Polymeric dyes with linker groups comprising deoxyribose
Compounds useful as fluorescent or colored dyes are disclosed. The compounds have the following structure (I): (I) or a stereoisomer, tautomer or salt thereof, wherein R 1 , R 2 , R 3 , R 4 , R 5 , L 1a , L 1b , L 2 , L 3 , L 4 , L 5 , L 6 , L 7 , M 1 , M2, q, w, 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 (Ia):
or a stereoisomer, salt or tautomer thereof, wherein:
M 1 is, at each occurrence, independently a moiety comprising a chromophore;
L 1a is, at each occurrence, independently a heteroarylene linker;
L 1b L 2 and L 3 are, at each occurrence, independently optional alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene or heteroalkynylene linkers;
L 4 is, at each occurrence, independently an alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene or heteroalkynylene linker;
R 1 and R 2 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 sulfhydryl, disulfide, activated ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, α-haloamide, biotin, amino or maleimide functional group;
L′, at each occurrence, independently comprises an alkylene or heteroalkylene linker covalently bonded to: Q, a targeting moiety selected from an antibody and a cell surface receptor antagonist, an amino acid or polymer thereof, an enzyme, a receptor, a receptor ligand, a glycoprotein, an aptamer and a prion, an analyte molecule selected from a nucleic acid or polymer thereof, a solid support selected from a polymeric bead and a non-polymeric bead, or a nucleoside;
m is, at each occurrence, an integer of one or greater; and
n is an integer of one or greater.
2. The compound of claim 1 , wherein L 1a has one of the following structures:
3. The compound of claim 1 , wherein at least one occurrence of L 3 is an alkylene linker, and at least one occurrence of L 4 comprises alkylene oxide.
4. The compound of claim 1 , wherein the compound has the following structure (Ib) or (Ic):
wherein:
L 1b is, at each occurrence, independently an alkylene or heteroalkylene linker.
5. The compound of claim 1 , wherein L 4 is polyethylene oxide, and the compound has the following structure (Id) or (Ie):
wherein:
z is an integer from 1 to 100.
6. The compound of claim 1 , wherein L 1b , at each occurrence, independently comprises an amide functional group or a triazolyl functional group.
7. The compound of claim 1 , wherein R 4 is, at each occurrence, oxo, and R 5 is, at each occurrence, independently OH, O − or OR d .
8. The compound of claim 1 , wherein R 1 and R 2 are each independently —OP(═R a )(R b )R c .
9. The compound of claim 8 , wherein R c is OL′, wherein L′ comprises a heteroalkylene linker to: Q, a targeting moiety, an analyte molecule, a solid support, a solid support residue or a nucleoside.
10. The compound of claim 9 , wherein L′ comprises an alkylene oxide or phosphodiester moiety, or combinations thereof.
11. The compound of claim 10 , wherein L′ has the following structure:
wherein:
m″ and n″ are independently an integer from 1 to 10;
R e is H, an electron pair or a counter ion; and
L″ is R e or a direct bond or comprises an alkylene linkage to: Q, a targeting moiety, an analyte molecule, a solid support or a nucleoside.
12. The compound of claim 11 , wherein the targeting moiety is an antibody or cell surface receptor antagonist.
13. The compound of claim 1 , wherein R 1 or R 2 has one of the following structures:
14. The compound of claim 1 , wherein Q is a moiety having one of the following structures:
wherein:
X is halo; and
EWG is an electron withdrawing group.
15. The compound of claim 1 , wherein n is an integer from 1 to 10 and m is an integer from 3 to 12.
16. The compound of claim 1 , wherein M 1 is, at each occurrence, independently pyrene, perylene, perylene monoimide or 6-carboxyfluorescein (6-FAM).
17. The compound of claim 1 , wherein M 1 , at each occurrence, independently has one of the following structures:
18. A compound having one of the following structures:
wherein:
F″ is
wherein R is H or a direct bond.
19. 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.
20. A method for visually detecting an analyte molecule, the method comprising:
(a) providing the compound of claim 1 , wherein R 1 or R 2 is a linker comprising a covalent bond to the analyte molecule; and
(b) detecting the compound by its visible properties.
21. A method for visually detecting an analyte molecule, the method comprising:
(a) admixing the compound of claim 1 , wherein R 1 or R 2 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.
22. A method for visually detecting an analyte, the method comprising:
(a) providing the compound of claim 1 , wherein R 1 or R 2 comprises a linker comprising a covalent bond to a targeting moiety having specificity for the analyte;
(b) admixing the compound and the analyte, thereby associating the targeting moiety and the analyte; and
(c) detecting the compound by its visible properties.
23. A composition comprising the compound of claim 1 and one or more analyte molecules.
24. A compound having the following structure (IIa):
or a stereoisomer, salt or tautomer thereof, wherein:
G 1 is, at each occurrence, independently a moiety comprising an aldehyde, oxime, hydrazone, alkyne, amine, azide, acylazide, acylhalide, nitrile, nitrone, sulfhydryl, disulfide, sulfonyl halide, isothiocyanate, imidoester, activated ester, ketone, α,β-unsaturated carbonyl, alkene, maleimide, α-haloimide, epoxide, aziridine, tetrazine, tetrazole, phosphine, biotin or thiirane functional group;
L 1a is, at each occurrence, independently a heteroarylene linker;
L 1b′ , L 2 and L 3 are, at each occurrence, independently optional alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene or heteroalkynylene linkers;
L 4 is, at each occurrence, independently an alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene or heteroalkynylene linker;
R 1 and R 2 are each independently H, OH, SH, alkyl, alkoxy, alkylether, heteroalkyl, —OP(═R a )(R b )R c , Q, or L′;
R 3 is, at each occurrence, independently H, alkyl or alkoxy;
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 sulfhydryl, disulfide, activated ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, α-haloamide, biotin, amino or maleimide functional group;
L′, at each occurrence, independently comprises an alkylene or heteroalkylene linker covalently bonded to: Q, a targeting moiety selected from an antibody and a cell surface receptor antagonist, an amino acid or polymer thereof, an enzyme, a receptor, a receptor ligand, a glycoprotein, an aptamer and a prion, an analyte molecule selected from a nucleic acid or polymer thereof, a solid support selected from a polymeric bead and a non-polymeric bead, or a nucleoside;
m is, at each occurrence, an integer of one or greater; and
n is an integer of one or greater.
25. A compound of structure (III) having one of the following structures:
wherein DMT is dimethoxytrityl.