Handbook of Biological Dyes and Stains

NameCAS Registry NumberMerck Index NumberChemical/Dye ClassMolecular Formula
Acid Funchsin3244-88-0107TriphenylmethaneC20H17N3Na2O9S3
Acridine Homodimer57576-49-5AcridineC38H42Cl2N6O2
Acridine Orange65-61-2AcridineC17H20ClN3
Alcian Blue 8GX33864-99-2218Copper phthalocyanineC56H68Cl4CuN16S4
Alizarin72-48-0251AnthraquinoneC14H8O4
Alizarin Red S130-22-38573AnthraquinoneC14H7NaO7S
Allura Red25956-17-6284AzoC18H14N2Na2O8S2
Amaranth915-67-3375AzoC20H11N2Na3O10S3
9-Amino-6-chloro-2-methoxyacridine (ACMA)3548-09-2AcridineC14H11ClN2O
Aniline Blue (Methyl Blue)28983-56-46028TriphenylmethaneC37H27N3Na2O9S3
Auramine O2465-27-2DiphenylmethaneC17H22ClN
Azure A531-53-3927PhenothiazineC14H14ClN3S
Azure B531-55-5928PhenothiazineC15H16ClN3S
BAPTA85233-19-8957AromaticC22H24N2O10
BAPTA M126150-97-8AromaticC34H40N2O18
Basic Fuchsin632-99-55652TriphenylmethaneC20H20ClN3
Bismark Brown Y10114-58-61253AzoC18H20Cl2N8
Blue Tetrazolium (BT)1871-22-39244Tetrazolium saltC40H32Cl2N8O2
BOBO 1169454-13-1CyanineC41H54I4N6S2
BOBO 3169454-17-5CyanineC45H58I4N6S2
Bodipy FL C5-Ceramide133867-53-5Organometallic, boron basedC34H54BF2N3O3
Brilliant Blue FCF3844-45-91373TriphenylmethaneC37H34N2Na2O9S3
Brilliant Cresyl Blue81029-05-2PhenoxazineC17H20ClN3O×0.5 ZnCl2
Brilliant Geen633-03-41374TriphenylmethaneC27H34N2O4S
BSPT38116-89-1Tetrazolium saltC24H16ClN7O2S
BTC154324-80-8BenzothiazolylcoumarinC33H29N3O12S
BTC AM176767-94-5BenzothiazolylcoumarinC45H45N3O20S
Calcein1461-15-0XantheneC30H26N2O13
Calcein AM148504-34-1XantheneC46H46N2O23
Calcein Blue54375-47-2CoumarinC15H15NO7
Calcein Blue AM168482-84-6CoumarinC21H23NO11
Calcium Green 1154719-40-1XantheneC43H27Cl2K6N3O16
Calcium Green 2170516-40-2XantheneC64H34Cl4K8N4O22
Calcium Green 5N153130-66-6XantheneC43H26Cl2K6N4O18
Carmine1390-65-4AnthraquinoneC44H43AlCaO32
Coelenterazine55779-48-1Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-oneC26H21N3O3
Coelenterazine cp123437-25-2Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-oneC25H25N3O3
Coelenterazine f123437-16-1Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-oneC26H20FN3O2
Coelenterazine h50909-86-9Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-oneC26H21N3O2
Coelenterazine hcp123437-32-1Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-oneC25H25N3O2
Coelenterazine n123437-22-9Heterocycle; Imidazo[1,2-α]pyrazin-3(7H)-oneC30H23N3O2
Congo Red573-58-02498AzoC32H22N6Na2O6S2
CoroNa Green690993-66-9XantheneC30H29F2NO9
CoroNa Green AM690993-67-0XantheneC33H33F2NO11
CoroNa Red481667-01-0XantheneC42H49ClN4O8
Cresyl Violet Acetate10510-54-0PhenoxazineC18H15N3O3
Crystal Violet548-62-94395TriphenylmethaneC25H30ClN3
Cyanotolyl Tetrazolium Chloride (CTC)90217-02-0Tetrazolium saltC16H14ClN5
DAF FM254109-20-1XantheneC21H14F2N2O5
Dansyl Cadaverine10121-91-2NaphthaleneC17H25N3O2S
DAPI28718-90-3IndoleC16H17Cl2N5
Darrow Red15391-59-0PhenoxazineC18H14ClN3O2
DASPEI3785-01-1StyrylC17H21IN2
DASPMI959-81-9StyrylC16H19IN2
Di-2-ANEPEQ160605-94-7StyrylC26H35Br2N3
Di-4-ANEPPS90134-00-2StyrylC28H36N2O3S
Di-8-ANEPPS157134-53-7StyrylC36H52N2O3S
DiBAC4(3)70363-83-6OxonolC27H40N4O6
DiBAC4(5)63560-89-4OxonolC29H42N4O6
DiD127274-91-3CyanineC61H99ClN2O4
Dihydroethidium104821-25-2PhenanthridineC21H21N3
Dihydrorhodamine 6G217176-83-5XantheneC28H32N2O3
Dihydrorhodamine 123109244-58-8XantheneC21H18N2O3
DiI41085-99-8CyanineC59H97ClN2O4
DiIC1(5)36536-22-8CyanineC27H31IN2
DiOC2(3)905-96-4CyanineC21H21IN2O2
DiOC5(3)53213-81-3CyanineC27H33IN2O2
DiOC6(3)53213-82-4CyanineC29H37IN2O2
DiOC7(3)53213-83-5CyanineC31H41IN2O2
DiSBAC2(3)47623-98-3OxonolC19H24N4O4S2
DiSC3(5)53213-94-8CyanineC25H27IN2S2
Eosin B548-24-33602XantheneC20H6Br2N2Na2O9
Eosin Y17372-87-13603XantheneC20H6Br4Na2O5
Erythrosin16423-68-03693XantheneC20H6I4Na2O5
Ethidium Bromide1239-45-84731PhenanthridineC21H20BrN3
Ethidium Homodimer-1 (EthD-1)61926-22-5PhenanthridineC46H50Cl4N8
Ethidium Homodimer-2 (EthD-2)180389-01-9PhenanthridineC51H60I4N8
Ethidium Monoazide (EMA)58880-05-0PhenanthridineC21H18BrN5
Ethyl Eosin6359-05-3XantheneC22H11Br4KO5
Fast Green FCF2353-45-93941TriphenylmethaneC37H34N2Na2O10S3
Fluo 3123632-39-3XantheneC36H30Cl2N2O13
Fluo 3 AM121714-22-5XantheneC51H50Cl2N2O23
Fluo 4273221-59-3XantheneC36H30F2N2O13
Fluo 4 AM273221-67-3XantheneC51H50F2N2O23
FluoZin 1411209-53-5XantheneC24H14F2K3NO8
FluoZin 2411209-54-6XantheneC32H18F2K4N2O11
FluoZin 3404335-95-1XantheneC34H24F2K4N2O12
FM 4-64162112-35-8StyrylC30H45Br2N3
Fura 2113694-64-7Not listed; 4293 for Free AcidBenzofuranC29H22K5N3O14
Fura 2 AM108964-32-5BenzofuranC44H47N3O24
Fura 2FF192140-58-2BenzofuranC28H18F2K5N3O14
Giemsa Stain51811-82-6PhenothiazineC14H14ClN3S
Hematoxylin517-28-24637FlavoneC16H14O6
Hexidium Iodide211566-66-4PhenanthridineC25H28IN3
Hoechst 3325823491-45-4BenzimidazoleC25H27Cl3N6O
Hoechst 3334223491-52-3BenzimidazoleC27H31Cl3N6O
Hoechst 3458023555-00-2BenzimidazoleC27H32Cl3N7
Indigo Carmine860-22-04944IndoleC16H8N2Na2O8S2
Indo 1132319-56-3Not listed (Free acid: 4960)IndoleC32H26K5N3O12
Indo 1 AM112926-02-0IndoleC47H51N3O22
Iodonitro Tetrazolium (INT)146-68-9Tetrazolium saltC19H13ClIN5O2
Janus Green B2869-83-25255PhenazineC30H31ClN6
JC 13520-43-2CyanineC25H27Cl4IN4
JC 9522592-13-8CyanineC27H21IN2O2
JOJO 1305801-87-0CyanineC47H56I4N8O2
JO-PRO 1305801-86-9CyanineC23H28I2N4O
Light Green SF Yellowish5141-20-85485TriphenylmethaneC37H34N2Na2O9S3
LOLO 1305802-06-6CyanineC47H54Br2I4N8S2
Lucifer Yellow CH67769-47-55594NaphthalimideC13H9Li2N5O9S2
Lucifer Yellow VS71231-14-65594NaphthalimideC20H12Li2N2O10S3
Lucigenin2315-97-1AcridineC28H22N4O6
Mag-Fura 2 (Furaptra)132319-57-4BenzofuranC18H10K4N2O11
Mag-Fura 2 AM130100-20-8BenzofuranC30H30N2O19
Mag-Indo 1132299-21-9IndoleC21H14K4N2O9
Mag-Indo 1 AM130926-94-2IndoleC33H34N2O17
Magnesium Green170516-41-3XantheneC33H17Cl2K5N2O13
Malachite Green569-64-25699TriphenylmethaneC23H25ClN2
Malachite Green Oxalate Salt2437-29-85699TriphenylmethaneC52H54N4O12
MEQ34373-76-7QuinolineC12H14INO
Methylene Blue61-73-46060PhenothiazineC16H18ClN3S
Methylene Blue Trihydrate7220-79-36060PhenothiazineC16H18ClN3S3H2O
Methylene Violet (Methylene Violet Bernthsen)2516-05-4PhenothiazineC14H12N2OS
Methyl Green7114-03-6TriphenylmethaneC27H35BrClN3 × ZnCl2
Methyl Orange (Orange III)547-58-06105AzoC14H14N3NaO3S
Methylthiazoletetrazolium (MTT)298-93-1Tetrazolium saltC18H16BrN5S
Methyl Violet 2B (Methyl Violet)8004-87-3TriphenylmethaneMixture (tetra, penta and hexa) of the hydrochloride salts of N-methylated forms of pararosanilines, predominantly the penta (chemical structure given above)
Monobromobimane (mBBr)71418-44-5PyrazoleC10H11BrN2O2
MQAE162558-52-3QuinolineC14H16BrNO3
NBD C6-Ceramide86701-10-2BenzoxadiazoleC30H49N5O6
NBD Methylhydrazine214147-22-5BenzoxadiazoleC7H7N5O3
Neotetrazolium (NT)298-95-36466Tetrazolium saltC38H28Cl2N8
Neutral Red553-24-26488PhenazineC15H17ClN4
Newport Green DCF288374-37-8XantheneC39H24Cl2K2N4O6
Newport Green PDX612502-05-3XantheneC31H21F2N3O3
Nigrosin8005-03-6AzineMixture, unspecified
Nile Blue A3625-57-8PhenoxazineC40H40N6O6S
Nitro Blue Tetrazolium (NBT)298-83-9Tetrazolium saltC40H30Cl2N10O6
Nonyl-Acridine Orange (NAO)75168-11-5AcridineC26H38BrN3
Nuclear Yellow74681-68-8BenzimidazoleC25H28Cl3N7O2S
Oil Red O1320-06-5AzoC26H24N4O
Orange II (Tropaeolin OOO)633-96-56858AzoC16H11N2NaO4S
Orange G1936-15-8AzoC16H10N2Na2O7S2
Orcein1400-62-06863PhenoxazineUnspecified (it is a mixture)
Oxonol V61389-30-8Oxonol; IsoxazoleC23H16N2O4
Oxonol VI64724-75-0Oxonol; IsoxazoleC17H20N2O4
Pararosaniline Hydrochloride569-61-9TriphenylmethaneC19H18ClN3
PBFI124549-11-7BenzofuranC46H46N2O16
PBFI AM124549-23-1BenzofuranC58H62N2O2
Phen Green SK234075-34-4XantheneC33H15Cl2K2N3O6
Phloxine B18472-87-2XantheneC20H2Br4Cl4Na2O5
Ponceau SX4548-53-27591AzoC18H14N2Na2O7S2
POPO 1169454-15-3CyanineC41H54I4N6O2
POPO 3154757-99-0CyanineC45H58I4N6O2
PO-PRO 1157199-56-9CyanineC20H27I2N3O
PO-PRO 3161016-55-3CyanineC22H29I2N3O
Propidium Iodide25535-16-4PhenanthridineC27H34I2N4
Pyronin B2150-48-38006XantheneC42H54Cl8Fe2N4O2
Pyronin Y92-32-08007XantheneC17H19ClN2O
QSY 7 Carboxylic Acid, Succinimidyl Ester304014-12-8XantheneC43H39ClN4O7S
QSY 9 Carboxylic Acid, Succinimidyl Ester700834-40-8XantheneC43H39ClN4O13S3
QSY 21 Carboxylic Acid, Succinimidyl Ester304014-13-9XantheneC45H39ClN4O7S
Quin 273630-23-68042QuinolineC26H23K4N3O10
Quin 2 AM83104-85-28042QuinolineC38H43N3O18
Redoxsensor Red CC-1296277-09-3XantheneC23H19F5N2O
Resazurin Sodium Salt62758-13-8PhenoxazineC12H6NNaO4
RH 23783668-91-1StyrylC29H40N2O3S
RH 414161433-30-3StyrylC28H43Br2N3
RH 421107610-19-5StyrylC29H42N2O3S
RH 795172807-13-5StyrylC26H39Br2N3O2
Rhodamine 6G989-38-8XantheneC28H31ClN2O3
Rhodamine 12362669-70-9XantheneC21H17ClN2O3
RhodZin 3677716-65-3XantheneC38H38K2N4O10
Rose Bengal632-69-98262XantheneC20H2Cl4I4Na2O5
Safranin O477-73-6PhenazineC20H19ClN4
SBFI124549-08-2BenzofuranC44H42N2O15
SBFI AM129423-53-6BenzofuranC56H58N2O23
SPQ83907-40-8QuinolineC13H15NO4S
Stains-All7423-31-6NaphthothiazoleC30H27BrN2S2
Stilbene Isothiocyanate Sulfonic Acid (SITS)51023-76-8StilbeneC17H12N2Na2O7S3
Sudan Black B4197-25-58885AzoC29H24N6
Sudan III85-86-98884AzoC22H16N4O
Sudan IV85-83-68393AzoC24H20N4O
Sunset Yellow FCF2783-94-09001AzoC16H10N2Na2O7S2
Tartrazine1934-21-09072AzoC16H9N4Na3O9S2
Tetranitro Blue Tetrazolium (TNBT)1184-43-6Tetrazolium saltC40H28Cl2N12O10
Tetrazolium Violet (TV)1719-71-7Tetrazolium saltC23H17ClN4
Thionin78338-22-4Not listed (Chloride listed: 9346)PhenothiazineC14H13N3O2S
TMRE115532-52-0XantheneC26H27ClN2O7
TMRM115532-50-8XantheneC25H25ClN2O7
Toluidine Blue O92-31-99520PhenothiazineC15H16ClN3S
TO-PRO 1157199-59-2CyanineC24H29I2N3S
TO-PRO 3157199-63-8CyanineC26H31I2N3S
TO-PRO 5177027-61-1CyanineC28H33I2N3S
TOTO 1143413-84-79308CyanineC49H58I4N6S2
TOTO 3166196-17-4CyanineC53H62I4N6S2
Triphenyl Tetrazolium Chloride (TTC)298-96-49744Tetrazolium saltC19H15ClN4
TSQ109628-27-59799QuinolineC17H16N2O3S
XTT11072-31-2Tetrazolium saltC22H16N7NaO13S2
YO-PRO 1152068-09-2CyanineC24H29I2N3O
YO-PRO 3157199-62-7CyanineC26H31I2N3O
YOYO 1143413-85-8CyanineC49H58I4N6O2
YOYO 3156312-20-8CyanineC53H62I4N6O2
Zinquin151606-29-010169QuinolineC19H18N2O5S
Zinquin Ester181530-09-610169QuinolineC21H22N2O5S


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