Cyanine dyes
A compound of the formula (I) wherein the variables are defined herein. Methods of dye-labeling biomolecules with the compound of formula (I) and dye-labeled biomolecules are also provided.
1. A dye-labeled biomolecule of formula (XV)
wherein Z is O, S, or NR 35 wherein R 35 is H or alkyl;
R 1 -R 5 are each independently H, alkyl, halo, carboxyl, amino, or SO 3 − Cat + , wherein Cat + is a cation and at least one of R 1 -R 5 is SO 3 − Cat + ;
R 6 and R 7 are each H, alkyl, or optionally, together with the
group to which they are bonded, form a ring;
m and n are each independently integers from 0 to 5;
X and Y are each independently CR 19 R 20 , wherein R 19 and R 20 are each independently alkyl, or optionally form a ring together with the carbon atom to which they are bonded;
R 8 is a member selected from the group consisting of alkyl, (CH 2 ) r R 25 , (CH 2 ) r R 18 , and R 30 —B, wherein r is an integer from 1 to 50, and R 25 is selected from the group consisting of hydroxyl, thioacetyl, sulfonato, and R 18 is selected from the group consisting of mercapto, amino, haloalkyl, phosporamidityl, N-hydroxy succinimidyl ester, sulfo N-hydroxy succinimidyl ester, isothiocyanato, iodoacetamidyl, and maleimidyl; and
R 9 -R 12 and R 14 -R 17 are each independently H, alkyl, halo, amino, sulfonato, R 21 COOH, R 21 OR 22 , R 21 SR 22 , or R 21 COOR 22 wherein R 21 is a bond or alkylene and R 22 is alkyl, or optionally R 11 and R 12 together with the atoms to which they are bonded form an aromatic ring, or optionally R 16 and R 17 together with the atoms to which they are bonded form an aromatic ring;
B is a biomolecule; and
R 30 is (CH 2 ) r L; wherein r is an integer from 1 to 50, and L is a linking group.
2. The dye-labeled biomolecule of claim 1 , wherein
Z is O;
R 1 -R 5 are each independently H, alkyl, halo, carboxyl, amino, or SO 3 − Cat + , wherein Cat + is a cation and at least one of R 1 -R 5 is SO 3 − Cat + ;
R 6 and R 7 are each H, alkyl, or optionally, together with the
group to which they are bonded, form a ring;
m and n are each independently integers from 0 to 5;
X and Y are CR 19 R 20 , wherein R 19 and R 20 are each independently alkyl, or optionally form a ring together with the carbon atom to which they are bonded;
R 8 is a member selected from the group consisting of alkyl, (CH 2 ) r R 25 , (CH 2 ) r R 18 , and R 30 —B; wherein r is an integer from 1 to 50, and R 25 is a functional group consisting of hydroxyl, thioacetyl, sulfonato, and R 18 is selected from the group consisting of mercapto, amino, haloalkyl, phosporamidityl, N-hydroxy succinimidyl ester, sulfo N-hydroxy succinimidyl ester, isothiocyanato, iodoacetamidyl, and maleimidyl and
R 9 -R 12 and R 14 -R 17 are each independently H, alkyl, halo, amino, sulfonato, R 21 COOH, R 21 OR 22 , R 21 SR 22 , or R 21 COOR 22 wherein R 21 is a bond or alkylene and R 22 is alkyl, or optionally R 11 and R 12 together with the atoms to which they are bonded form an aromatic ring, or optionally R 16 and R 17 together with the atoms to which they are bonded form an aromatic ring;
B is a biomolecule; and
R 30 is (CH 2 ) r L; wherein r is an integer from 1 to 50, and L is a linking group.
3. The dye-labeled biomolecule of claim 1 , wherein R 3 is SO 3 − Cat + .
4. The dye-labeled biomolecule of claim 3 , wherein Cat + is H + .
5. The dye-labeled biomolecule of claim 3 , wherein Cat + is a metal ion.
6. The dye-labeled biomolecule of claim 5 , wherein Cat + is an alkali metal ion.
7. The dye-labeled biomolecule of claim 1 , wherein R 6 and R 7 are lower alkyl.
8. The dye-labeled biomolecule of claim 1 , wherein R 6 and R 7 , together with the
group to which they are bonded, form a ring, said ring being optionally substituted.
9. The dye-labeled biomolecule of claim 8 , wherein the ring that includes R 6 and R 7 is substituted with sulfonate.
10. The dye-labeled biomolecule of claim 8 , wherein the ring that includes R 6 and R 7 has 4 to 10 members.
11. The dye-labeled biomolecule of claim 8 , wherein the ring that includes R 6 and R 7 has 5 or 6 members.
12. The dye-labeled biomolecule of claim 8 , wherein the ring that includes R 6 and R 7 contains a heteroatom.
13. The dye-labeled biomolecule of claim 8 , wherein the ring that includes R 6 and R 7 is substituted in at least one position with an alkyl, amino, or a sulfonate group.
14. The dye-labeled biomolecule of claim 1 , wherein m and n are both 0.
15. The dye-labeled biomolecule of claim 1 , wherein the sum of m+n is less than 3.
16. The dye-labeled biomolecule of claim 1 , wherein at least one of R 19 and R 20 is lower alkyl.
17. The dye-labeled biomolecule of claim 16 , wherein both R 19 and R 20 are methyl.
18. The dye-labeled biomolecule of claim 1 , wherein R 8 is (CH 2 ) r R 25 and wherein R 25 is thioacetyl or sulfonato.
19. The dye-labeled biomolecule of claim 1 , wherein r is an integer from 1 to 5.
20. The dye-labeled biomolecule of claim 1 , wherein R 9 -R 12 are each H.
21. The dye-labeled biomolecule of claim 1 , wherein one of R 9 -R 12 is sulfonato.
22. The dye-labeled biomolecule of claim 1 , wherein R 14 -R 17 are each H.
23. The dye-labeled biomolecule of claim 1 , wherein one of R 14 -R 17 is sulfonato.
24. The dye-labeled biomolecule of claim 1 , wherein the biomolecule is selected from the group consisting of a protein, a peptide, an enzyme substrate, a hormone, an antibody, an antigen, an hapten, an avidin, a streptavidin, a carbohydrate, an oligosaccharide, a polysaccharide, a nucleic acid, a deoxy nucleic acid, a fragment of DNA, a fragment of RNA, nucleotide triphosphates, acyclo terminator triphosphates, and PNA.
25. The dye-labeled biomolecule of claim 1 , wherein at least one of R 9 -R 12 is alkyl, halo, amino, R 21 COOH, R 21 OR 22 , R 21 SR 22 , or R 21 COOR 22 wherein R 21 is a bond or alkylene and R 22 is alkyl.
26. The dye-labeled biomolecule of claim 1 , wherein at least one of R 14 -R 17 is alkyl, halo, amino, R 21 COOH, R 21 OR 22 , R 21 SR 22 , or R 21 COOR 22 wherein R 21 is a bond or alkylene and R 22 is alkyl.
27. A dye-labeled biomolecule of formula
wherein Cat + is a cation;
X and Y are each (CH 3 ) 2 C; and
R 8 is a member selected from the group consisting of alkyl, (CH 2 ) r R 25 , (CH 2 ) r R 18 and R 30 —B; wherein r is an integer from 1 to 50, and R 25 is a member selected from the group consisting of hydroxyl, thioacetyl, sulfonato, and R 18 is selected from the group consisting of mercapto, amino, haloalkyl, phosporamidityl, N-hydroxy succinimidyl ester, sulfo N-hydroxy succinimidyl ester, isothiocyanato, iodoacetamidyl, and maleimidyl,
R 11 and R 12 are either H, sulfonato, or together with the atoms to which they are bonded form an aromatic ring;
R 16 and R 17 are either H, sulfonato, or together with the atoms to which they are bonded form an aromatic ring;
B is a biomolecule; and
R 30 is (CH 2 ) r L; wherein r is an integer from 1 to 50, and L is a linking group.
28. The dye-labeled biomolecule of claim 27 , wherein Cat + is H + or a metal ion.
29. The dye-labeled biomolecule of claim 27 , wherein r is an integer from 1 to 5.
30. The dye-labeled biomolecule of claim 27 , wherein R 8 is (CH 2 ) r R 18 .
31. The dye-labeled biomolecule of claim 1 , wherein the compound has the structure of:
32. The dye-labeled biomolecule of claim 27 , wherein
R 8 is (CH 2 ) r R 25 ; and
R 11 and R 16 are each sulfonato.
33. The dye-labeled biomolecule of claim 27 , wherein the biomolecule is selected from the group consisting of a protein, a peptide, an enzyme substrate, a hormone, an antibody, an antigen, an hapten, an avidin, a streptavidin, a carbohydrate, an oligosaccharide, a polysaccharide, a nucleic acid, a deoxy nucleic acid, a fragment of DNA, a fragment of RNA, nucleotide triphosphates, acyclo terminator triphosphates, and PNA.
34. The dye-labeled biomolecule of claim 32 , wherein said biomolecule is a carbohydrate.