Compositions comprising a polymeric dye and a cyclodextrin and uses thereof
Compositions comprising a polymeric dye and a cyclodextrin are provided. Methods associated with preparation and use of such compounds, for example in methods for detection of any analyte molecule, are also provided.
1. A composition comprising a polymeric dye and a cyclodextrin, wherein the polymeric dye is a compound having the following structure (I):
or a stereoisomer, salt or tautomer thereof, wherein:
M is, at each occurrence, independently a bivalent pyrene, 6-FAM, 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 moiety, p-terphenyl, perylene, azobenzene, phenazine, phenanthroline, acridine, thioxanthrene, chrysene, rubrene, coronene, cyanine, perylene imide, perylene monoimide, 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;
L 1 is at each occurrence, independently an optional alkylene or heteroalkylene linker;
L 3 is, at each occurrence, independently an optional alkylene linker;
L 4 is, at each occurrence, independently an alkylene oxide linker of greater than three atoms in length;
R 2 and R 3 are each independently H, OH, SH, alkyl, alkoxy, alkylether, heteroalkyl, —OP(═R a )(R b )R c , Q, or a protected form thereof, or L′;
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 sulfhydryl, disulfide, N-succinimide ester, imidoester, polyfluorophenyl ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, α-haloamide, biotin, amino or maleimide functional group;
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 is, at each occurrence, independently an integer of zero or greater, provided that at least one occurrence of m is an integer of one or greater; and
n is an integer of one or greater.
2. The composition of claim 1 , wherein the cyclodextrin is α-cyclodextrin, β-cyclodextrin or γ-cyclodextrin.
3. The composition of claim 1 , wherein the cyclodextrin is β-cyclodextrin.
4. The composition of claim 1 , wherein each M is independently a fluorescent moiety.
5. The composition of claim 1 , wherein the polymeric dye comprises from 2 to 10 M moieties.
6. The compound of claim 1 , wherein M, at each occurrence, independently has one of the following structures:
7. The composition of claim 1 , wherein the polymeric dye compound has the following structure (IA):
wherein z is an integer from 2 to 100.
8. The composition of claim 7 , wherein:
L 1 comprises one of the following structures:
R 2 comprises one of the following structures:
wherein:
A is an antibody; and
m″ is 1, 4, or 10,
R 3 comprises one of the following structures:
wherein dT has the following structure:
M comprises one of the following structures:
m is 2, 3, 4, or 5; and
n is 1-10.
9. A method of staining a sample, comprising adding to said sample the composition of claim 1 in an amount sufficient to produce an optical response when said sample is illuminated at an appropriate wavelength.
10. A method for visually detecting an analyte molecule, the method comprising:
(a) providing the composition of claim 1 , wherein the polymeric dye comprises a covalent bond to the analyte molecule; and
(b) detecting the compound by its visible properties.
11. A method for visually detecting an analyte molecule, the method comprising:
(a) admixing the composition of claim 1 , wherein the polymeric dye comprises a covalent bond to a moiety Q comprising a reactive group capable of forming a covalent bond with the analyte molecule, with the analyte molecule;
(b) forming a conjugate of the compound and the analyte molecule; and
(c) detecting the conjugate by its visible properties.
12. A method for determining the presence of dead cells in a sample, the method comprising contacting the sample with the composition of claim 1 , thereby binding or associating the polymeric dye with the dead cells, and observing a fluorescent signal from the polymeric dye bound or associated with the dead cells.
13. The composition of claim 1 , wherein R 2 and R 3 are each independently OH or —OP(═R a )(R b )R c .
14. The composition 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.
15. The composition 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 analyte molecule, targeting moiety or a linker comprising a covalent bond to a solid support.
16. The composition of claim 1 , wherein M is, at each occurrence, independently a moiety comprising four or more aryl or heteroaryl rings, or combinations thereof.
17. The composition of claim 1 , wherein Q comprises one of the following structures:
wherein:
X is halo; and
EWG is an electron withdrawing group.