Ultra bright dimeric or polymeric dyes and methods for preparation of the same
Dimeric and/or polymeric dyes and compounds and methods for preparation of the same are disclosed.
1. A compound having one of the following structures (III) or (IV):
wherein:
A 1 , A 2 and A 3 are each independently alkyne, OH, —OP(═R a )(R b )R c or Q, wherein: R a is O; R b is O − or OR d ; R c is O − , OR d or OL′; and R d is a counter ion;
G 1 , G 2 , and G 3 are each independently moieties selected from the group consisting of a urea, carbamate, urethane, thiocarbamate, amino-alcohol, thioether-alcohol, ether-alcohol, amine, thioether, thioester, double-stranded nucleic acid, and triazole functional group;
M is, at each occurrence, independently a fluorescent or colored dye moiety or Q, wherein at least one occurrence of M is a fluorescent or colored dye moiety for at least one integral value of a and b;
R 1 is, at each occurrence, independently H, alkyl or alkoxy;
Q is, at each occurrence, independently a moiety having one of the following structures:
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 (III) or (IV);
L 1 and L 2 are, at each occurrence, independently optional bivalent linker moieties;
L 3 , at each occurrence, independently has the following structure:
wherein:
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; and
m 1 and x 1 are, at each occurrence, independently an integer from 0 to 10;
L 5 is an alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, heteroalkynylene, carbocyclic or heterocyclic linker;
L 4 is an optional multivalent linker moiety;
a, b and c are independently an integer of 1 or greater;
each x is independently an integer of 1 or greater; and
y is an integer of 1 or greater.
2. A compound having one of the following structures:
wherein:
Hex has the following structure:
bB has the following structure:
sF has the following structure:
Alk has the following structure:
and
F has the following structure:
3. The compound of claim 1 , wherein M, at each occurrence, independently has one of the following structures:
4. The compound of claim 1 , wherein L 4 is alkylene.
5. The compound of claim 1 , wherein L 3 is, at each occurrence, independently an amino acid or peptide linker.
6. The compound of claim 1 , wherein L 3 is, at each occurrence, independently a linker comprising one or more charged moieties.
7. The compound of claim 1 , wherein R 1 is H.
8. The compound of claim 1 , wherein A 1 , A 2 and A 3 are each independently OH or —OP(═R a )(R b )R c .
9. A composition comprising the compound of claim 1 and one or more analyte molecules.
10. 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.
11. A method for preparing the compound of structure (III) of claim 1 , the method comprising:
reacting a second and third compound of structure (I):
with a fourth compound of structure (II):
wherein:
A 1 and A 2 are each independently, alkyne, OH, —OP(═R a )(R b )R c , Q, or a moiety comprising a first functional group having complementary reactivity to B 1 , B 2 or both, provided at least one of A 1 and A 2 is a moiety comprising a first functional group having complementary reactivity to B 1 , B 2 or both, wherein: R a is O; R b is O − or OR d ; R c is O − , OR d , or OL′; and R d is a counter ion;
B 1 and B 2 are each independently a second functional group having complementary reactivity to the first functional group;
M is, at each occurrence, independently a fluorescent or colored dye moiety or Q, provided at least one occurrence of M is a fluorescent or colored dye moiety;
R 1 is, at each occurrence, independently H, alkyl or alkoxy;
Q is, at each occurrence, independently a moiety having one of the following structures:
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);
L 1 and L 2 are, at each occurrence, independently optional bivalent linker moieties;
L 3 , at each occurrence, independently has the following structure:
wherein:
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; and
m 1 and x 1 are, at each occurrence, independently an integer from 0 to 10;
L 5 is an alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, heteroalkynylene, carbocyclic or heterocyclic linker;
L 4 is an optional multivalent linker moiety; and
x, y and z are independently an integer of 1 or greater,
thereby: i) forming a first bond between the second compound of structure (I) and the fourth compound of structure (II) by reaction of B 1 with the first functional group of the second compound of structure (I); and ii) forming a second bond between the third compound of structure (I) and the fourth compound of structure (II) by reaction of B 2 with the first functional group of the third compound of structure (I).
12. The method of claim 11 , wherein A 1 , A 2 are each independently a nucleophilic functional group, wherein the nucleophilic functional group is amino, alkylamino, sulfhydryl or hydroxyl.
13. The method of claim 11 , wherein B 1 and B 2 are each independently an electrophilic functional group, wherein the electrophilic functional group is an acid halide, N-hydroxysuccinimide ester, isocycanate, isothiocyanate, epoxide, halide, tosylate, mesylate, triflate, maleimide, phosphate or alkene.
14. The method of claim 11 , wherein A 1 , A 2 are each independently an electrophilic functional group, wherein the electrophilic functional group is an N-hydroxysuccinimide ester, phenolate ester, halide, tosylate, mesylate, phosphate or triflate.
15. The method of claim 11 , wherein B 1 and B 2 are each independently nucleophilic functional group, wherein the nucleophilic functional group is amino, alkylamino, sulfhydryl or hydroxyl.
16. The method of claim 11 , wherein A 1 and A 2 are each independently an alkyne and B 1 and B 2 are each independently an azide or A 1 and A 2 are each independently an azide and B 1 and B 2 are each independently an alkyne.
17. The method of claim 11 , wherein A 1 and A 2 comprise an aryl halide, boronic acid, boronic ester, alkylstannane, arylstannane, amine, and each of B 1 and B 2 are alkene or alkyne functional groups, aryl halide or alkyl halide functional groups.
18. The method of claim 11 , wherein L 4 is alkylene.