Fluorescent imaging with substituted cyanine dyes

1. A compound of Formula I:

wherein

Q is a portion of a polymethine bridge having the formula:

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

each R 1 is a member selected from the group consisting of -L-Y—Z and an alkyl that is additionally substituted with from 0 to 1 R 14 and from 0 to 1 -L-Y—Z; 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, or sulfonatoalkyl; wherein a carbon of the member is additionally substituted with from 0 to 1 -L-Y—Z; or, alternatively, an 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 -L-Y—Z, or an exocyclic alkene, wherein the exocyclic alkene is additionally substituted with from 0 to 2 R 14 and from 0 to 1 -L-Y—Z;

each R 3 , R 4 , R 5 , and R 6 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 13 or from 0 to 1 -L-Y—Z; or, alternatively, a pair of said members that is selected from the group consisting of an R 3 and R 4 , an R 4 and R 5 , and an R 5 and R 6 , 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 -L-Y—Z;

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 -L-Y—Z; 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 -L-Y—Z;

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 at least one member selected from the group consisting of R 8 , R 9 , and R 10 is halo;

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

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

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 ;

or 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 o-diarylphosphino 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 1 , 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 a member independently selected from the group consisting of azido, alkynyl, cycloalkynyl, a pegylated azido, a pegylated alkynyl, a pegylated cycloalkynyl, and an o-diarylphosphino aryl ester.

5. The compound of claim 1 , wherein at least one member selected from the group consisting of R 8 , R 9 , and R 10 is chloro or fluoro.

6. The compound of claim 5 , wherein at least one member selected from the group consisting of R 8 , R 9 , and R 10 is fluoro.

7. The compound of claim 5 , wherein at least one member selected from the group consisting of R 8 , R 9 , and R 10 is chloro.

8. The compound of claim 1 , wherein each R 3 , R 4 , R 5 , and R 6 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 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.

10. The compound of claim 9 , wherein r is 2, 3, or 4.

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

12. The compound of claim 1 , wherein R 8 , R 9 , or R 10 is -L-Y—Z.

13. The compound of claim 12 , wherein L is (CH 2 ) t or (CH 2 ) t X(CH 2 ) s

wherein Y is a bond;

wherein Z is carboxyl or activated acyl;

wherein t is an integer from 0 to 10;

wherein s is an integer from 0 to 10;

wherein the sum of s and t is at most 14; and

wherein X is a heteroatom selected from the group consisting of O, S, or NR 15 .

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

wherein M is a cationic counterion.

15. The compound of claim 14 , wherein M is a hydrogen or an alkali metal ion.

16. The compound of claim 1 , wherein R 8 , R 9 , R 10 , R 11 , and R 12 are each a member independently selected from the group consisting of hydrogen, alkyl, alkoxyalkyl, carboxyalkyl, alkoxycarbonyl, alkoxycarbonylalkyl, amido, halo, and sulfonato.

17. The compound of claim 1 , wherein 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; and

wherein said ring is additionally substituted with from 0 to 3 R 14 ; and from 0 to 1 -L-Y—Z.

18. The compound of claim 17 , wherein both R 7 , together with the intervening segment of the polyene to which both R 7 are bonded, join to form a ring selected from the group consisting of a five-membered ring and a six-membered ring, wherein said ring is additionally substituted with from 0 to 3 R 14 .

19. A method of imaging, wherein said method comprises administering a compound of claim 1 to a tissue or organism; and deleting optical responses to thereby image said tissue or organism.