SULFONATED FLUOROPHORE COMPOUNDS

1 . A compound, or a salt thereof, having the formula:

wherein

R 1 is hydrogen, halogen, —CX 1 3 , —CHX 1 2 , —CH 2 X 1 , —OCX 1 3 , —OCH 2 X 1 , —OCHX 1 2 ,

—CN, —SO n1 R 1D , —SO v1 NR 1A R 1B , —NR 1C NR 1A R 1B ,

—ONR 1A R 1B , —NR 1C C(O)NR 1A R 1B , —N(O) m1 ,

—NR 1A R 1B , —C(O)R 1C , —C(O)OR 1C , —OC(O)R 1C , —OC(O)OR 1C , —C(O)NR 1A R 1B , —OC (O)NR 1A R 1B ,

—OR 1D , —SR 1D , —NR 1A SO 2 R 1D , —NR 1A C(O)R 1C , —NR 1A C(O)OR 1C , —NR 1A OR 1C , —SF 5 , —N 3 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;

R 2 is hydrogen, halogen, —CX 2 3 , —CHX 2 2 , —CH 2 X 2 , —OCX 2 3 , —OCH 2 X 2 , —OCHX 2 2 ,

—CN, —SO n2 R 2D , —SO v2 NR 2A R 2B , NR 2C NR 2A R 2B ,

—ONR 2A R 2B , —NR 2C C(O)NR 2A R 2B , —N(O) m2 ,

—NR 2A R 2B , —C(O)R 2C , —C(O)OR 2C , —OC(O)R 2C , —OC(O)OR 2C , —C(O)NR 2A R 2B , —OC (O)NR 2A R 2B ,

—OR 2D , —SR 2D , —NR 2A SO 2 R 2D , —NR 2A C(O)R 2C , —NR 2A C(O)OR 2C , —NR 2A OR 2C , —SF 5 , —N 3 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;

R 1A , R 1B , R 1C , R 1D , R 2A , R 2B , R 2C , and R 2D are independently hydrogen, —CCl 3 ,

—CBr 3 , —CF 3 , —CI 3 , —CHCl 2 , —CHBr 2 , —CHF 2 , —CHI 2 , —CH 2 Cl, —CH 2 Br, —CH 2 F, —CH 2 I, —CN, —OH,

—NH 2 , —COOH, —CONH 2 , —OCCl 3 , —OCF 3 , —OCBr 3 , —OCI 3 , —OCHCl 2 , —OCHBr 2 , —O CHI 2 ,

—OCHF 2 , —OCH 2 Cl, —OCH 2 Br, —OCH 2 I, —OCH 2 F, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R 1A and R 1B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R 1A and R 2B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;

each X 1 and X 2 is independently —F, —Cl, —Br, or —I;

n1 and n2 are independently an integer from 0 to 4; and

m1, m2, v, and v2 are independently 1 or 2.

2 . The compound of claim 1 , having the formula:

3 . The compound of claim 1 , having the formula:

4 . The compound of claim 1 , wherein R 1 is —OR 1D , —NR 1A R 1B , or substituted or unsubstituted 2 to 16 membered heteroalkyl.

5 . The compound of claim 1 , wherein R 1 is —OH or

6 . The compound of claim 1 , wherein R 2 is —SR 2D or substituted or unsubstituted 2 to 16 membered heteroalkyl.

7 . The compound of claim 1 , wherein R 2 is

8 . A biomolecule covalently attached to a compound, wherein the compound has the formula:

where L is a covalent linker.

9 . The biomolecule of claim 8 , wherein the biomolecule is streptavidin.

10 . The biomolecule of claim 8 , wherein the biomolecule is an oligonucleotide.

11 . The biomolecule of claim 8 , wherein L 1 comprises a substituted alkylene or heteroalkylene.

12 . The biomolecule of claim 8 , wherein L 1 is

13 . A method of detecting the presence of an agent, wherein said agent is covalently bound to a monovalent form of the compound of claim 1 , or a salt thereof, and wherein said agent is an oligonucleotide, protein, or compound.

14 . The method of claim 13 , wherein said agent is an oligonucleotide.

15 . The method of claim 13 , wherein said agent is a protein.