Cyanine dyes and their conjugates

1. A compound of Formula I:

wherein

Q is a portion of a polymethine bridge selected from the group consisting of:

wherein Q is the central portion of either a five- or a seven- polymethine-carbon polymethine bridge;

each R 1 is a member independently selected from the group consisting of -L-Y—Z and an alkyl that is additionally substituted with from 0 to 1 R 13 and from 0 to 1 R 16 , wherein the alkyl is optionally interrupted by at least one heteroatom;

each R 2a and R 2b is a member independently selected from the group consisting of alkyl, alkenyl, hydroxyalkyl, alkoxyalkyl, aminoalkyl, amidoalkyl, alkylthioalkyl, carboxyalkyl, alkoxycarbonylalkyl, and sulfonatoalkyl; wherein a carbon of the member is additionally substituted with from 0 to 1 R 16 ; or, alternatively, a R 2a and R 2b pair, together with the ring carbon to which the R 2a and R 2b are bonded, join to form a spirocycloalkyl ring, wherein the spirocycloalkyl ring is additionally substituted with from 0 to 6 R 14 and from 0 to 1 R 16 , or an exocyclic alkene, wherein the exocyclic alkene is additionally substituted with from 0 to 2 R 14 and from 0 to 1 R 16 ;

each R 3 , R 4a , R 4b , R 5a , R 5b , R 6a , and R 6b is a member independently selected from the group consisting of hydrogen, alkyl, alkenyl, halo, hydroxyl, alkoxy, amino, cyano, carboxyl, alkoxycarbonyl, amido, sulfonato, alkoxyalkyl, carboxyalkyl, alkoxycarbonylalkyl, and sulfonatoalkyl; wherein a carbon of the member is additionally substituted with from 0 to 1 R 16 ; or, alternatively, a pair of said members that is selected from the group consisting of R 3 and R 4a , an R 4a and R 5a , and an R 5a and R 6a , together with the pair of atoms to which the pair of said members is bonded, joins to form an aryl ring, wherein the aryl ring is additionally substituted with from 0 to 2 R 14 and from 0 to 1 R 16 ;

each R 7 is a member independently selected from the group consisting of hydrogen and alkyl; wherein the alkyl is additionally substituted with from 0 to 3 R 14 and from 0 to 1 R 16 ; or, alternatively, both R 7 , together with the intervening segment of the polyene to which both R 7 are bonded, join to form a ring, wherein said ring is selected from the group consisting of a cycloalkyl and a heterocyclyl ring; wherein the ring is additionally substituted with from 0 to 3 R 14 and from 0 to 1 R 16 ;

R 8 , R 9 , R 10 , R 11 and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, alkenyl, halo, alkoxy, sulfonato, sulfonatoalkyl, hydroxyl, amino, carboxyl, alkoxycarbonyl, cyano, amido, thioacetyl, and -L-Y—Z; wherein, if present, at least one member selected from the group consisting of R 8 , R 9 , and R 10 is -L-Y—Z;

each R 13 is a member independently selected from the group consisting of hydroxyl, amino, carboxyl, alkoxycarbonyl, cyano, amido, sulfonato, and thioacetyl;

each R 14 is a member independently selected from the group consisting of alkyl, alkenyl, halo, hydroxyl, alkoxy, amino, cyano, carboxyl, alkoxycarbonyl, amido, sulfonato, alkoxycarbonylalkyl, and alkoxyalkyl; wherein the alkyl or alkenyl is additionally substituted with from 0 to 1 R 13 and from 0 to 1 R 16 ;

each L is an optional member independently selected from the group consisting of a bond, a C 1 -C 20 alkylene, and a C 1 -C 20 alkenylene; wherein the alkylene or alkenylene is optionally interrupted by at least one heteroatom;

each Y is an optional member independently selected from the group consisting of a bond, —O—, —S—, —NH—, —NHC(O)—, —C(O)NH—, —NR 15 —, —NR 15 C(O)—, —C(O)NR 15 —, —N(Z)—, —N(Z)C(O)—, and —C(O)N(Z)—;

each Z is independently selected from the group consisting of -L-R 13 and -L-R 16 ,

alternatively, —Y—Z is a member selected from the group consisting of —N(Z) 2 , —N(Z)C(O)Z, and —C(O)N(Z) 2 , and the two Z groups may optionally be linked to form a cycloalkynyl group;

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

each R 16 is independently a member selected from the group consisting of activated acyl, acrylamido, optionally substituted alkylsulfonate ester, azido, optionally substituted arylsulfonate ester, optionally substituted amino, aziridino, boronato, cycloalkynyl, cycloalkynylcarbonyl, diazo, formyl, glycidyl, halo, haloacetamidyl, haloalkyl, haloplatinato, halotriazino, hydrazinyl, imido ester, isocyanato, isothiocyanato, maleimidyl, mercapto, phosphoramidityl, a photoactivatable moiety, vinyl sulfonyl, alkynyl, cycloalkynyl, spirocycloalkynyl, a pegylated azido, a pegylated alkynyl, a pegylated cycloalkynyl, a pegylated spirocycloalkynyl, an ortho substituted phosphinyl aryl ester, and an ortho substituted phosphine oxide aryl ester; and

wherein said compound has a balanced charge.

2. The compound of claim 1 , wherein each R 16 is independently a member selected from the group consisting of activated acyl, acrylamido, optionally substituted alkylsulfonate ester, azido, optionally substituted arylsulfonate ester, amino, aziridino, boronato, diazo, formyl, glycidyl, halo, haloacetamidyl, haloalkyl, haloplatinato, halotriazino, hydrazinyl, imido ester, isocyanato, isothiocyanato, maleimidyl, mercapto, phosphoramidityl, a photoactivatable moiety, and vinyl sulfonyl.

3. The compound of claim 2 , wherein when —Y—Z is a member selected from the group consisting of —N(Z) 2 , —N(Z)C(O)Z, and —C(O)N(Z) 2 , the two Z groups are not linked to form a cycloalkynyl group.

4. The compound of claim 1 , wherein at least one R 16 is independently a member selected from the group consisting of azido, alkynyl, cycloalkynyl, a pegylated azido, a pegylated alkynyl, a pegylated cycloalkynyl and an ortho substituted phosphinyl aryl ester.

5. The compound of claim 1 , wherein each R 1 is independently an alkyl that is additionally substituted with from 0 to 1 R 13 and from 0 to 1 R 16 , wherein the alkyl is optionally interrupted by at least one heteroatom.

6. The compound of claim 2 , wherein Q is:

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

wherein M is an alkali metal ion.

8. The compound of claim 1 , wherein each R 3 , R 4a , R 4b , R 5a , R 5b , R 6a , and R 6b is a member independently selected from the group consisting of hydrogen, alkyl, alkenyl, halo, alkoxy, cyano, carboxyl, alkoxycarbonyl, amido, sulfonato, alkoxyalkyl, carboxyalkyl, alkoxycarbonylalkyl, and sulfonatoalkyl.

9. The compound of claim 6 ,

wherein each R 1 is an independently selected sulfonatoalkyl or an independently selected alkyl that is additionally substituted with from 0 to 1 R 13 ;

each R 2a and R 2b is a member independently selected from the group consisting of alkyl, carboxyalkyl, and sulfonatoalkyl;

each R 3 , R 4a , R 4b , R 5a , R 5b , R 6a , and R 6b is a member independently selected from the group consisting of hydrogen, alkyl, carboxy, carboxyalkyl, halo, sulfonato, and sulfonatoalkyl;

R 8 , R 9 , R 10 , R 11 and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, sulfonato, sulfonatoalkyl, and -L-Y—Z; wherein at least one member selected from the group consisting of R 8 , R 9 , and R 10 is -L-Y—Z;

each R 13 is a member independently selected from the group consisting of hydroxyl, amino, and carboxyl;

each R 14 is a member independently selected from the group consisting of alkyl, alkenyl, carboxyl, alkoxycarbonyl, amido, alkoxycarbonylalkyl, and halo;

each L is a member independently selected from the group consisting of a bond, a C 1 —C 20 alkylene, and a C 1 —C 20 alkenylene;

each Y is a member independently selected from the group consisting of a bond, —O—, —NHC(O)—, —C(O)NH—, —NR 15 C(O)—, —C(O)NR 15 —, —N(Z)—, —N(Z)C(O)—, and —C(O)N(Z)—;

alternatively, —Y—Z is a member selected from the group consisting of —N(Z) 2 , —N(Z)C(O)Z, and —C(O)N(Z) 2 , and the two Z groups may optionally be linked to form a cycloalkynyl group;

each R 15 is an independently selected alkyl; and

each R 16 is independently a member selected from the group consisting of activated acyl, maleimidyl, phosphoramidityl, and glycidyl.

10. The compound of claim 1 , wherein R 2a and R 2b are methyl.

11. The compound of claim 1 , wherein R 1 is (CH 2 ) r SO 3 H or (CH 2 ) r SO 3 —; and

wherein r is an integer from 1 to 20.

12. The compound of claim 11 , wherein r is 2, 3, or 4.

13. The compound of claim 1 , wherein -L-Y— is (CH 2 ) t ;

wherein Z is carboxyl or activated acyl; and

wherein t is an integer from 0 to 10.

14. The compound of claim 2 , wherein R 8 is -L-Y—Z.

15. The compound of claim 14 , wherein R 9 , R 10 , R 11 , and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, sulfonato, and sulfonatoalkyl.

16. The compound of claim 2 , wherein R 10 is -L-Y—Z.

17. The compound of claim 16 , wherein R 9 , R 10 , R 11 , and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, sulfonato, and sulfonatoalkyl.

18. The compound of claim 2 , wherein R 9 is -L-Y—Z.

19. The compound of claim 18 , wherein R 8 , R 10 , R 11 , and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, sulfonato, and sulfonatoalkyl.

20. The compound of claim 2 , having the formula:

wherein M is a cationic counterion.

21. The compound of claim 20 , having the formula:

22. The compound of claim 1 , wherein:

each R 1 is an independently selected sulfonatoalkyl;

each R 2a and R 2b is an independently selected alkyl;

each R 3 , R 4a , R 4b , R 5a , R 5b , R 6a , R 6b is a member independently selected from the group consisting of hydrogen, alkyl, carboxy, carboxyalkyl, halo, sulfonato, and sulfonatoalkyl; or, alternatively, a pair of said members that is selected from the group consisting of R 3 and R 4a , an R 4a and R 5a , and an R 5a and R 6a , together with the pair of atoms to which the pair of said members is bonded, joins to form an aryl ring, wherein the aryl ring is additionally substituted with from 0 to 2 R 14 and from 0 to 1 R 16 ;

each R 7 is a member independently selected from the group consisting of hydrogen, alkyl, carboxyalkyl, and sulfonatoalkyl; or, alternatively, both R 7 , together with the intervening segment of the polyene to which both R 7 are bonded, join to form a ring, wherein said ring is selected from the group consisting of a cycloalkyl and a heterocyclyl ring; wherein the ring is additionally substituted with from 0 to 3 R 14 and from 0 to 1 R 16 ;

R 8 , R 9 , R 10 , R 11 and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, halo, sulfonato, sulfonatoalkyl, and -L-Y—Z; wherein at least one member selected from the group consisting of R 8 , R 9 , and R 10 is -L-Y—Z;

each R 13 is a member independently selected from the group consisting of hydroxyl, amino, and carboxyl;

each R 14 is a member independently selected from the group consisting of alkyl, alkenyl, carboxyl, alkoxycarbonyl, amido, alkoxycarbonylalkyl, and halo;

each L is a member independently selected from the group consisting of a bond, a C 1 -C 20 alkylene and a C 1 -C 20 alkenylene;

each Y is a member independently selected from the group consisting of a bond, —O—, —NHC(O)—, —C(O)NH—, —NR 15 C(O)—, —C(O)NR 15 —, —N(Z)—, —N(Z)C(O)—, and —C(O)N(Z)—;

alternatively, —Y—Z is a member selected from the group consisting of —N(Z) 2 , —N(Z)C(O)Z, and —C(O)N(Z) 2 , and the two Z groups may optionally be linked to form a cycloalkynyl group;

each R 14 is a member independently selected from the group consisting of alkyl, alkenyl, carboxyl, carboxyalkyl, alkoxycarbonyl, amido, alkoxycarbonylalkyl hydroxyalkyl, halo, sulfonato, and sulfonatoalkyl; and

each R 15 is a member independently selected from the group consisting of alkyl and alkoxycarbonylalkyl.

23. A bioconjugate compound of Formula II:

wherein

Q L is a portion of a polymethine bridge selected from the group consisting of:

wherein Q L is the central portion of either a five- or a seven- polymethine-carbon polymethine bridge;

each R 1 is a member independently selected from the group consisting of -L-Y—Z and alkyl that is additionally substituted with from 0 to 1 R 13 and from 0 to 1 R L ; wherein the alkyl is optionally interrupted by at least one heteroatom;

each R 2a and R 2b is a member independently selected from the group consisting of alkyl, alkenyl, hydroxyalkyl, alkoxyalkyl, aminoalkyl, amidoalkyl, alkylthioalkyl, carboxyalkyl, alkoxycarbonylalkyl, and sulfonatoalkyl; wherein a carbon of the member is additionally substituted with from 0 to 1 R L ; or, alternatively, a R 2a and R 2b pair, together with the ring carbon to which the R 2a and R 2b are bonded, join to form a spirocycloalkyl ring, wherein the spirocycloalkyl ring is additionally substituted with from 0 to 6 R 14 and from 0 to 1 R L , or an exocyclic alkene, wherein the exocyclic alkene is additionally substituted with from 0 to 2 R 14 and from 0 to 1 R L ;

each R 3 , R 4a , R 4b , R 5a , R 5b , R 6a , R 6b is a member independently selected from the group consisting of hydrogen, alkyl, alkenyl, halo, hydroxyl, alkoxy, amino, cyano, carboxyl, alkoxycarbonyl, amido, sulfonato, alkoxyalkyl, carboxyalkyl, alkoxycarbonylalkyl, and sulfonatoalkyl; wherein a carbon of the member is additionally substituted with from 0 to 1 R L ; or, alternatively, a pair of said members that is selected from the group consisting of R 3 and R 4a , an R 4a and R 5a , and an R 5a and R 6a , together with the pair of atoms to which the pair of said members is bonded, joins to form an aryl ring, wherein the aryl ring is additionally substituted with from 0 to 2 R 14 and from 0 to 1 R L ;

each R 7 is a member independently selected from the group consisting of hydrogen and alkyl; wherein the alkyl is additionally substituted with from 0 to 3 R 14 and from 0 to 1 R L ; or, alternatively, both R 7 , together with the intervening segment of the polyene to which both R 7 are bonded, join to form a ring, wherein said ring is selected from the group consisting of a cycloalkyl and a heterocyclyl ring; wherein the ring is additionally substituted with from 0 to 3 R 14 and from 0 to 1 R L ;

R 8 , R 9 , R 10 , R 11 and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, alkenyl, halo, alkoxy, sulfonato, hydroxyl, amino, carboxyl, alkoxycarbonyl, cyano, amido, thioacetyl, and -L-Y—Z; wherein, if present, at least one member selected from the group consisting of R 8 , R 9 , and R 10 is -L-Y—Z;

each R 13 is a member independently selected from the group consisting of hydroxyl, amino, carboxyl, alkoxycarbonyl, cyano, amido, sulfonato, and thioacetyl;

each R 14 is a member independently selected from the group consisting of alkyl, alkenyl, halo, hydroxyl, alkoxy, amino, cyano, carboxyl, alkoxycarbonyl, amido, sulfonato, alkoxycarbonylalkyl, and alkoxyalkyl; wherein the alkyl or alkenyl is additionally substituted with from 0 to 1 R 13 and from 0 to 1 R L ;

each L is an optional member independently selected from the group consisting of a bond, a C 1 -C 20 alkylene, and a C 1 -C 20 alkenylene; wherein the alkylene or alkenylene is optionally interrupted by at least one heteroatom;

each Y is an optional member independently selected from the group consisting of a bond, —O—, —S—, —NH—, —NHC(O)—, —C(O)NH—, —NR 15 —, —NR 15 C(O)—, —C(O)NR 15 —, —N(Z)—, —N(Z)C(O)—, and —C(O)N(Z)—;

each Z is independently selected from the group consisting of -L-R 13 and -L-R L ;

alternatively, —Y—Z is a member selected from the group consisting of —N(Z) 2 , —N(Z)C(O)Z, and —C(O)N(Z) 2 , and the two Z groups may optionally be linked to form a cycloalkynyl group;

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

each R L comprises a linking group and a biomolecule connected thereby, wherein the compound comprises at least one R L ; and

wherein said compound has a balanced charge.

24. A method of labeling a biomolecule, wherein said method comprises reacting a compound of claim 1 with a biomolecule.