Modified carbocyanine dyes and their conjugates

A compound having the formula:

• and its salts, wherein
• R3 comprises an acrylamide, an activated ester of a carboxylic acid, an acyl azide, an acyl nitrile, an aldehyde, an alkyl halide, an amine, an anhydride, an aniline, an aryl halide, an azide, an aziridine, a boronate, a carboxylic acid, a diazoalkane, a haloacetamide, a halotriazine, a hydrazide, an imido ester, an isocyanate, an isothiocyanate, a maleimide, a phosphoramidite, a sulfonyl halide, a thiol group, a protein, avidin or streptavidin, biotin, or tyramide;
• R4 is C1-C22 alkyl or C7-C22 arylalkyl, each alkyl portion of which optionally incorporates up to six hetero atoms, selected from N, O and S, and each alkyl portion of which is optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxy, sulfo, phosphate, amino, sulfate, phosphonate, cyano, nitro, azido, C1-C6 alkoxy, C1-C6 alkylamino, or C2-C12 dialkylamino, or C3-C18 trialkylammonium;
• or
• R3 and R4 taken in combination complete a five- or six-membered saturated or unsaturated ring that is substituted by a group comprising an acrylamide, an activated ester of a carboxylic acid, an acyl azide, an acyl nitrile, an aldehyde, an alkyl halide, an amine, an anhydride, an aniline, an aryl halide, an azide, an aziridine, a boronate, a carboxylic acid, a diazoalkane, a haloacetamide, a halotriazine, a hydrazide, an imido ester, an isocyanate, an isothiocyanate, a maleimide, a phosphoramidite, a sulfonyl halide, a thiol group, a protein, avidin or streptavidin, biotin, or tyramide;
• R2 is C1-C22 alkyl or C7-C22 arylalkyl, each alkyl portion of which optionally incorporates up to six hetero atoms, selected from N, O and S, and each alkyl portion of which is optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxy, sulfo, phosphate, amino, sulfate, phosphonate, cyano, nitro, azido, C1-C6 alkoxy, C1-C6 alkylamino, C2-C12 dialkylamino, or C3-C18 trialkylammonium;
• R6 is H, amino, sulfo, trifluoromethyl, halogen, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 alkylamino, or C2-C12 dialkylamino, each alkyl portion of which is optionally further substituted by substituents selected from the group consisting of carboxy, sulfo, amino, and hydroxyl;
• R7 is H, amino, sulfo, trifluoromethyl, halogen, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 alkylamino, or C2-C12 dialkylamino, each alkyl portion of which is optionally further substituted by substituents selected from the group consisting of carboxy, sulfo, amino, and hydroxyl;
• R8 is H, amino, sulfo, trifluoromethyl, halogen, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 alkylamino, or C2-C12 dialkylamino, each alkyl portion of which is optionally further substituted by substituents selected from the group consisting of carboxy, sulfo, amino, and hydroxyl;
• R9 is H, amino, sulfo, trifluoromethyl, halogen, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 alkylamino, or C2-C12 dialkylamino, each alkyl portion of which is optionally further substituted by substituents selected from the group consisting of carboxy, sulfo, amino, and hydroxyl;
• R16 is H, amino, sulfo, trifluoromethyl, halogen, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 alkylamino, or C2-C12 dialkylamino, each alkyl portion of which is optionally further substituted by substituents selected from the group consisting of carboxy, sulfo, amino, and hydroxyl;
• R17 is H, amino, sulfo, trifluoromethyl, halogen, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 alkylamino, or C2-C12 dialkylamino, each alkyl portion of which is optionally further substituted by substituents selected from the group consisting of carboxy, sulfo, amino, and hydroxyl;
• R18 is H, amino, sulfo, trifluoromethyl, halogen, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 alkylamino, or C2-C12 dialkylamino, each alkyl portion of which is optionally further substituted by substituents selected from the group consisting of carboxy, sulfo, amino, and hydroxyl;
• or
• a member independently selected from
• R6 in combination with R7;
• R7 in combination with R8;
• R8 in combination with R9;
• R16 in combination with R17;
• and
• R17 in combination with R18;
• together with the atoms to which they are joined, form an aromatic ring comprising —CH or —CR1 wherein R1 is amino, sulfo, trifluoromethyl, halogen, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 alkylamino, or C2-C12 dialkylamino, wherein each alkyl portion of which is optionally substituted by substituents selected from the group consisting of carboxy, sulfo, amino, and hydroxyl;
• n is 1, 2 or 3;
• R12 is C1-C22 alkyl or C7-C22 arylalkyl, each alkyl portion of which optionally incorporates up to six hetero atoms, selected from the group consisting of N, O and S, and each alkyl portion of which is optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxy, sulfo, phosphate, amino, sulfate, phosphonate, cyano, nitro, azido, C1-C6 alkoxy, C1-C6 alkylamino, C2-C12 dialkylamino, or C3-C18 trialkylammonium;
• R13 is C1-C22 alkyl or C7-C22 arylalkyl, each alkyl portion of which optionally incorporates up to six hetero atoms, selected from the group consisting of N, O and S, and each alkyl portion of which is optionally substituted one or more times by substituents selected from the group consisting of F, Cl, Br, I, hydroxy, carboxy, sulfo, phosphate, amino, sulfate, phosphonate, cyano, nitro, azido, C1-C6 alkoxy, C1-C6 alkylamino, C2-C12 dialkylamino, and C3-C18 trialkylammonium;
• R14 is C1-C22 alkyl or C7-C22 arylalkyl, each alkyl portion of which optionally incorporates up to six hetero atoms, selected from the group consisting of N, O and S, and each alkyl portion of which is optionally substituted one or more times by substituents selected from the group consisting of F, Cl, Br, I, hydroxy, carboxy, sulfo, phosphate, amino, sulfate, phosphonate, cyano, nitro, azido, C1-C6 alkoxy, C1-C6 alkylamino, C2-C12 dialkylamino, and C3-C18 trialkylammonium,
• or R13 and R14 taken in combination complete a five- or six-membered saturated or unsaturated ring that is optionally substituted;
• and
• wherein sulfo is sulfonic acid or sulfonate.