Modified carbocyanine dyes and their conjugates

1. A compound having the formula:

and its salts, wherein

R 3 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 reactive platinum complex, a sulfonyl halide, a thiol group, a photoactivatable group, a protein, a peptide, an amino acid, a dextran, a hormone, a lectin, a lipopolysaccharide, a biological cell, a non-biological microparticle, a nucleotide, an oligonucleotide, a small-molecule drug, avidin or streptavidin, biotin, or tyramide;

R 4 is a C 1 -C 22 alkyl or C 7 -C 22 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, or C 2 -C 12 dialkylamino, or C 3 -C 18 trialkylammonium; or

R 3 and R 4 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 reactive platinum complex, a sulfonyl halide, a thiol group, a photoactivatable group, a protein, a peptide, an amino acid, a dextran, a hormone, a lectin, a lipopolysaccharide, a biological cell, a non-biological microparticle, a nucleotide, an oligonucleotide, a small -molecule drug, avidin or streptavidin, biotin, or tyramide;

R 2 is a C 1 -C 22 alkyl or C 7 -C 22 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, or C 3 -C 18 trialkylammonium;

R 6 is H;

R 7 is sulfo;

R 8 is H;

R 9 is H;

n is 0, 1, 2 or 3;

δ is 0 or 1, and δ+β′=1;

R 12 is C 1 -C 22 alkyl or C 7 -C 22 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, or C 3 -C 18 trialkylammonium;

R 13 is a C 1 -C 22 alkyl and C 7 -C 22 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 independently and 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, and C 3 -C 18 trialkylammonium;

R 14 is a C 1 -C 22 alkyl and C 7 -C 22 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 independently and 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, and C 3 -C 18 trialkylammonium,

or R 13 and R 14 taken in combination complete a five- or six-membered saturated or unsaturated ring that is optionally substituted;

R 16 is H;

R 17 is H, amino, sulfo, trifluoromethyl, halogen, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, and C 2 -C 12 dialkylamino, each alkyl portion of which is optionally further substituted by substituents selected from the group consisting of carboxy, sulfo, amino, or hydroxyl;

R 18 is H.

2. The compound according to claim 1 , wherein R 3 comprises a protein, a peptide, an amino acid, a dextran, a hormone, a lectin, a lipopolysaccharide, a biological cell, a non -biological microparticle, a nucleotide, an oligonucleotide, a small-molecule drug, avidin or streptavidin, biotin, or tyramide.

3. The compound according to claim 1 , wherein R 3 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 reactive platinum complex, a sulfonyl halide, a thiol group, or a photoactivatable group.

4. The compound according to claim 1 , wherein R 3 comprises an antibody or fragment thereof, a blood component protein, a blood vessel proliferation inhibition factor, an enzyme, an enzyme inhibitor, a hormone, an IgG-binding protein, a fluorescent protein, a growth factor, a metal -binding protein, a microorganism or portion thereof, a neuropeptide, a peptide toxin, a phospholipid -binding protein, or a structural protein.

5. A compound having the formula:

and its salts, wherein

R 3 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 reactive platinum complex, a sulfonyl halide, a thiol group, a photoactivatable group, a protein, a peptide, an amino acid, a dextran, a hormone, a lectin, a lipopolysaccharide, a biological cell, a non-biological microparticle, a nucleotide, an oligonucleotide, a small-molecule drug, avidin or streptavidin, biotin, or tyramide;

R 4 is a C 1 -C 22 alkyl or C 7 -C 22 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, or C 2 -C 12 dialkylamino, or C 3 -C 18 trialkylammonium; or

R 3 and R 4 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 reactive platinum complex, a sulfonyl halide, a thiol group, a photoactivatable group, a protein, a peptide, an amino acid, a dextran, a hormone, a lectin, a lipopolysaccharide, a biological cell, a non-biological microparticle, a nucleotide, an oligonucleotide, a small -molecule drug, avidin or streptavidin, biotin, or tyramide;

R 2 is a C 1 -C 22 alkyl or C 7 -C 22 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, or C 3 -C 18 trialkylammonium;

R 6 is H;

R 7 is sulfo;

R 8 is H;

R 9 is H;

R 16 is H;

R 17 is H, amino, sulfo, trifluoromethyl, halogen, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, and C 2 -C 12 dialkylamino, each alkyl portion of which is optionally further substituted by substituents selected from the group consisting of carboxy, sulfo, amino, or hydroxyl;

R 18 is H;

n is 0, 1, 2 or 3;

R 12 is C 1 -C 22 alkyl or C 7 -C 22 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, or C 3 -C 18 trialkylammonium;

R 13 is a C 1 -C 22 alkyl and C 7 -C 22 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 independently and 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, and C 3 -C 18 trialkylammonium;

R 14 is a C 1 -C 22 alkyl and C 7 -C 22 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 independently and 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, and C 3 -C 18 trialkylammonium,

or R 13 and R 14 taken in combination complete a five- or six-membered saturated or unsaturated ring that is optionally substituted.

6. The compound according to claim 5 , wherein R 3 comprises a carboxylic acid, a succinimidyl ester of a carboxylic acid, hydrazide, a maleimide, an antibody or fragment thereof, a fluorescent protein, a lectin, a nucleotide, an oligonucleotide, a peptide, protein, a small -molecule drug, or a tyramide.

7. The compound according to claim 5 , wherein

R 4 , R 13 and R 14 are each methyl;

R 6 , R 8 , R 9 , R 16 , R 17 and R 18 are each H;

R 7 is sulfo;

R 2 and R 12 are independently methyl or sulfopropyl; and

n is 2.

8. A kit for fluorescent labeling of a biological sample, comprising:

a dye solution comprising a compound having the formula:

and its salts, wherein

R 3 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 reactive platinum complex, a sulfonyl halide, a thiol group, a photoactivatable group, a protein, a peptide, an amino acid, a dextran, a hormone, a lectin, a lipopolysaccharide, a biological cell, a non-biological microparticle, a nucleotide, an oligonucleotide, a small-molecule drug, avidin or streptavidin, biotin, or tyramide;

R 4 is a C 1 -C 22 alkyl or C 7 -C 22 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, or C 2 -C 12 dialkylamino, or C 3 -C 18 trialkylammonium; or

R 3 and R 4 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 reactive platinum complex, a sulfonyl halide, a thiol group, a photoactivatable group, a protein, a peptide, an amino acid, a dextran, a hormone, a lectin, a lipopolysaccharide, a biological cell, a non-biological microparticle, a nucleotide, an oligonucleotide, a small -molecule drug, avidin or streptavidin, biotin, or tyramide;

R 2 is a C 1 -C 22 alkyl or C 7 -C 22 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, or C 3 -C 18 trialkylammonium;

R 6 is H;

R 7 is sulfo;

R 8 is H;

R 9 is H;

n is 0, 1, 2 or 3;

δ is 0 or 1, and δ+β′=1;

R 12 is C 1 -C 22 alkyl or C 7 -C 22 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, or C 3 -C 18 trialkylammonium;

R 13 is a C 1 -C 22 alkyl and C 7 -C 22 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 independently and 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, and C 3 -C 18 trialkylammonium;

R 14 is a C 1 -C 22 alkyl and C 7 -C 22 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 independently and 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, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, C 2 -C 12 dialkylamino, and C 3 -C 18 trialkylammonium,

or R 13 and R 14 taken in combination complete a five- or six-membered saturated or unsaturated ring that is optionally substituted;

R 16 is H;

R 17 is H, amino, sulfo, trifluoromethyl, halogen, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 1 -C 6 alkylamino, and C 2 -C 12 dialkylamino, each alkyl portion of which is optionally further substituted by substituents selected from the group consisting of carboxy, sulfo, amino, or hydroxyl;

R 18 is H; and

a buffer.