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, L 1 , L 2 , L 3 , L 4 , M, M′, m 1 , m 2 , n, x, y and z 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 salt or tautomer thereof, wherein:
M is, at each occurrence, independently a monovalent moiety comprising two or more carbon-carbon double bonds and at least one degree of conjugation;
M′ is, at each occurrence, independently a divalent moiety having one of the following structures:
L is, at each occurrence, independently an alkylene or alkenylene linker, wherein the alkylene or alkenylene linker is unsubstituted;
L 2 and L 3 are, at each occurrence, independently an optional alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, heteroalkynylene or heteroatomic linker;
L 1 is at each occurrence, independently either: i) an optional alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, heteroalkynylene or heteroatomic linker; or ii) a linker comprising a functional group capable of formation by reaction of two complementary reactive groups;
L 4 is, at each occurrence, independently an alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, carbocyclic or heterocyclic linker;
R 1 is, at each occurrence, independently H, alkyl or alkoxy;
R 2 and R 3 are each independently H, OH, SH, alkyl, alkoxy, alkylether, heteroalkyl, —OP(═R a )(R b )R c , Q or L′;
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;
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 , OL′, SR d , alkyl, alkoxy, heteroalkyl, heteroalkoxy, alkylether, alkoxyalkylether, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether;
R d is a counter ion;
Q is, at each occurrence, independently a moiety comprising a reactive group, or protected analogue thereof, capable of forming a covalent bond with an analyte molecule, a targeting moiety, a solid support or a complementary reactive group Q′;
L′ is, at each occurrence, independently a linker comprising a covalent bond to Q, a linker comprising a covalent bond to a targeting moiety, a linker comprising a covalent bond to an analyte molecule, a linker comprising a covalent bond to a solid support, a linker comprising a covalent bond to a solid support residue, a linker comprising a covalent bond to a nucleoside or a linker comprising a covalent bond to a further compound of structure (I);
m 1 and m 2 are, at each occurrence, independently an integer of zero or greater;
n, x and y are each independently an integer of zero or greater for each integral value of z; and
z is an integer of 1 or greater,
provided that x is 1 or greater for at least one integral value of z, and at least one of n or y is 1 or greater for at least one integral value of z.
2. The compound of claim 1 , having the following structure (IA):
wherein y is an integer of 1 or greater.
3. The compound of claim 1 , wherein M′, at each occurrence, has the following structure:
4. The compound of claim 1 , wherein R 4 is, at each occurrence, independently OH, O − or OR d .
5. The compound of claim 1 , wherein R 5 is, at each occurrence, oxo.
6. The compound of claim 1 , wherein R 2 and R 3 are each independently OH or —OP(═R a )(R b )R c .
7. 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.
8. The compound of claim 1 , wherein Q is a moiety having one of the following structures:
9. 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 a linker comprising a covalent bond to an enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer or prion or a linker comprising a covalent bond to a solid support.
10. The compound of claim 1 , wherein M is, at each occurrence, independently a dimethylaminostilbene, quinacridone, fluorophenyl-dimethyl-BODIPY, bis-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.
11. The compound of claim 1 , wherein M is, at each occurrence, independently pyrene, perylene, perylene monoimide or 6-carboxyfluorescein (6-FAM) or a derivative thereof.
12. The compound of claim 1 , wherein M, at each occurrence, independently has one of the following structures:
13. A compound having the following structure:
wherein y is an integer greater than 1.
14. 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.
15. 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.
16. A method for determining the presence of dead cells in a sample, the method comprising contacting the sample with a compound of claim 1 , thereby binding or associating the compound with the dead cells, and observing a fluorescent signal from the compound bound or associated with the dead cells.
17. A composition comprising a compound of claim 1 and a cyclodextrin.