4,7-DICHLORORHODAMINE DYES
A set of 4,7-dichlororhodamine compounds useful as fluorescent dyes are disclosed having the structures wherein R 1 -R 6 are hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy, linking group, or, when taken together, R 1 and R 6 is benzo, or, when taken together, R 4 and R 5 is benzo; R 7 -R 10 , R 12 -R 16 and R 18 may be hydrogen, fluorine, chlorine, lower alkyl lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy, linking group; R 11 and R 17 may be hydrogen, lower alkyl lower alkene, lower alkyne, phenyl, aryl, linking group; Y 1 -Y 4 are hydrogen, lower alkyl or cycloalkyl, or, when taken together, Y 1 and R 2 , Y 2 and R 1 Y 3 and R 3 , and/or Y 4 and R 4 is propano, ethano, or substituted forms thereof, and X 1 -X 3 taken separately are hydrogen, chlorine, fluorine, lower alkyl, carboxylate, sulfonate, hydroxymethyl, and linking group, or any combinations thereof. In another aspect, the invention includes reagents labeled with the 4,7-dichlororhodamine dye compounds, including deoxynucleotides, dideoxynucleotides, and polynucleotides. In an additional aspect, the invention includes methods utilizing such dye compounds and reagents including dideoxy polynucleotide sequencing and fragment analysis methods.
1 . A labeled nucleotide according to structural formula (VII):
wherein:
B is selected from the group consisting of a 7-deazapurine nucleotide base attached to the illustrated furan at its N9 position, a purine nucleotide base attached to the furan of structural formula (VII) at its N9 position and a pyrimidine nucleotide base attached to the furan of structural formula (VII) at its N1 position;
D is a 4,7-dichlororhodamine dye according to structural formula (VI):
wherein:
R 7 , R 8 , R 9 , R 10 , R 12 , R 13 R 14 , R 15 , R 16 and R 18 are each, independently of one another, selected from the group consisting of hydrogen, fluorine, chlorine, methyl, ethyl, lower alkyl, lower alkene, lower alkyne, cycloalkyl, phenyl, aryl, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy and combinations thereof, or, alternatively, R 7 and R 8 or R 13 and R 14 may be taken together for form an oxo, sulfoxo, imminium or alkyliminium group;
R 11 and R 17 are each, independently of one another, selected from the group consisting of hydrogen, lower alkyl, alkyl sulfonate, alkyl carboxylate, lower alkene, lower alkyne, cycloalkyl, phenyl, aryl and combinations thereof, and
X 1 , X 2 and X 3 are each, independently of one another, selected from the group consisting of hydrogen, chlorine, fluorine, lower alkyl, amine, amide, carboxylate, sulfonate and hydroxymethyl,
with the proviso that one of R 7 , R 8 , R 9 , R 10 , R 11 , R 12 , R 13 , R 14 , R 15 , R 16 , R 17 , R 18 , X 1 , X 2 or X 3 comprises a linkage linking D to B;
W 1 and W 2 are each, independently of one another, selected from the group consisting of hydrogen and OH;
W 3 is selected from the group consisting of OH, OPO 3 , OP 2 O 6 , OP 3 O 9 , and analogs thereof.
2 . The labeled nucleotide of claim 1 in which D is linked to the 8-position of B when B is a purine nucleotide base, D is linked to the 7-position of B when B is a 7-deazapurine nucleotide base and D is linked to the 5-position of B when B is a pyrimidine nucleotide base.
3 . The labeled nucleotide of claim 1 in which W 3 is selected from the group consisting of phosphorothioate, phosphoroanilidate, phosphoroanilothioate and phosphoramidate.
4 . The labeled nucleotide of claim 1 in which W 1 is hydrogen, W 2 is OH and W 3 is OP 3 O 9 .
5 . The labeled nucleotide of claim 1 in which W 1 and W 2 are each hydrogen and W 3 is OP 3 O 9 .
6 . The labeled nucleotide of claim 1 in which the linkage linking B and D comprises a acetylenic amido or an alkenic amido linkage.
7 . The labeled nucleotide of claim 1 in which the linkage linking B and D is selected from the group consisting of —C≡C—CH 2 —NH—C(O)—, —C≡C—CH 2 —NH—C(O)—(CH 2 ) 5 —NH—C(O)—, —CH═CH—C(O)—NH—(CH 2 ) 5 —NH—C(O)—, —C≡C—CH 2 —O—CH 2 CH 2 —NH—C(O)—, —C≡C—CH 2 —O—CH 2 CH 2 —O—CH 2 CH 2 —NH—C(O)— and —C≡C-Ph-O—CH 2 CH 2 —NH—C(O)—, where Ph is 1,4-phenylene.
8 . The labeled nucleotide of any one of claims 1 - 7 in which X 1 is carboxylate; one of X 2 or X 3 is hydrogen and the other one of X 2 or X 3 comprises the linkage linking D to B.
9 . The labeled nucleotide of any one of claims 1 - 7 in which R 7 , R 8 , R 9 , R 10 , R 13 , R 14 , R 15 and R 16 are each, independently of one another, selected from the group consisting of hydrogen, methyl and ethyl.
10 . The labeled nucleotide of any one of claims 1 - 7 in which R 11 and R 12 are each, independently of one another, selected from the group consisting of methyl and phenyl.
11 . The labeled nucleotide of any one of claims 1 - 7 in which R 7 , R 8 , R 9 , R 10 , R 13 , R 14 , R 15 and R 16 are each, independently of one another, selected from hydrogen, methyl and ethyl.
12 . The labeled nucleotide of any one of claims 1 - 7 in which R 7 , R 8 , R 10 , R 13 , R 14 and R 17 are each, independently of one another, selected from the group consisting of hydrogen and methyl; R 9 and R 15 are each hydrogen; R 11 and R 16 are each methyl or phenyl; and R 12 and R 18 are each hydrogen.
13 . A labeled polynucleotide containing a nucleotide according to structural formula (XI):
wherein:
B is selected from the group consisting of a 7-deazapurine nucleotide base attached to the illustrated furan at its N9 position, a purine nucleotide base attached to the furan of structural formula (XI) at its N9 position and a pyrimidine nucleotide base attached to the furan of structural formula (XI) at its N1 position;
D is a 4,7-dichlororhodamine dye according to structural formula (VI):
wherein:
R 7 , R 8 , R 9 , R 10 , R 12 , R 13 , R 14 , R 15 , R 16 and R 18 are each, independently of one another, selected from the group consisting of hydrogen, fluorine, chlorine, methyl, ethyl, lower alkyl, lower alkene, lower alkyne, cycloalkyl, phenyl, aryl, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy and combinations thereof, or, alternatively, R 7 and R 8 or R 13 and R 14 may be taken together for form an oxo, sulfoxo, imminium or alkyliminium group;
R 11 and R 17 are each, independently of one another, selected from the group consisting of hydrogen, lower alkyl, alkyl sulfonate, alkyl carboxylate, lower alkene, lower alkyne, cycloalkyl, phenyl, aryl and combinations thereof; and
X 1 , X 2 and X 3 are each, independently of one another, selected from the group consisting of hydrogen, chlorine, fluorine, lower alkyl, amine, amide, carboxylate, sulfonate and hydroxymethyl,
with the proviso that one of R 7 , R 8 , R 9 , R 10 , R 11 , R 12 , R 13 , R 14 R 15 R 16 , R 17 , R 18 , X 1 , X 2 or X 3 comprises a linkage linking D to B
Z 1 is selected from the group consisting of hydrogen, OH and OCH 3 ;
Z 2 is selected from the group consisting of hydrogen, OH, OPO 3 , OP 2 O 6 , OP 3 O 9 and Nuc 1 , where Nuc 1 is a nucleoside, nucleotide or polynucleotide which is linked to structural formula (XI) by a phosphodiester linkage or an analog thereof, the linkage being attached to the 5′-position of Nuc 1 ; and
Z 3 is selected from the group consisting of hydrogen, PO 3 , phosphate analogs and Nuc 2 , where Nuc 2 is a nucleoside, nucleotide or polynucleotide which is linked to structural formula (XI) by a phosphodiester linkage or an analog thereof, the linkage being attached to the 3′-position of Nuc 2 .
14 . The labeled polynucleotide of claim 13 in which D is linked to the 8-position of B when B is a purine nucleotide base, D is linked to the 7-position of B when B is a 7-deazapurine nucleotide base and D is linked to the 5-position of B when B is a pyrimidine nucleotide base.
15 . The labeled polynucleotide of claim 13 in which the illustrated nucleotide is a 5′-terminal nucleotide.
16 . The labeled polynucleotide of claim 13 in which the illustrated nucleotide is a 3′-terminal nucleotide.
17 . The labeled polynucleotide of claim 13 in which the illustrated nucleotide is an internal nucleotide of the polynucleotide.
18 . The labeled polynucleotide of claim 13 in which the linkage linking B and D comprises a acetylenic amido or an alkenic amido linkage.
19 . The labeled polynucleotide of claim 13 in which the linkage linking B and D is selected from the group consisting of —C≡C—CH 2 —NH—C(O)—, —C≡C—CH 2 —NH—C(O)—(CH 2 ) 5 —NH—C(O)—, —CH═CH—C(O)—NH—(CH 2 ) 5 —NH—C(O)—, —C≡C—CH 2 —O—CH 2 CH 2 —NH—C(O)—, —C≡C—CH 2 —O—CH 2 CH 2 —O—CH 2 CH 2 —NH—C(O)— and —C≡C-Ph-O—CH 2 CH 2 —NH—C(O)—, where Ph is 1,4-phenylene.
20 . The labeled nucleotide of any one of claims 13 - 19 in which X 1 is carboxylate; one of X 2 or X 3 is hydrogen and the other one of X 2 or X 3 comprises the linkage linking D to B.
21 . The labeled polynucleotide of any one of claims 13 - 19 in which R 7 , R 8 , R 9 , R 10 , R 13 , R 14 , R 15 and R 16 are each, independently of one another, selected from the group consisting of hydrogen, methyl and ethyl.
22 . The labeled nucleotide of any one of claims 13 - 19 in which R 11 and R 12 are each, independently of one another, selected from the group consisting of methyl and phenyl.
23 . The labeled nucleotide of any one of claims 13 - 19 in which R 7 , R 8 , R 9 , R 10 , R 13 , R 14 , R 15 and R 16 are each, independently of one another, selected from hydrogen, methyl and ethyl.
24 . The labeled nucleotide of any one of claims 13 - 19 in which R 7 , R 8 , R 10 , R 13 , R 14 and R 17 are each, independently of one another, selected from the group consisting of hydrogen and methyl; R 9 and R 15 are each hydrogen; R 11 and R 16 are each methyl or phenyl; and R 12 and R 18 are each hydrogen.
25 . A labeled nucleotide according to structural formula (VII):
wherein:
B is selected from the group consisting of a 7-deazapurine nucleotide base attached to the illustrated furan at its N9 position, a purine nucleotide base attached to the furan of structural formula (VII) at its N9 position and a pyrimidine nucleotide base attached to the furan of structural formula (VII) at its N1 position;
D is a 4,7-dichlororhodamine dye according to structural formula (I):
wherein:
R 1 , R 2 , R 3 , R 4 , R 5 and R 6 , when taken alone, are each, independently of one another, selected from the group consisting of hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, cycloalkyl, phenyl, aryl, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy and combinations thereof, or, alternatively, R 1 and R 6 and/or R 4 and R 5 are taken together to form a benzo group;
Y 1 , Y 2 , Y 3 and Y 4 , when taken alone, are each, independently of one another, selected from the group consisting of hydrogen, lower alkyl, alkyl sulfonate, alkyl carboxylate and cycloalkyl, or, alternatively, Y 1 and R 2 , Y 2 and R 1 , Y 3 and R 3 and/or Y 4 and R 4 , are taken together and are each, independently of one another selected from the group consisting of ethano, propano and substituted forms thereof;
X 1 , X 2 and X 3 are each, independently of one another, selected from the group consisting of hydrogen, chlorine, fluorine, lower alkyl, carboxylate, sulfonate and hydroxymethyl,
with the proviso that one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , X 1 , X 2 or X 3 comprises a linkage linking D to B;
W 1 and W 2 are each, independently of one another, selected from the group consisting of hydrogen and OH;
W 3 is selected from the group consisting of OH, OPO 3 , OP 2 O 6 , OP 3 O 9 , and analogs thereof.
26 . The labeled nucleotide of claim 25 in which D is linked to the 8-position of B when B is a purine nucleotide base, D is linked to the 7-position of B when B is a 7-deazapurine nucleotide base and D is linked to the 5-position of B when B is a pyrimidine nucleotide base.
27 . The labeled nucleotide of claim 25 in which W 3 is selected from the group consisting of phosphorothioate, phosphoroanilidate, phosphoroanilothioate and phosphoramidate.
28 . The labeled nucleotide of claim 25 in which W 1 is hydrogen, W 2 is OH and W 3 is OP 3 O 9 .
29 . The labeled nucleotide of claim 25 in which W 1 and W 2 are each hydrogen and W 3 is OP 3 O 9 .
30 . The labeled nucleotide of claim 25 in which the linkage linking B and D comprises a acetylenic amido or an alkenic amido linkage.
31 . The labeled nucleotide of claim 25 in which the linkage linking B and D is selected from the group consisting of —C≡C—CH 2 —NH—C(O)—, —C≡C—CH 2 —NH—C(O)—(CH 2 ) 5 —NH—C(O)—, —CH═CH—C(O)—NH—(CH 2 ) 5 —NH—C(O)—, —C≡C—CH 2 —O—CH 2 CH 2 —NH—C(O)—, —C═C—CH 2 —O—CH 2 CH 2 —O—CH 2 CH 2 —NH—C(O)— and —C—C-Ph-O—CH 2 CH 2 —NH—C(O)—, where Ph is 1,4-phenylene.
32 . The labeled nucleotide of any one of claims 25 - 31 in which X 1 is carboxylate; one of X 2 or X 3 is hydrogen and the other one of X 2 or X 3 comprises the linkage linking D to B.
33 . The labeled nucleotide of any one of claims 25 - 31 in which R 2 , R 3 , R 5 , R 6 , Y 1 and Y 3 are each hydrogen; Y 2 and R 1 are taken together to form a propano group; Y 4 and R 4 are taken together to form a propano group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.
34 . The labeled nucleotide of any one of claims 25 - 31 in which R 2 , R 3 , R 5 and R 6 are each hydrogen; Y 1 and Y 3 are each methyl; Y 2 and R 1 are taken together to form an propane group; Y 4 and R 4 are taken together to from a propane group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.
35 . The labeled nucleotide of any one of claims 25 - 31 in which R 1 , R 4 , R 5 and R 6 are each hydrogen; Y 2 and Y 4 are each ethyl; Y 1 and R 2 are taken together to form an ethano group; Y 3 and R 3 are taken together to form an ethano group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.
36 . The labeled nucleotide of any one of claims 25 - 31 in which R 1 , R 4 , R 5 and R 6 are each hydrogen; Y 2 and Y 4 are each —(CH 2 ) 5 —COOH; Y 1 and R 2 are taken together to form a —CH 2 —C(CH 3 ) 2 — group; Y 3 and R 3 are taken together to form a —CH 2 —C(CH 3 ) 2 — group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.
37 . The labeled nucleotide of any one of claims 25 - 31 in which R 1 , R 4 , R 5 and R 6 are each hydrogen; Y 2 and Y 4 are each —CH 2 -Ph-COOH, where Ph is 1,4-phenylene; Y 1 and R 2 are taken together to form a —CH 2 —C(CH 3 ) 2 — group; Y 3 and R 3 are taken together to form a —CH 2 —C(CH 3 ) 2 — group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.
38 . The labeled nucleotide of any one of claims 25 - 31 in which R 1 , R 2 , R 3 , R 4 , R 5 and R 6 are each hydrogen; Y 1 and Y 2 are taken together to form a butano group; Y 3 and Y 4 are taken together to form a butano group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.
39 . A labeled polynucleotide containing a nucleotide according to structural formula (XI):
wherein:
B is selected from the group consisting of a 7-deazapurine nucleotide base attached to the furan of structural formula (XI) at its N9 position, a purine nucleotide base attached to the furan of structural formula (XI) at its N9 position, and a pyrimidine nucleotide base attached to the furan of structural formula (XI) at its N1 position;
D is a 4,7-dichlororhodamine dye according to structural formula (I):
wherein:
R 1 , R 2 , R 3 , R 4 , R 5 and R 6 , when taken alone, are each, independently of one another, selected from the group consisting of hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, cycloalkyl, phenyl, aryl, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy and combinations thereof, or, alternatively, R 1 and R 6 and/or R 4 and R 5 are taken together to form a benzo group;
Y 1 , Y 2 , Y 3 and Y 4 , when taken alone, are each, independently of one another, selected from the group consisting of hydrogen, lower alkyl, alkyl sulfonate, alkyl carboxylate and cycloalkyl, or, alternatively, Y 1 and R 2 , Y 2 and R 1 , Y 3 and R 3 and/or Y 4 and R 4 , are taken together and are each, independently of one another selected from the group consisting of ethano, propano and substituted forms thereof;
X 1 , X 2 and X 3 are each, independently of one another, selected from the group consisting of hydrogen, chlorine, fluorine, lower alkyl, carboxylate, sulfonate and hydroxymethyl,
with the proviso that one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , X 1 , X 2 or X 3 comprises a linkage linking D to B;
Z 1 is selected from the group consisting of hydrogen and OH;
Z 2 is selected from the group consisting of hydrogen, OH, OPO 3 , OP 2 O 6 , OP 3 O 9 and Nuc 1 , where Nuc 1 is a nucleoside, nucleotide or polynucleotide which is linked to structural formula (XI) by a phosphodiester linkage or an analog thereof; the linkage being attached to the 5′-position of Nuc 1 ; and
Z 3 is selected from the group consisting of hydrogen, PO 3 , phosphate analogs and Nuc 2 , where Nuc 2 is a nucleoside, nucleotide or polynucleotide which is linked to structural formal (XI) by a phosphodiester linkage or an analog thereof, the linkage being attached to the 3′-position of Nuc 2 .
40 . The labeled polynucleotide of claim 39 in which D is linked to the 8-position of B when B is a purine nucleotide base, D is linked to the 7-position of B when B is a 7-deazapurine nucleotide base and D is linked to the 5-position of B when B is a pyrimidine nucleotide base.
41 . The labeled polynucleotide of claim 39 in which the illustrated nucleotide is a 5′-terminal nucleotide.
42 . The labeled polynucleotide of claim 39 in which the illustrated nucleotide is a 3′-terminal nucleotide.
43 . The labeled polynucleotide of claim 39 in which the illustrated nucleotide is an internal nucleotide of the polynucleotide.
44 . The labeled polynucleotide of claim 39 in which the linkage linking B and D comprises a acetylenic amido or an alkenic amido linkage.
45 . The labeled polynucleotide of claim 39 in which the linkage linking B and D is selected from the group consisting of —C≡C—CH 2 —NH—C(O)—, —C≡C—CH 2 —NH—C(O)—(CH 2 ) 5 —NH—C(O)—, —CH═CH—C(O)—NH—(CH 2 ) 5 —NH—C(O)—, —C≡C—CH 2 —O—CH 2 CH 2 —NH—C(O)—, —C≡C—CH 2 —O—CH 2 CH 2 —O—CH 2 CH 2 —NH—C(O)— and —C≡C-Ph-O—CH 2 CH 2 —NH—C(O)—, where Ph is 1,4-phenylene.
46 . The labeled nucleotide of any one of claims 39 - 45 in which X 1 is carboxylate; one of X 2 or X 3 is hydrogen and the other one of X 2 or X 3 comprises the linkage linking D to B.
47 . The labeled nucleotide of any one of claims 39 - 45 in which R 2 , R 3 , R 5 , R 6 , Y 1 and Y 3 are each hydrogen; Y 2 and R 1 are taken together to form a propano group; Y 4 and R 4 are taken together to form a propano group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.
48 . The labeled nucleotide of any one of claims 39 - 45 in which R 2 , R 3 , R 5 and R 6 are each hydrogen; Y 1 and Y 3 are each methyl; Y 2 and R 1 are taken together to form an propane group; Y 4 and R 4 are taken together to from a propane group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.
49 . The labeled nucleotide of any one of claims 39 - 45 in which R 1 , R 4 , R 5 and R 6 are each hydrogen; Y 2 and Y 4 are each ethyl; Y 1 and R 2 are taken together to form an ethano group; Y 3 and R 3 are taken together to form an ethano group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.
50 . The labeled nucleotide of any one of claims 39 - 45 in which R 1 , R 4 , R 5 and R 6 are each hydrogen; Y 2 and Y 4 are each —(CH 2 ) 5 —COOH; Y 1 and R 2 are taken together to form a —CH 2 —C(CH 3 ) 2 — group; Y 3 and R 3 are taken together to form a —CH 2 —C(CH 3 ) 2 — group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.
51 . The labeled nucleotide of any one of claims 39 - 45 in which R 1 , R 4 , R 5 and R 6 are each hydrogen; Y 2 and Y 4 are each —CH 2 -Ph-COOH, where Ph is 1,4-phenylene; Y 1 and R 2 are taken together to form a —CH 2 —C(CH 3 ) 2 — group; Y 3 and R 3 are taken together to form a —CH 2 —C(CH 3 ) 2 — group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.
52 . The labeled nucleotide of any one of claims 39 - 45 in which R 1 , R 2 , R 3 , R 4 , R 5 and R 6 are each hydrogen; Y 1 and Y 2 are taken together to form a butano group; Y 3 and Y 4 are taken together to form a butano group; X 1 is carboxylate; and one of X 2 and X 3 is hydrogen and the other comprises the linkage to B.