Water soluble fluorescent or colored dyes and methods for their use
Compounds useful as fluorescent or colored dyes are disclosed. The compounds have the following structure (I): including stereoisomers, salts and tautomers thereof, R 1 , R 2 , R 3 , L 1 , L 2 , L 3 , L 4 , L 5 , L 6 , M 1 , M 2 , A, q, w and n are as defined herein. Methods associated with preparation and use of such compounds are also provided.
1. A compound having the following structure (IV):
wherein:
M 1 is, at each occurrence, independently a fluorescent or colored moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M 1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
L 1 , L 3 , and L 7 are, at each occurrence, independently optional alkylene or heteroalkylene linkers;
R 1 is, at each occurrence, independently H, alkyl or alkoxy;
R 2 is phospho, thiophospho, alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, or R 2 is a linker comprising a covalent bond to a biomolecule or microparticle;
R 3 is H, OH, SH, —NH 2 , alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, phosphate, thiophosphate, alkylphospho, alkylthiophospho, -Oalkylphospho, -Oalkylthiophospho, alkyletherphospho, alkyletherthiophospho, -Oalkyletherphospho, -Oalkyletherthiophospho phosphoalkyl, phosphoalkylether, thiophosphoalkyl, thiophosphoalkylether, -Ophosphoalkyl, O-phosphoalkylether, -Othiophosphoalkyl or -Othiophosphoalkylether;
R 4 is O − , S − , OZ, SZ or N(R 6 ) 2 , where Z is a cation and each R 6 is independently H or alkyl;
R 5 is oxo, thioxo or absent;
n is an integer from 1 to 20.
2. The compound of claim 1 , wherein R 2 is alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, wherein R 2 is optionally substituted with a substituent selected from —OH, —NH 2 , and —SH.
3. The compound of claim 2 , wherein R 2 has one of the following structures:
wherein:
R 2a is —OH, —SH, —NH 2 , phosphate or thiophosphate;
R 4a and R 4b are independently O − , S − , OZ or SZ, where Z is a cation;
R 5a and R 5b are independently oxo, or thioxo; and
a, b and c are each independently integers from 1 to 10.
4. The compound of 1 , wherein R 3 is OH.
5. The compound of claim 1 , wherein R 3 is, phosphate, thiophosphate, phospho, thiophospho, -Oalkylphospho, -Oalkylthiophospho, -Oalkyletherphospho, -Oalkyletherthiophosp ho, -Ophosphoalkyl, -Ophosphoalkylether, -Othiophosphoalkyl or -Othiophosphoalkylether optionally substituted with a substituent selected from —OH, —NH 2 , and —SH.
6. The compound of claim 5 , wherein R 3 has one of the following structures:
wherein:
R 3a is —OH, —SH, —NH 2 , phosphate or thiophosphate;
R 4a and R 4b are independently O − , S − , OZ or SZ, where Z is a cation;
R 5a and R 5b are independently oxo, or thioxo; and
b and c are each independently integers from 1 to 10.
7. The compound of claim 1 , wherein R 4 is O − and R 5 is oxo.
8. The compound of claim 1 , wherein L 1 , L 3 and L 7 are each alkylene linkers.
9. The compound of claim 1 , wherein L 1 and L 3 are each alkylene linkers and L 7 is absent.
10. The compound of claim 8 , wherein alkylene is methylene.
11. A compound having the following structure (Ih):
wherein:
M 1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
R 1 is H, C 1 -C 6 alkyl or alkoxy;
R 2 is H, an electron pair or a cation;
R 3 is OH;
R 4 is O − , S − , OZ, SZ where Z is a cation;
R 5 is oxo or thioxo;
R 7 , R 8 , R 9 , R 10 , R 11 and R 12 are, at each occurrence, independently H or alkyl; and
x, y and z are, at each occurrence, independently an integer from 0 to 5.
12. The compound of claim 11 , wherein x, y and z are each 1.
13. The compound of claim 11 , wherein x is 0 and y and z are each 1.
14. The compound of claim 1 , wherein at least one M 1 is, is a moiety comprising four or more aryl or heteroaryl rings, or combinations thereof.
15. The compound of claim 1 , wherein at least one M 1 is a dimethylaminostilbene, quinacridone, fluorophenyl-dimethyl-BODIPY, his-fluorophenyl-BODIPY, acridine, terrylene, sexiphenyl, porphyrin, benzopyrene, (fluorophenyl-dimethyl-difluorobora-diaza-indacene)phenyl, (bis-fluorophenyl-difluorobora-diaza-indacene)phenyl, quaterphenyl, bi-benzothiazole, ter-benzothiazole, bi-naphthyl, bi-anthracyl, squaraine, squarylium, 9,10-ethynylanthracene or ter-naphthyl moiety.
16. The compound of claim 1 , wherein at least one M 1 is p-terphenyl, perylene, azobenzene, phenazine, phenanthroline, acridine, thioxanthrene, chrysene, rubrene, coronene, cyanine, perylene imide, or perylene amide or derivative thereof.
17. The compound of claim 1 , wherein at least one M 1 is a coumarin dye, resorufin dye, dipyrrometheneboron difluoride dye, ruthenium bipyridyl dye, energy transfer dye, thiazole orange dye, polymethine or N-aryl-1,8-naphthalimide dye.
18. The compound of claim 1 , wherein each M 1 is pyrene, perylene, perylene monoimide or 6-FAM or derivative thereof.
19. The compound of claim 1 , wherein M 1 has one of the following structures:
20. A method for visually detecting a biomolecule, the method comprising:
(a) admixing the compound of claim 1 , with one or more biomolecules; and
(b) detecting the compound by its visible properties.