Cyanine dyes

1. A cyanine compound having the structure of Formula (I) or (II):

wherein

n is an integer selected from 1, 2 and 3;

e is an integer selected from 0, 1 and 2;

R f , R g , R h , and R i are members independently selected from halogen, substituted or unsubstituted alkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heteroalkyl, or a bond to M;

R c , and R d are independently selected from a bond to M, and alkyl substituted with a member selected from sulfonic acid, carboxylic acid, phosphonic acid, phosphoric acid and heteroalkyl, substituted with a member selected from sulfonic acid, carboxylic acid, phosphonic acid, phosphoric acid;

R a and R e , are independently selected from C(O)R 9 , OR 12 , NR 12 R 13 , CR 12 C(O)R 13 , NR 12 C(O) 2 R 13 , SO 3 H, and C(O)NR 12 R 13 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and a bond to M,

wherein

R 9 is a member selected from OR 10 , and a bond to M

wherein

R 10 is a member selected from H and substituted or unsubstituted alkyl; and

R 12 and R 13 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and a bond to M,

wherein

M comprises a linker bound to a carrier molecule, and at least one of R a , R c , R d , R e , R f , R g , R h , R i , R 9 , R 12 and R 13 is a bond to M.

2. The cyanine compound according to claim 1 , wherein said linker bound to a carrier molecule is a linker bound to a moiety having the structure of Formula III:

wherein

u is an integer selected from 1, 2, 3, 4, 5, 6, 7 and 8;

r is 0 or 1; and

Y is a nucleobase.

3. The cyanine compound according to claim 1 , said compound having the structure of Formula IV:

4. The cyanine compound of claim 1 , wherein the linker of the M moiety comprises the structure C(O)NH(CH 2 ) t , wherein the index t is an integer selected from 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12.

5. The cyanine compound of claim 1 , wherein the linker of the M moiety comprises a polyvalent scaffold.

6. The cyanine compound according to claim 5 , wherein said polyvalent scaffold is a polyvalent arylene scaffold.

7. The cyanine compound of claim 5 , wherein the polyvalent scaffold comprises a second cyanine moiety bound thereto, said second cyanine moiety having a structure according to Formula I or Formula II.

8. The cyanine compound of claim 1 , wherein the linker of the M moiety comprises biotin bound to streptavidin.

9. A cyanine compound according to one of the following formulae:

wherein M comprises a linker bound to a carrier molecule.

10. A cyanine compound according to one of the following formulae:

wherein Y is a nucleobase.

11. The cyanine compound according to claim 1 , having the formula:

M-(R D ) 2

wherein

each R D has a structure independently selected from Formula I and Formula II.

12. The cyanine compound according to claim 6 , wherein M comprises the polyvalent arylene scaffold moiety:

13. The cyanine compound according to claim 12 , having the formula:

wherein

each R D has a structure independently selected from Formula I and Formula II.

14. The cyanine compound according to claim 2 , having at least one Y moiety comprising a natural nucleobase.

15. The cyanine compound according to claim 1 , wherein the carrier molecule comprises a member selected from a nucleic acid, a protein, a glycoprotein, a peptide, a saccharide, a hormone, a receptor, an antigen, a substrate, metabolite, a transition state analog, a cofactor, an inhibitor, a drug, a dye, a nutrient, and a growth factor.

16. The cyanine compound according to claim 1 , wherein the carrier molecule comprises a member selected from a solid support, a virus and a microorganism.

17. A method of monitoring an enzyme reaction, said method comprising:

(a) forming a reaction mixture by contacting said enzyme with a cyanine compound according to claim 1 , wherein said cyanine compound is a substrate for said enzyme under conditions sufficient for said enzyme and said cyanine compound to react; and

(b) monitoring fluorescence of said reaction mixture, thereby monitoring said enzyme reaction.

18. The method according to claim 17 , wherein said enzyme is a DNA polymerase and said cyanine compound comprises a nucleic acid moiety, which is said substrate for said enzyme.

19. The method according to claim 17 , wherein said enzyme reaction is template directed DNA synthesis.

20. The method according to claim 17 , wherein said reaction is a component of a single molecule DNA sequencing analysis.

21. A cyanine compound according to formula II:

wherein

n is an integer selected from 1, 2 and 3;

e is an integer selected from 0, 1 and 2;

R f , R g , R h , and R i are members independently selected from halogen, substituted or unsubstituted alkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heteroalkyl, or a bond to M;

R c , and R d are independently selected from a bond to M, and alkyl substituted with a member selected from sulfonic acid, carboxylic acid, phosphonic acid, phosphoric acid and heteroalkyl, substituted with a member selected from sulfonic acid, carboxylic acid, phosphonic acid, phosphoric acid;

R a and R e , are independently selected from C(O)R 9 , OR 12 , NR 12 R 13 , CR 12 C(O)R 13 , NR 12 C(O) 2 R 13 , SO 3 H, and C(O)NR 12 R 13 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and a bond to M,

wherein

R 9 is a member selected from OR 10 , and a bond to M

wherein

R 10 is a member selected from H and substituted or unsubstituted alkyl; and

R 12 and R 13 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and a bond to M,

wherein

M comprises a linker bound to a carrier molecule.