Polymeric tandem dyes with linker groups
Compounds useful as fluorescent or colored dyes are disclosed. In some embodiments, 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 1 , M 2 , m, and n are as defined herein. Methods associated with preparation and use of such compounds is also provided.
1. A compound having the following structure (I):
or a stereoisomer, salt, or tautomer thereof, wherein:
M 1 and M 2 are, at each occurrence, independently a chromophore, provided that at least one of M 1 and M 2 is a FRET donor, and another one of M 1 and M 2 is a corresponding FRET acceptor, and at least one occurrence a FRET donor is positioned between two FRET acceptors;
L 1 is, at each occurrence, an optional linker, provided that at least one occurrence of L 1 is present and comprises oxygen, wherein at least one occurrence of L′ is a linker comprising a triazolyl functional 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 or heteroalkylene 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 a protected form thereof, 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 form 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 is, at each occurrence, independently an integer of zero or greater; and
n is an integer of two or greater.
2. The compound of claim 1 , wherein the compound has the following structure (IA):
wherein:
z is, at each occurrence, independently an integer from 1 to 100; and
m is, at each occurrence, independently an integer from 0 to 6.
3. The compound of claim 2 , wherein z is, at each occurrence, independently an integer from 1 to 30.
4. The compound of claim 2 , wherein m is, at each occurrence, independently an integer from 2-4.
5. The compound of claim 2 , wherein the compound has the following structure (IB):
wherein:
x 1 , x 2 , x 3 , and x 4 are, at each occurrence, independently an integer from 0 to 6.
6. The compound of claim 1 , wherein at least one occurrence of L 1 -M 1 or L 1 -M 2 comprises one of the following structures:
wherein L a and L b are each independently optional linkers.
7. The compound of claim 6 , wherein L a or L b , or both, is absent.
8. The compound of claim 6 , wherein L a or L b , or both, is present.
9. The compound of claim 8 , wherein L a and L b , when present, are each independently alkylene or heteroalkylene.
10. The compound of claim 8 , wherein L a and L b independently have one of the following structures:
11. The compound of claim 1 , wherein R 4 is, at each occurrence, independently OH, O − or OR d ; R 5 is, at each occurrence, oxo; and R 1 is, at each occurrence, H.
12. 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.
13. The compound of claim 1 , wherein Q has one of the following structures:
wherein each X is independently a halogen.
14. 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 analyte molecule or a linker comprising a covalent bond to a solid support.
15. The compound of claim 1 , wherein R 2 or R 3 has one of the following structures:
16. The compound of claim 1 , wherein at least one combination of M 1 and M 2 is a FRET pair with a J-value greater than about 1×10 10 .
17. The compound of claim 1 , wherein M 1 and M 2 are, at each occurrence, independently selected from the group consisting of:
i) 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, and ter-naphthyl moiety;
ii) p-terphenyl, perylene, azobenzene, phenazine, phenanthroline, acridine, thioxanthrene, chrysene, rubrene, coronene, cyanine, perylene imide, perylene amide, and derivatives thereof;
iii) a coumarin dye, resorufin dye, dipyrrometheneboron difluoride dye, ruthenium bipyridyl dye, thiazole orange dye, polymethine, and N-aryl-1,8-naphthalimide dye; or
iv) a coumarin dye, boron-dipyrromethene, rhodamine, cyanine, pyrene, perylene, perylene monoimide, 6-FAM, 5-FAM, 6-FITC, 5-FITC, and derivatives thereof.
18. The compound of claim 1 , wherein M 1 and M 2 form a FRET pair, wherein M 1 and M 2 at each occurrence, independently have one of the following structures:
19. A composition comprising the compound of claim 1 and one or more analyte molecules.