Ultra bright dimeric or polymeric dyes
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 2 , L 3 , L 4 , M, m 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 (I):
or a stereoisomer, salt or tautomer thereof, wherein:
M is, at each occurrence, independently a moiety comprising two or more carbon-carbon double bonds and at least one degree of conjugation, and at least one occurrence of M is a moiety comprising three or more rings selected from aryl and heteroaryl rings;
L 1 is, at each occurrence, independently a linker comprising an alkene, ester, amide, thioester, disulfide, carbocyclic, heterocyclic or heteroaryl group;
L 2 and L 3 are, at each occurrence, independently an optional alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, heteroalkynylene or heteroatomic linker;
L 4 is, at each occurrence, independently an alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene or heteroalkynylene linker;
R 1 is, at each occurrence, independently H, alkyl or alkoxy;
one of R 2 and R 3 is OH or —OP(═R a )(R b )R c , and the other one of R 2 and R 3 is Q, a linker comprising a covalent bond to Q, a linker comprising a covalent bond to an analyte molecule or a linker comprising a covalent bond to a solid support, wherein: R a is O or S; R b is OH, SH, O − , S − , OR d or SR d ; R c is OH, SH, O − , S − , OR d , SR d , alkyl, alkoxy, alkylether, alkoxyalkylether, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether; and R d is a counter ion;
R 4 is, at each occurrence, independently OH, SH, O − , S − , OR d or SR d ;
R 5 is, at each occurrence, independently oxo, thioxo or absent;
Q is, at each occurrence, independently a moiety comprising a sulfhydryl, disulfide, activated ester, isothiocyanate azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, α-haloamide, biotin, amino or maleimide functional group;
m is, at each occurrence, independently an integer of zero or greater, wherein at least one occurrence of m is an integer of two or greater; and
n is an integer of one or greater.
2. The compound of claim 1 , wherein for at least one occurrence of L 1 , the functional group can be formed by reaction of an alkyne and azide.
3. The compound of claim 1 , wherein the compound has the following structure (IC):
wherein:
x 1 , x 2 , x 3 and x 4 are, at each occurrence, independently an integer from 0 to 6; and
y is, at each occurrence, independently an integer from 1 to 6.
4. The compound of claim 1 , wherein the compound has one of the following structures (ID) or (IE):
5. The compound of claim 1 , wherein one of R 2 or R 3 is OH or —OP(═R a )(R b )R c , and the other of R 2 or R 3 is Q or a linker comprising a covalent bond to Q.
6. The compound of claim 1 , wherein Q has one of the following structures:
wherein
X is halo; and
EWG is an electron withdrawing group.
7. The compound of claim 1 , wherein one of R 2 and R 3 is OH or —OP(═R a )(R b )R c , and the other of R 2 and R 3 is a linker comprising a covalent bond to an analyte molecule or a linker comprising a covalent bond to a solid support.
8. The compound of claim 7 , wherein the analyte molecule is an enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer or prion.
9. The compound of claim 1 , wherein m is, at each occurrence, independently an integer from 3 to 10.
10. The compound of claim 1 , wherein m is, at each occurrence, independently an integer from 7 to 9.
11. The compound of claim 1 , wherein M is, at each occurrence, independently fluorescent or colored.
12. The compound of claim 1 , wherein M is, at each occurrence, independently 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, thioxanthrene, chrysene, rubrene, coronene, cyanine, perylene imide, perylene amide, coumarin dye, resorufin dye, dipyrrometheneboron difluoride dye, ruthenium bipyridyl dye, energy transfer dye, thiazole orange dye, polymethine or N-aryl-1,8-naphthalimide dye moiety.
13. The compound of claim 1 , wherein M is, at each occurrence, independently pyrene, perylene, perylene monoimide or 6-FAM or derivative thereof.
14. The compound of claim 1 , wherein M, at each occurrence, independently has one of the following structures:
15. The compound of claim 1 , wherein the compound is selected from one of the following compounds:
wherein:
L 1 is, at each occurrence, independently a linker comprising a functional group capable of formation by reaction of two complementary reactive groups;
F has the following structure:
E has the following structure:
Y has the following structure:
16. A method of staining a sample, comprising adding to said sample the compound of claim 1 in an amount sufficient to produce an optical response when said sample is illuminated at an appropriate wavelength.
17. A method for visually detecting an analyte molecule, the method comprising:
(a) providing the compound of claim 1 , wherein R 2 or R 3 is a linker comprising a covalent bond to the analyte molecule; and
(b) detecting the compound by its visible properties.
18. A method for visually detecting an analyte molecule, the method comprising:
(a) admixing the compound of claim 1 , wherein R 2 or R 3 is Q or a linker comprising a covalent bond to Q, with the analyte molecule;
(b) forming a conjugate of the compound and the analyte molecule; and
(c) detecting the conjugate by its visible properties.
19. A composition comprising the compound of claim 1 and one or more analyte molecules.
20. The compound of claim 1 , wherein the analyte molecule is a nucleic acid, a nucleic acid polymer, an amino acid or an amino acid polymer.