Fluorescent dyes and related methods

1. A compound having the general formula (I):

wherein

each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted, methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl,

or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;

each of R 3A , R 3B , R 3C , R 3D , R 3E and R 3F are independently selected from the group consisting of hydrogen, a halide, —OH, —NH 2 , —CN, —SH, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;

R 4A and R 4D are hydrogen;

each of R 4B and R 4C are independently hydrogen or —CN;

and salts and isomers thereof;

or the general formula (II):

wherein

each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl,

or wherein R 1 and R 2 are joined together to form substituted or unsubstituted heterocycloalkyl, or substituted or unsubstituted heteroaryl;

each of R 3A , R 3B , R 3C , R 3D , R 3E and R 3F are independently selected from the group consisting of hydrogen, a halide, —OH, —NH 2 , —CN, —SH, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;

R 4A , R 4D are hydrogen;

each of R 4B and R 4C are independently hydrogen or —CN;

R 5 is selected from the group consisting of a halide, —CN, —NO 2 , fluorinated alkyl, fluorinated heteroalkyl, fluorinated acyl, fluorinated alkoxy, fluorinated cycloalkyl, fluorinated heterocycloalkyl, fluorinated aryl, fluorinated heteroaryl, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted acyl, unsubstituted alkoxy, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, and unsubstituted heteroaryl;

and salts and isomers thereof;

provided that

when R 4A , R 4B , R 4C and R 4D are hydrogen, R 1 and R 2 are not phenyl.

2. The compound of claim 1 , wherein each of R 1 and R 2 are independently selected from substituted or unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, unsubstituted acyl, substituted or unsubstituted alkoxy, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, substituted or unsubstituted aryl, and unsubstituted heteroaryl.

3. The compound of claim 1 , wherein each of R 1 and R 2 are unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.

4. The compound of claim 1 , wherein R 5 is unsubstituted C 1 -C 10 alkyl.

5. The compound of claim 1 , wherein R 5 is selected from the group consisting of substituted or unsubstituted alkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, and substituted or unsubstituted aryl.

6. The compound of claim 1 , wherein the compound of general formula (II) comprises a salt including a counterion selected from the group consisting of a halide, acetate, halogen-substituted acetate and tosylate.

7. The compound of claim 1 , wherein the compound of general formula (II) comprises a salt including a counterion selected from the group consisting of a halide, acetate and trifluoroacetate.

8. The compound of claim 1 , wherein the compound of general formula (II) comprises a salt including a counterion selected from the group consisting of I − , O(C═O)CH 3 − , and O(C═O)CF 3 − .

9. The compound of claim 1 , having any one of the following formulas:

10. A method for detecting a nucleic acid molecule in a sample, the method comprising:

combining the sample and a compound to form a complex including the compound and the nucleic acid molecule; and

detecting the nucleic acid molecule the complex including the compound and the nucleic acid molecule, thereby detecting the nucleic acid molecule,

wherein the compound has the genera formula (I):

wherein

each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl,

or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;

each of R 3A , R 3B , R 3C , R 3D , R 3E and R 3F are independently selected from the group consisting of hydrogen, a halide, —OH, —NH 2 , —CN, —SH, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;

R 4A , R 4D are hydrogen;

each of R 4B and R 4C are independently hydrogen or —CN;

and salts and isomers thereof;

or the general formula (II):

wherein

each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl,

or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;

each of R 3A , R 3B , R 3C , R 3D , R 3E and R 3F are independently selected from the group consisting of hydrogen, a halide, —OH, —NH 2 , —CN, —SH, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;

R 4A , R 4B are hydrogen;

each of R 4C and R 4D are independently hydrogen or —CN;

R 5 is selected from the group consisting of a halide, —CN, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;

and salts and isomers thereof;

provided that

when R 4A , R 4B , R 4C and R 4D are hydrogen, R 1 and R 2 are not phenyl.

11. The method of claim 10 , wherein each of R 1 and R 2 are independently selected from substituted or unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, unsubstituted acyl, substituted or unsubstituted alkoxy, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, substituted or unsubstituted aryl, and unsubstituted heteroaryl.

12. The method of claim 10 , wherein each of R 1 and R 2 are unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.

13. The method of claim 10 , wherein R 5 is fluorinated alkyl, fluorinated heteroalkyl, fluorinated acyl, fluorinated alkoxy, fluorinated cycloalkyl, fluorinated heterocycloalkyl, fluorinated aryl, or fluorinated heteroaryl.

14. The method of claim 10 , wherein R 5 is unsubstituted C 1 -C 10 alkyl.

15. The method of claim 10 , wherein R 5 is selected from the group consisting of substituted or unsubstituted alkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, and substituted or unsubstituted aryl.

16. The method of claim 10 , wherein the compound of general formula (II) comprises a salt including a counterion selected from the group consisting of a halide, acetate, halogen-substituted acetate and tosylate.

17. The method of claim 10 , wherein the compound of general formula (II) comprises a salt including a counterion selected from the group consisting of halide, acetate and trifluoroacetate.

18. The method of claim 10 , having any one of the following formulas:

19. A method of determining a quantity of a nucleic acid molecule in a sample, the method comprising:

contacting the nucleic acid molecule in the sample with a compound to form a complex including the compound and the nucleic acid molecule; and

determining the quantity of the nucleic acid molecule in the sample by at least measuring an amount of the compound complexed with the nucleic acid molecule,

wherein the compound has the general formula (I):

wherein

each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl,

or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;

each of R 3A , R 3B , R 3C , R 3D , R 3E and R 3F are independently selected from the group consisting of hydrogen, a halide, —OH, —NH 2 , —CN, —SH, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;

R 4A , R 4D are hydrogen;

each of R 4B and R 4C are independently hydrogen or —CN;

and salts and isomers thereof;

or the general formula (II):

wherein

each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl,

or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;

each of R 3A , R 3B , R 3C , R 3D , R 3E and R 3F are independently selected from the group consisting of hydrogen, a halide, —OH, —NH 2 , —CN, —SH, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;

R 4A , R 4D are hydrogen;

each of R 4B and R 4C are independently hydrogen or —CN;

R 5 is selected from the group consisting of a halide, —CN, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;

and salts and isomers thereof;

provided that

when R 4A , R 4B , R 4C and R 4D are hydrogen, R 1 and R 2 are not phenyl.

20. The method of claim 19 , wherein the determining comprises measuring an amount of fluorescence emission from the compound complexed with the nucleic acid molecule, wherein the amount of fluorescence emission corresponds to the amount of the compound complexed with the nucleic acid molecule.

21. The compound of claim 1 , wherein

each of R 1 and R 2 are independently hydrogen, substituted or unsubstituted-methyl, ethyl, propyl, isopropyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, and substituted or unsubstituted heteroaryl,

or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl.

22. The compound of claim 1 , wherein

each of R 1 and R 2 are independently hydrogen, methyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, and substituted or unsubstituted heteroaryl,

or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl.

23. The compound of claim 1 , wherein R 5 is selected from the group consisting of substituted or unsubstituted alkyl and substituted or unsubstituted acyl.

24. The compound of claim 1 , wherein

each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted methyl, ethyl, hexyl, heptyl, octyl, nonyl, decyl and unsubstituted acyl,

or wherein R 1 and R 2 are joined together to form an unsubstituted heterocycloalkyl.

25. The compound of claim 1 , wherein

each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted methyl, ethyl, hexyl, heptyl, octyl, nonyl, decyl and unsubstituted acyl,

or wherein R 1 and R 2 are joined together to form an unsubstituted heterocycloalkyl; and

R 5 is selected from the group consisting of substituted or unsubstituted alkyl and substituted or unsubstituted acyl.

26. The compound of claim 1 , wherein

each of R 1 and R 2 are independently hydrogen or unsubstituted methyl; and

R 5 is selected from the group consisting of R 5 is unsubstituted C 1 -C 10 alkyl and substituted or unsubstituted acyl.