Carboxy X rhodamine analogs

1. A method to detect a selected molecule in a sample, comprising:

a) contacting a sample suspected of containing the selected molecule with a composition comprising a dye conjugate according to formula (IIIa), (IIIb) or (IIIc) so as to yield a mixture:

wherein

R 11 is independently H or C 1-4 alkyl or L-C s ;

L is a covalent linkage that is linear or branched, cyclic or heterocyclic saturated or unsaturated, having 1-16 non hydrogen atoms such that the linkage contains any combination of ester, acid, amine, amide, alcohol, ether, thioether or halide groups or single, double, triple or aromatic carbon-carbon bond;

C s is a conjugated substance selected from the group consisting of solid supports, resin particles, beads, assay plates, proteins, nucleotides, polynucleotides, enzyme substrates, nanobodies, polypeptides, amino acids, lipids, carbohydrates, haptens, drugs, ion-complexing agents, microparticles, polymers, cells, viruses, fluorophores, chloroalkanes, and cyanobenzothiazoles;

R 2 and R 16 can be independently H, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, or L-C s ;

R 3 and R 4 are H, alkyl, L-C s , L-CO 2 H, L-SO 3 H or together form a carbocyclic, aryl, heteroaryl, or heterocyclic ring;

alternatively, R 2 and R 3 and independently R 4 and R 16 together form a carbocyclic, heterocyclic, aryl or heteroaryl ring;

R 5 , R 12 , R 13 , R 14 and R 15 are independently H, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, or L-C s ;

R 20 , R 21 , R 22 and R 23 are independently H or C 1-6 alkyl or one or more of R 20 and R 21 , R 21 and R 22 , R 22 and R 23 , together form an aryl, heteroaryl, carbocyclic or heterocyclic ring;

alternatively R 11 and R 12 together form a carbocyclic, heterocyclic, aryl or heteroaryl ring;

R 6-10 are independently H, F, Cl, Br, I, OH, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, or L-C s ;

X is CHR 23 , O, S or NR 30 ; and

R 30 is H, C1-4 alkyl or —C(O)C1-4 alkyl; and

b) detecting the presence or amount of the dye conjugate in the mixture, thereby detecting the selected molecule in the sample.

2. The method of claim 1 , wherein at least one of R 2-16 is -L-C s .

3. The method of claim 1 , wherein C s is a polynucleotide.

4. A method of detecting the presence of a nucleic acid polymer in a sample comprising:

a) contacting a sample suspected of containing a nucleic acid polymer with a composition comprising a dye conjugate according to formula (IIIa), (IIIb) or (IIIc) so as to yield a mixture:

wherein

R 11 is independently H, C 1-4 alkyl, or L-C s ;

L is a covalent linkage that is linear or branched, cyclic or heterocyclic saturated or unsaturated, having 1-16 non hydrogen atoms such that the linkage contains any combination of ester, acid, amine, amide, alcohol, ether, thioether or halide groups or single, double, triple or aromatic carbon-carbon bond;

C s is an oligonucleotide;

R 2 and R 16 can be independently H, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, or L-C s ;

R 3 and R 4 are H, alkyl, L-C s , L-CO 2 H, L-SO 3 H or together form a carbocyclic, aryl, heteroaryl, or heterocyclic ring;

alternatively, R 2 and R 3 and independently R 4 and R 16 together form a carbocyclic, heterocyclic, aryl or heteroaryl ring;

R 5 , R 12 , R 13 , R 14 and R 15 are independently H, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, or L-C s ;

R 20 , R 21 , R 22 and R 23 are independently H or C 1-6 alkyl or one or more of R 20 and R 21 , R 21 and R 22 , R 22 and R 23 , together form an aryl, heteroaryl, carbocyclic or heterocyclic ring;

alternatively, R 11 and R 12 together form a carbocyclic, heterocyclic, aryl or heteroaryl ring;

R 6-10 are independently H, F, Cl, Br, I, OH, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, or L-C s ;

X is CHR 23 , O, S or NR 30 ; and

R 30 is H, C 1-4 alkyl or —C(O)C 1-4 alkyl; and

b) detecting the presence or amount of the dye conjugate in the mixture, thereby detecting the presence of the nucleic acid polymer in the sample.

5. The method of claim 4 , wherein more than one nucleic acid polymer in a sample is detected in a single reaction.

6. The method of claim 5 , wherein the more than one nucleic acid polymer is detected by capillary electrophoresis.

7. A method of labeling a biomolecule comprising:

a) contacting a sample suspected of containing the biomolecule with a composition comprising a dye conjugate according to formula (IIIa), (IIIb) or (IIIc) so as to yield a mixture:

wherein

R 11 is independently H or C 1-4 alkyl, or L-C s ;

L is a covalent linkage that is linear or branched, cyclic or heterocyclic saturated or unsaturated, having 1-16 non hydrogen atoms such that the linkage contains any combination of ester, acid, amine, amide, alcohol, ether, thioether or halide groups or single, double, triple or aromatic carbon-carbon bond;

C s is a conjugated substance selected from the group consisting of solid supports, resin particles, beads, assay plates, proteins, nucleotides, polynucleotides, enzyme substrates, nanobodies, polypeptides, amino acids, lipids, carbohydrates, haptens, drugs, ion-complexing agents, microparticles, polymers, cells, viruses, fluorophores, chloroalkanes, and cyanobenzothiazoles;

R 2 and R 16 can be independently H, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, or L-C s ;

R 3 and R 4 are H, alkyl, L-C s , L-CO 2 H, L-SO 3 H or together form a carbocyclic, aryl, heteroaryl, or heterocyclic ring;

alternatively, R 2 and R 3 and independently R 4 and R 16 together form a carbocyclic, heterocyclic, aryl or heteroaryl ring;

R 5 , R 12 , R 13 , R 14 and R 15 are independently H, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, or L-C s ;

R 20 , R 21 , R 22 and R 23 are independently H or C 1-6 alkyl or one or more of R 20 and R 21 , R 21 and R 22 , R 22 and R 23 , together form an aryl, heteroaryl, carbocyclic or heterocyclic ring;

alternatively R 11 and R 12 together form a carbocyclic, heterocyclic, aryl or heteroaryl ring;

R 6-10 are independently H, F, Cl, Br, I, OH, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, or L-C s ;

X is CHR 23 , O, S or NR 30 ; and

R 30 is H, C 1-4 alkyl or —C(O)C 1-4 alkyl;

b) detecting the presence or amount of the dye conjugate, thereby detecting the presence or amount of the labeled biomolecule in the mixture.

8. The method of claim 7 , wherein the dye conjugate contains a cyanobenzothiazole.

9. The method of claim 7 , wherein the biomolecule is a protein.

10. The method of claim 9 , wherein the protein comprises an N-terminal cysteine.

11. The method of claim 10 , wherein the protein comprising an N-terminal cysteine is labeled with the dye conjugate comprising a cyanobenzothiazole.

12. The method of claim 4 , wherein L is —CO—, —SCH 2 CO—, or —SO 2 —.

13. The method of claim 12 , wherein L is —SCH 2 CO— and L is bonded to a nucleotide base in the oligonucleotide to form a group

14. The method of claim 4 , wherein L is a group

bonded to a 5′-position of the oligonucleotide.

15. The method of claim 4 , wherein L is a self-immolative linker selected from the group consisting of

16. The method of claim 1 , wherein the protein is an antibody.

17. The method of claim 1 , wherein the polypeptide is a polypeptide-based toxin.

18. The method of claim 7 , wherein the protein is an antibody.

19. The method of claim 7 , wherein the polypeptide is a polypeptide-based toxin.