Fluorescent imaging with substituted cyanine dyes

1. A compound of Formula I:

wherein

R 1 is sulfonato;

r is 2, 3, or 4;

R 3 , R 4 , R 5 , and R 6 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, alkoxy, sulfonato, alkoxyalkyl, and sulfonatoalkyl; or, alternatively, R 5 and R 6 , together with a pair of atoms to which they are bonded, join to form an aryl ring, wherein each said aryl ring is additionally substituted with from 1 to 2 R 14 ;

R 8 , R 10 , R 11 , and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, alkoxy, and sulfonato;

each R 14 is a member independently selected from the group consisting of alkyl, halo, hydroxyl, alkoxy, amino, carboxyl, and sulfonato;

t is an integer from 1 to 10;

R 16 is carboxyl, maleimidyl, alkynyl, azido, or activated acyl;

wherein at least one substituent that is selected from the group consisting of R 3 , R 4 , R 5 , R 6 , and R 14 is sulfonato; and

wherein said compound has a balanced charge.

2. The compound of claim 1 , wherein R 3 , R 4 , R 5 , and R 6 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, alkoxy, sulfonato, alkoxyalkyl, and sulfonatoalky.

3. The compound of claim 1 , wherein R 8 , R 10 , R 11 , and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, and sulfonato.

4. The compound of claim 3 , having the formula:

5. The compound of claim 1 ,

wherein t is 4; wherein R 16 is carboxyl; and wherein R 3 , R 4 , R 5 , and R 6 are each a member independently selected from the group consisting of hydrogen and sulfonato.

6. The compound of claim 5 , having the formula:

7. The compound of claim 1 , wherein R 16 is maleimidyl.

8. The compound of claim 1 , wherein R 16 is alkynyl or azido.

9. The compound of claim 1 , having Formula Ia:

10. The compound of claim 9 , wherein R 16 is maleimidyl.

11. The compound of claim 9 , wherein R 16 is alkynyl or azido.

12. The compound of claim 9 , wherein R 8 , R 10 , R 11 , and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, and sulfonato.

13. The compound of claim 12 , having the formula:

14. The compound of claim 12 , having the formula:

15. The compound of claim 12 ,

wherein t is 4; wherein R 16 is carboxyl; and wherein each R 14 is a member independently selected from the group consisting of hydrogen and sulfonato.

16. The compound of claim 15 , having the formula:

17. The compound of claim 15 , having the formula:

18. The compound of claim 1 , wherein the compound fluoresces at a wavelength within the range of about 550 nm to about 1000 nm.

19. The compound of claim 1 , wherein the compound fluoresces at a wavelength within the range of about 600 nm to about 850 nm.

20. The compound of claim 1 , wherein the compound fluoresces at a wavelength within the range of about 600 nm to about 725 nm.

21. The compound of claim 1 , wherein the compound fluoresces at a wavelength within the range of about 725 nm to about 850 nm.

22. A bioconjugate compound of Formula II:

wherein

R 1 is sulfonato;

r is 2, 3, or 4;

R 3 , R 4 , R 5 , and R 6 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, alkoxy, sulfonato, alkoxyalkyl, and sulfonatoalkyl; or, alternatively, a pair of said members that is R 5 and R 6 , together with a pair of atoms to which they are bonded, join to form an aryl ring, wherein each said aryl ring is additionally substituted with from 1 to 2 R 14 ;

R 8 , R 10 , R 11 , and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, alkenyl, halo, alkoxy, and sulfonato;

each R 14 is a member independently selected from the group consisting of alkyl, halo, hydroxyl, alkoxy, amino, carboxyl, and sulfonato;

t is an integer from 1 to 10;

R L comprises a linking group and a biomolecule connected thereby;

wherein at least one substituent that is selected from the group consisting of R 3 , R 4 , R 5 , R 6 , and R 14 is sulfonato; and

wherein said compound has a balanced charge.

23. A method of labeling a biomolecule, said method comprising reacting a compound of claim 1 with a biomolecule.

24. A method of labeling a biomolecule, said method comprising:

reacting a compound of claim 1 with the biomolecule;

wherein said biomolecule is selected from the group consisting of somatostatin, endostatin, a carbohydrate, an oligosaccharide, an aptamer, a liposome, PEG, an angiopoietin, angiostatin, angiotensin II, α 2 -antiplasmin, annexin V, β-cyclodextrin tetradecasulfate, endoglin, endosialin, endostatin, epidermal growth factor, fibrin, fibrinopeptide β, fibroblast growth factor, FGF-3, basic fibronectin, fumagillin, heparin, hepatocycte growth factor, hyaluronan, an insulin-like growth factor, an interferon-α, βinhibitor, IL inhibitor, laminin, leukemia inhibitory factor, linomide, a metalloproteinase, a metalloproteinase inhibitor, an antibody, an antibody fragment, an acyclic RGD peptide, a cyclic RGD peptide, placental growth factor, placental proliferin-related protein, plasminogen, plasminogen activator, plasminogen activator inhibitor-1, a platelet activating factor antagonist, platelet-derived growth factor, a platelet-derived growth factor receptor, a platelet-derived growth factor receptor, platelet-derived endothelial cell growth factor, pleiotropin, proliferin, proliferin-related protein, a selectin, SPARC, a snake venom, substance P, suramin, a tissue inhibitor of a metalloproteinase, thalidomide, thrombin, thrombin-receptor-activating tetradecapeptide, transformin growth factor-α, β, transforming growth factor receptor, tumor growth factor-α, tumor necrosis factor, vitronectin, and calcein.

25. A method of imaging, said method comprising: administering a compound of claim 1 to a tissue or an organism.

26. A method of imaging, said method comprising administering a compound of claim 22 to a tissue or an organism.

27. A compound of Formula I′:

wherein

R 1 is sulfonato;

r is 2, 3, or 4;

R 3 , R 4 , R 5 , and R 6 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, alkoxy, sulfonato, alkoxyalkyl, and sulfonatoalkyl; or, alternatively, R 5 and R 6 , together with a pair of atoms to which they are bonded, join to form an aryl ring, wherein each said aryl ring is additionally substituted with from 1 to 2 R 14 ;

R 8 , R 10 , R 11 , and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, alkoxy, and sulfonato;

each R 14 is a member independently selected from the group consisting of alkyl, halo, hydroxyl, alkoxy, amino, carboxyl, and sulfonato;

t is an integer from 1 to 10;

Y is selected from the group consisting of —O—, —S—, —NH—, —NHC(O)—, —C(O)NH—, —NR 15 —, —NR 15 C(O)—, -and —C(O)NR 15 —;

R 15 is selected from the group consisting of alkyl and alkoxycarbonylalkyl; wherein the alkyl is optionally interrupted by at least one heteroatom;

Z is a C 1 -C 10 alkyl that is substituted with R 16 ; wherein the alkyl is optionally interrupted by at least one heteroatom;

R 16 is carboxyl, maleimidyl, alkynyl, azido, or activated acyl;

wherein at least one substituent that is selected from the group consisting of R 3 , R 4 , R 5 , R 6 , and R 14 is sulfonato; and

wherein said compound has a balanced charge.

28. The compound of claim 27 , wherein Y is selected from the group consisting of —NHC(O)—, —C(O)NH—, —NR 15 C(O)—, -and —C(O)NR 15 —;

R 15 is alkyl optionally interrupted by at least one heteroatom; and

Z is a C 1 -C 10 alkyl that is substituted with R 16 ; wherein Z is optionally interrupted by at least one ether group.

29. The compound of claim 28 , wherein Y is selected from the group consisting of —NHC(O)—, —C(O)NH—, —NR 15 C(O)—, —and —C(O)NR 15 —;

R 15 is alkyl; and

Z is a C 1 -C 10 alkyl that is substituted with R 16 .