Water soluble fluorescent or colored dyes comprising conjugating groups
Compounds useful as fluorescent or colored dyes are disclosed. The compounds have the following structure (I): or a stereoisomer, tautomer or salt thereof, wherein R 1 , R 2 , R 3 , R 4 , R 5 , L 1 , L 3 , L 4 , L 6 , L 7 , L 8 , M 1 , M 2 , 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 (Ia):
or a salt or stereoisomer thereof, 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 fluorescent or colored moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
L 1 is, at each occurrence, independently an optional alkylene linker;
L 3 and L 7 are, at each occurrence, independently alkylene linkers;
R 1 is, at each occurrence, independently H, alkyl or alkoxy;
R 2 is -L 9 -(L 10 ) z -L 11 -Q;
R 3 is OH, SH, —NH 2 , alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, cyanoalkyl, —Oaralkyl, phosphate, thiophosphate, alkylphospho, alkylthiophospho, —Oalkylphospho, —Oalkylthiophospho, alkyletherphospho, alkyletherthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho phosphoalkyl, phosphoalkylether, thiophosphoalkyl, thiophosphoalkylether, —Ophosphoalkyl, —Ophosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether;
R 4 is, at each occurrence, independently O − , or OZ, where Z is a cation;
R 5 is, at each occurrence, independently oxo;
L 9 is an optional C 1 -C 6 alkylene linker;
L 11 is an optional linker;
(L 10 ) z has one of the following structures:
where b is an integer from 2 to 10;
Q is sulfhydryl, disulfide, activated ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, α-haloamide, biotin, amino or a maleimide; and
n is an integer from 1 to 20.
2. The compound of claim 1 , wherein the compound has the following structure (Ia):
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 fluorescent or colored moiety comprising four or more aryl or heteroaryl rings, or combinations thereof;
L 1 is, at each occurrence, independently an alkylene linker;
L 7 and L 3 are, at each occurrence, independently alkylene linkers;
R 1 is, at each occurrence, independently H, alkyl or alkoxy;
R 2 is -L 9 -(L 10 ) z -L 11 -Q;
R 3 is OH, SH, —NH 2 , alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, cyanoalkyl, —Oaralkyl, phosphate, thiophosphate, alkylphospho, alkylthiophospho, —Oalkylphospho, —Oalkylthiophospho, alkyletherphospho, alkyletherthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho phosphoalkyl, phosphoalkylether, thiophosphoalkyl, thiophosphoalkylether, —Ophosphoalkyl, —Ophosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether;
R 4 is, at each occurrence, independently O − , or OZ, where Z is a cation;
R 5 is, at each occurrence, independently oxo;
L 9 is an optional C 1 -C 6 alkylene linker;
L 11 is an optional linker;
(L 10 ) z has one of the following structures:
where b is an integer from 2 to 10;
Q is sulfhydryl, disulfide, activated ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, α-haloamide, biotin, amino, or a maleimide; and
n is an integer from 1 to 10.
3. The compound of claim 2 , wherein the compound has the following structure (Ib):
wherein:
R 7 , R 8 , R 9 , R 10 , R 11 and R 12 are, at each occurrence, independently H or alkyl; and
x 1 , y 1 and z 1 are, at each occurrence, independently an integer from 0 to 5.
4. The compound of claim 1 , wherein R 2 is -L 9 -(L 10 ) z -L 11 -Q, and R 3 is OH or phosphate.
5. The compound of claim 1 , wherein R 2 is -L 9 -(L 10 ) z -L 11 -Q, and R 3 is phosphate, thiophosphate, phospho, thiophospho, —Oalkylphospho, —Oalkylthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho, —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 n is an integer from 2 to 15.
8. The compound of claim 1 , wherein each M 1 comprises a fluorescent or colored fused-multicyclic aryl moiety.
9. 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,ter-naphthyl, p-terphenyl, perylene, azobenzene, phenazine, phenanthroline, acridine, thioxanthrene, chrysene, rubrene, coronene, cyanine, perylene imide, perylene amide, 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.
10. The compound of claim 1 , wherein Q has one of the following structures:
11. The compound of claim 1 , wherein M 1 has one of the following structures:
12. The compound of claim 1 , having one of the following structures:
or a salt or stereoisomer thereof.
13. 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.