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, wherein 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 water soluble, oligomeric dye compound having the following structure:
wherein:
M 1 is, at each occurrence, independently a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
L 1 , L 2 , and L 3 are, at each occurrence, independently optional linkers comprising atoms selected from C, O, S, N and P;
R 1 is, at each occurrence, independently H, alkyl, or alkoxy;
R 2 and R 3 are independently H, OH, SH, NH 2 , alkyl, alkylether, hydroxlalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, phosphate, thiophosphate, alkylphospho, alkylthiophospho, —Oalkylphospho, —Oalkylthiophospho, alkyletherphospho, alkyletherthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho phosphoalkyl, phosphoalkylether, thiophosphoalkyl, thiophosphoalkylether, —Ophosphoalkyl, O-phosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether or a linker comprising a covalent bond to a biomolecule or microparticle; and
n is an integer from 2 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 claim 1 , wherein R 2 is a linker comprising a covalent bond to a biomolecule or microparticle, and R 3 is H, OH, phosphate, thiophosphate, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether.
5. The compound of claim 4 , wherein R 2 is a linker comprising a covalent linkage to a biomolecule.
6. The compound of claim 5 , wherein the biomolecule is a nucleic acid, amino acid or a polymer thereof.
7. The compound of claim 5 , wherein the biomolecule is an enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer or prion.
8. The compound of claim 1 , wherein at least one occurrence of L 3 is a heteroalkylene linker.
9. The compound of claim 1 , wherein L 3 , at each occurrence, comprises an alkylenether.
10. The compound of claim 1 , wherein L 3 comprises at least one —O—P—O— bond and at least one an alkylenether.
11. The compound of claim 1 , wherein L 3 comprises the following structure:
12. The compound of claim 1 , wherein M 1 is, at each occurrence, independently fluorescent or colored.
13. The compound of claim 1 , wherein M 1 has one of the following structures:
14. The compound of claim 1 , wherein n is an integer from 2 to 5.
15. The compound of claim 1 , wherein L 1 is a methylene linker.
16. The compound of claim 1 , wherein R 1 is H.
17. A method of staining a sample, comprising adding to the sample a compound of claim 1 in an amount sufficient to produce an optical response when the sample is illuminated at an appropriate wavelength.
18. A method for visually detecting a biomolecule, the method comprising:
a) providing the compound of claim 1 ; and
b) detecting the compound by its visible properties.
19. 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.
20. A composition comprising the compound of claim 1 and one or more biomolecules.