Fast Green FCF | 2353-45-9 | 3941 | Triphenylmethane | C37H34N2Na2O10S3 |
| Fluo 3 | 123632-39-3 | — | Xanthene | C36H30Cl2N2O13 |
| Fluo 3 AM | 121714-22-5 | — | Xanthene | C51H50Cl2N2O23 |
| Fluo 4 | 273221-59-3 | — | Xanthene | C36H30F2N2O13 |
| Fluo 4 AM | 273221-67-3 | — | Xanthene | C51H50F2N2O23 |
| FluoZin 1 | 411209-53-5 | — | Xanthene | C24H14F2K3NO8 |
| FluoZin 2 | 411209-54-6 | — | Xanthene | C32H18F2K4N2O11 |
| FluoZin 3 | 404335-95-1 | — | Xanthene | C34H24F2K4N2O12 |
| FM 4-64 | 162112-35-8 | — | Styryl | C30H45Br2N3 |
| Fura 2 | 113694-64-7 | Not listed; 4293 for Free Acid | Benzofuran | C29H22K5N3O14 |
| Fura 2 AM | 108964-32-5 | — | Benzofuran | C44H47N3O24 |
| Fura 2FF | 192140-58-2 | — | Benzofuran | C28H18F2K5N3O14 |
| Giemsa Stain | 51811-82-6 | — | Phenothiazine | C14H14ClN3S |
| Hematoxylin | 517-28-2 | 4637 | Flavone | C16H14O6 |
| Hexidium Iodide | 211566-66-4 | — | Phenanthridine | C25H28IN3 |
| Hoechst 33258 | 23491-45-4 | — | Benzimidazole | C25H27Cl3N6O |
| Hoechst 33342 | 23491-52-3 | — | Benzimidazole | C27H31Cl3N6O |
| Hoechst 34580 | 23555-00-2 | — | Benzimidazole | C27H32Cl3N7 |
| Indigo Carmine | 860-22-0 | 4944 | Indole | C16H8N2Na2O8S2 |
| Indo 1 | 132319-56-3 | Not listed (Free acid: 4960) | Indole | C32H26K5N3O12 |
| Indo 1 AM | 112926-02-0 | — | Indole | C47H51N3O22 |
| Iodonitro Tetrazolium (INT) | 146-68-9 | — | Tetrazolium salt | C19H13ClIN5O2 |
| Janus Green B | 2869-83-2 | 5255 | Phenazine | C30H31ClN6 |
| JC 1 | 3520-43-2 | — | Cyanine | C25H27Cl4IN4 |
| JC 9 | 522592-13-8 | — | Cyanine | C27H21IN2O2 |
| JOJO 1 | 305801-87-0 | — | Cyanine | C47H56I4N8O2 |
| JO-PRO 1 | 305801-86-9 | — | Cyanine | C23H28I2N4O |
| Light Green SF Yellowish | 5141-20-8 | 5485 | Triphenylmethane | C37H34N2Na2O9S3 |
| LOLO 1 | 305802-06-6 | — | Cyanine | C47H54Br2I4N8S2 |
| Lucifer Yellow CH | 67769-47-5 | 5594 | Naphthalimide | C13H9Li2N5O9S2 |
| Lucifer Yellow VS | 71231-14-6 | 5594 | Naphthalimide | C20H12Li2N2O10S3 |
| Lucigenin | 2315-97-1 | — | Acridine | C28H22N4O6 |
| Mag-Fura 2 (Furaptra) | 132319-57-4 | — | Benzofuran | C18H10K4N2O11 |
| Mag-Fura 2 AM | 130100-20-8 | — | Benzofuran | C30H30N2O19 |
| Mag-Indo 1 | 132299-21-9 | — | Indole | C21H14K4N2O9 |
| Mag-Indo 1 AM | 130926-94-2 | — | Indole | C33H34N2O17 |
| Magnesium Green | 170516-41-3 | — | Xanthene | C33H17Cl2K5N2O13 |
| Malachite Green | 569-64-2 | 5699 | Triphenylmethane | C23H25ClN2 |
| Malachite Green Oxalate Salt | 2437-29-8 | 5699 | Triphenylmethane | C52H54N4O12 |
| MEQ | 34373-76-7 | — | Quinoline | C12H14INO |
| Methylene Blue | 61-73-4 | 6060 | Phenothiazine | C16H18ClN3S |
| Methylene Blue Trihydrate | 7220-79-3 | 6060 | Phenothiazine | C16H18ClN3S3H2O |
| Methylene Violet (Methylene Violet Bernthsen) | 2516-05-4 | — | Phenothiazine | C14H12N2OS |
| Methyl Green | 7114-03-6 | — | Triphenylmethane | C27H35BrClN3 × ZnCl2 |
| Methyl Orange (Orange III) | 547-58-0 | 6105 | Azo | C14H14N3NaO3S |
| Methylthiazoletetrazolium (MTT) | 298-93-1 | — | Tetrazolium salt | C18H16BrN5S |
| Methyl Violet 2B (Methyl Violet) | 8004-87-3 | — | Triphenylmethane | Mixture (tetra, penta and hexa) of the hydrochloride salts of N-methylated forms of pararosanilines, predominantly the penta (chemical structure given above) |
| Monobromobimane (mBBr) | 71418-44-5 | — | Pyrazole | C10H11BrN2O2 |
| MQAE | 162558-52-3 | — | Quinoline | C14H16BrNO3 |
| NBD C6-Ceramide | 86701-10-2 | — | Benzoxadiazole | C30H49N5O6 |
| NBD Methylhydrazine | 214147-22-5 | — | Benzoxadiazole | C7H7N5O3 |
| Neotetrazolium (NT) | 298-95-3 | 6466 | Tetrazolium salt | C38H28Cl2N8 |
| Neutral Red | 553-24-2 | 6488 | Phenazine | C15H17ClN4 |
| Newport Green DCF | 288374-37-8 | — | Xanthene | C39H24Cl2K2N4O6 |
| Newport Green PDX | 612502-05-3 | — | Xanthene | C31H21F2N3O3 |
| Nigrosin | 8005-03-6 | — | Azine | Mixture, unspecified |
| Nile Blue A | 3625-57-8 | — | Phenoxazine | C40H40N6O6S |
| Nitro Blue Tetrazolium (NBT) | 298-83-9 | — | Tetrazolium salt | C40H30Cl2N10O6 |
| Nonyl-Acridine Orange (NAO) | 75168-11-5 | — | Acridine | C26H38BrN3 |
| Nuclear Yellow | 74681-68-8 | — | Benzimidazole | C25H28Cl3N7O2S |
| Oil Red O | 1320-06-5 | — | Azo | C26H24N4O |
| Orange II (Tropaeolin OOO) | 633-96-5 | 6858 | Azo | C16H11N2NaO4S |
| Orange G | 1936-15-8 | — | Azo | C16H10N2Na2O7S2 |
| Orcein | 1400-62-0 | 6863 | Phenoxazine | Unspecified (it is a mixture) |
| Oxonol V | 61389-30-8 | — | Oxonol; Isoxazole | C23H16N2O4 |
| Oxonol VI | 64724-75-0 | — | Oxonol; Isoxazole | C17H20N2O4 |
| Pararosaniline Hydrochloride | 569-61-9 | — | Triphenylmethane | C19H18ClN3 |
| PBFI | 124549-11-7 | — | Benzofuran | C46H46N2O16 |
| PBFI AM | 124549-23-1 | — | Benzofuran | C58H62N2O2 |
| Phen Green SK | 234075-34-4 | — | Xanthene | C33H15Cl2K2N3O6 |
| Phloxine B | 18472-87-2 | — | Xanthene | C20H2Br4Cl4Na2O5 |
| Ponceau SX | 4548-53-2 | 7591 | Azo | C18H14N2Na2O7S2 |
| POPO 1 | 169454-15-3 | — | Cyanine | C41H54I4N6O2 |
| POPO 3 | 154757-99-0 | — | Cyanine | C45H58I4N6O2 |
| PO-PRO 1 | 157199-56-9 | — | Cyanine | C20H27I2N3O |
| PO-PRO 3 | 161016-55-3 | — | Cyanine | C22H29I2N3O |
| Propidium Iodide | 25535-16-4 | — | Phenanthridine | C27H34I2N4 |
| Pyronin B | 2150-48-3 | 8006 | Xanthene | C42H54Cl8Fe2N4O2 |
| Pyronin Y | 92-32-0 | 8007 | Xanthene | C17H19ClN2O |
| QSY 7 Carboxylic Acid, Succinimidyl Ester | 304014-12-8 | — | Xanthene | C43H39ClN4O7S |
| QSY 9 Carboxylic Acid, Succinimidyl Ester | 700834-40-8 | — | Xanthene | C43H39ClN4O13S3 |
| QSY 21 Carboxylic Acid, Succinimidyl Ester | 304014-13-9 | — | Xanthene | C45H39ClN4O7S |
| Quin 2 | 73630-23-6 | 8042 | Quinoline | C26H23K4N3O10 |
| Quin 2 AM | 83104-85-2 | 8042 | Quinoline | C38H43N3O18 |
| Redoxsensor Red CC-1 | 296277-09-3 | — | Xanthene | C23H19F5N2O |
| Resazurin Sodium Salt | 62758-13-8 | — | Phenoxazine | C12H6NNaO4 |
| RH 237 | 83668-91-1 | — | Styryl | C29H40N2O3S |
| RH 414 | 161433-30-3 | — | Styryl | C28H43Br2N3 |
| RH 421 | 107610-19-5 | — | Styryl | C29H42N2O3S |
| RH 795 | 172807-13-5 | — | Styryl | C26H39Br2N3O2 |
| Rhodamine 6G | 989-38-8 | — | Xanthene | C28H31ClN2O3 |
| Rhodamine 123 | 62669-70-9 | — | Xanthene | C21H17ClN2O3 |
| RhodZin 3 | 677716-65-3 | — | Xanthene | C38H38K2N4O10 |
| Rose Bengal | 632-69-9 | 8262 | Xanthene | C20H2Cl4I4Na2O5 |
| Safranin O | 477-73-6 | — | Phenazine | C20H19ClN4 |
| SBFI | 124549-08-2 | — | Benzofuran | C44H42N2O15 |
| SBFI AM | 129423-53-6 | — | Benzofuran | C56H58N2O23 |
| SPQ | 83907-40-8 | — | Quinoline | C13H15NO4S |
| Stains-All | 7423-31-6 | — | Naphthothiazole | C30H27BrN2S2 |
| Stilbene Isothiocyanate Sulfonic Acid (SITS) | 51023-76-8 | — | Stilbene | C17H12N2Na2O7S3 |
| Sudan Black B | 4197-25-5 | 8885 | Azo | C29H24N6 |
| Sudan III | 85-86-9 | 8884 | Azo | C22H16N4O |
| Sudan IV | 85-83-6 | 8393 | Azo | C24H20N4O |
| Sunset Yellow FCF | 2783-94-0 | 9001 | Azo | C16H10N2Na2O7S2 |
| Tartrazine | 1934-21-0 | 9072 | Azo | C16H9N4Na3O9S2 |
| Tetranitro Blue Tetrazolium (TNBT) | 1184-43-6 | — | Tetrazolium salt | C40H28Cl2N12O10 |
| Tetrazolium Violet (TV) | 1719-71-7 | — | Tetrazolium salt | C23H17ClN4 |
| Thionin | 78338-22-4 | Not listed (Chloride listed: 9346) | Phenothiazine | C14H13N3O2S |
| TMRE | 115532-52-0 | — | Xanthene | C26H27ClN2O7 |
| TMRM | 115532-50-8 | — | Xanthene | C25H25ClN2O7 |
| Toluidine Blue O | 92-31-9 | 9520 | Phenothiazine | C15H16ClN3S |
| TO-PRO 1 | 157199-59-2 | — | Cyanine | C24H29I2N3S |
| TO-PRO 3 | 157199-63-8 | — | Cyanine | C26H31I2N3S |
| TO-PRO 5 | 177027-61-1 | — | Cyanine | C28H33I2N3S |
| TOTO 1 | 143413-84-7 | 9308 | Cyanine | C49H58I4N6S2 |
| TOTO 3 | 166196-17-4 | — | Cyanine | C53H62I4N6S2 |
| Triphenyl Tetrazolium Chloride (TTC) | 298-96-4 | 9744 | Tetrazolium salt | C19H15ClN4 |
| TSQ | 109628-27-5 | 9799 | Quinoline | C17H16N2O3S |
| XTT | 11072-31-2 | — | Tetrazolium salt | C22H16N7NaO13S2 |
| YO-PRO 1 | 152068-09-2 | — | Cyanine | C24H29I2N3O |
| YO-PRO 3 | 157199-62-7 | — | Cyanine | C26H31I2N3O |
| YOYO 1 | 143413-85-8 | — | Cyanine | C49H58I4N6O2 |
| YOYO 3 | 156312-20-8 | — | Cyanine | C53H62I4N6O2 |
| Zinquin | 151606-29-0 | 10169 | Quinoline | C19H18N2O5S |
| Zinquin Ester | 181530-09-6 | 10169 | Quinoline | C21H22N2O5S |
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