Fluorinated xanthene derivatives
AssigneeMolecular Probes, Inc.
InventorsKyle R. Gee, Martin Poot, Dieter H. Klaubert, Wei-Chuan Sun, Richard P. Haugland, Fei Mao
Life of this patent
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Abstract
The family of dyes of the invention are fluoresceins and rhodols that are directly substituted on one or more aromatic carbons by fluorine. These fluorine-substituted fluorescent dyes possess greater photostability and have lower sensitivity to pH changes in the physiological range of 6-8 than do non-fluorinated dyes, exhibit less quenching when conjugated to a substance, and possess additional advantages. The dyes of the invention are useful as detectable tracers and for preparing conjugates of organic and inorganic substances.
Claims107
A compound having the formula ##STR10## or the formula ##STR11## wherein R.sup.1 and R.sup.6 are independently H, F, Cl, Br, I, C.sub.1 -C.sub.18 alkyl or C.sub.1 -C.sub.18 alkoxy;
- R.sup.2, R.sup.3, R.sup.4 and R.sup.5 are independently H, F, Cl, Br, I, CN;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy or C.sub.1 -C.sub.18 alkylthio, where each alkyl, alkoxy or alkylthio is optionally further substituted by F, Cl, Br, I, sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 where R.sup.18 is a C.sub.1 -C.sub.4 alkyl;
- or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
- or one or both of R.sup.3 and R.sup.4 are --CH.sub.2 N(CH.sub.2 COOR.sup.17).sub.2, where R.sup.17 is H, a biologically compatible counterion, a linear or branched alkyl having 1-6 carbons, or --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- A is OR.sup.7 or NR.sup.8 R.sup.9,
- where each R.sup.7 is independently H, C.sub.1 -C.sub.18 alkyl, a C.sub.1 -C.sub.18 acyl wherein each alkyl group independently has 1-6 carbons and is optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or a trialkylsilyl wherein each alkyl group independently has 1-6 carbons;
- R.sup.8 and R.sup.9 are independently H, C.sub.1 -C.sub.6 alkyl, C.sub.1 -C.sub.6 carboxyalkyl, C.sub.1 -C.sub.6 sulfoalkyl, a salt of C.sub.1 -C.sub.6 carboxyalkyl, a salt of C.sub.1 -C.sub.6 sulfoalkyl, or C.sub.1 -C.sub.18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.8 in combination with R.sup.2, or R.sup.9 in combination with R.sup.3, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
- or R.sup.8 in combination with R.sup.9 forms a saturated 5- or 6-membered heterocycle that is a piperidine, a morpholine, a pyrrolidine or a piperazine, each of which is optionally substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- R.sup.10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.10 is C.sub.1 -C.sub.18 alkyl, alkenyl or alkynyl that is optionally substituted one or more times by F, Cl, Br, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
- or R.sup.10 has the formula ##STR12## where R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 are independently H, F, Cl, Br, I;
- or sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, CN, nitro, hydroxy, azido, amino, hydrazino;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy, C.sub.1 -C.sub.18 alkylthio, C.sub.1 -C.sub.18 alkylamino, C.sub.1 -C.sub.18 alkylester, C.sub.1 -C.sub.18 alkylamido or C.sub.1 -C.sub.18 arylamido, the alkyl or aryl portions of which are optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, dialkylamino or alkoxy, the alkyl portions of each having 1-6 carbons;
- or one pair of adjacent substituents R.sup.13 and R.sup.14, R.sup.14 and R.sup.15 or R.sup.15 and R.sup.16, when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- and
- R.sup.11 is H, hydroxy, CN or a C.sub.1 -C.sub.6 alkoxy;
- or R.sup.10 in combination with R.sup.11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
- or R.sup.11 in combination with R.sup.12 forms a 5- or 6-membered spirolactone ring or a 5- or 6-membered spirosultone ring that is optionally and independently substituted by H, F or CH.sub.3 ;
- or R.sup.10 when taken in combination with R.sup.11 is a carbonyl oxygen;
- provided that at least one of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.6, and R.sup.10 is F, or at least three of R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 are F.
A compound having the formula ##STR14## or the formula ##STR15## wherein R.sup.1 and R.sup.6 are independently H, F, Cl, Br, I, C.sub.1 -C.sub.18 alkyl or C.sub.1 -C.sub.18 alkoxy;
- R.sup.2, R.sup.3, R.sup.4 and R.sup.5 are independently H, F, Cl, Br, I, CN;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy or C.sub.1 -C.sub.18 alkylthio, where each alkyl, alkoxy or alkylthio is optionally further substituted by F, Cl, Br, I, sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 where R.sup.18 is a C.sub.1 -C.sub.4 alkyl;
- or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
- or one or more of R.sup.2, R.sup.3, R.sup.4, and R.sup.5 is --L--R.sub.x ;
- A is OR.sup.7 or NR.sup.8 R.sup.9,
- where each R.sup.7 is independently H, C.sub.1 -C.sub.18 alkyl, a C.sub.1 -C.sub.18 acyl wherein each alkyl group independently has 1-6 carbons and is optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or a trialkylsilyl wherein each alkyl group independently has 1-6 carbons;
- or R.sup.7 is an --L--R.sub.x ;
- R.sup.8 and R.sup.9 are independently H, C.sub.1 -C.sub.6 alkyl, C.sub.1 -C.sub.6 carboxyalkyl, C.sub.1 -C.sub.6 sulfoalkyl, a salt of C.sub.1-C.sub.6 carboxyalkyl, a salt of C.sub.1 -C.sub.6 sulfoalkyl, or C.sub.1 -C.sub.18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.8 in combination with R.sup.2, or R.sup.9 in combination with R.sup.8, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
- or R.sup.8 in combination with R.sup.9 forms a saturated 5- or 6-membered heterocycle that is a piperidine, a morpholine, a pyrrolidine or a piperazine, each of which is optionally substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or one of R.sup.8 and R.sup.9 is --L--R.sub.x ;
- and
- R.sup.10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.10 is C.sub.1 -C.sub.18 alkyl, alkenyl or alkynyl that is optionally substituted one or more times by F, Cl, Br, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
- or R.sup.10 is an --L--R.sub.x ;
- or R.sup.10 has the formula ##STR16## where R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 are independently H, F, Cl, Br, I;
- or sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, CN, nitro, hydroxy, azido, amino, hydrazino;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy, C.sub.1 -C.sub.18 alkylthio, C.sub.1 -C.sub.18 alkylamino, C.sub.1 -C.sub.18 alkylester, C.sub.1 -C.sub.18 alkylamido or C.sub.1 -C.sub.18 arylamido, the alkyl or aryl portions of which are optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, dialkylamino or alkoxy, the alkyl portions of each having 1-6 carbons;
- or one pair of adjacent substituents R.sup.13 and R.sup.14, R.sup.14 and R.sup.15 or R.sup.15 and R.sup.16, when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or one or more of R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 is --L--R.sub.x ;
- R.sup.11 is H, hydroxy, CN or a C.sub.1 -C.sub.6 alkoxy;
- or R.sup.10 in combination with R.sup.11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
- or R.sup.11 in combination with R.sup.12 forms a 5- or 6-membered spirolactone ring or a 5- or 6-membered spirosultone ring that is optionally and independently substituted by H, F or CH.sub.3 ;
- or R.sup.10 when taken in combination with R.sup.11 is a carbonyl oxygen;
- provided that at least one of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.6, and R.sup.10 is F, or at least three of R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 are F;
- and
- further provided that at least one of R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.7, R.sup.8, R.sup.9, R.sup.10, R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 is --L--R.sub.x, where each --L--R.sub.x is optionally the same or different;
- wherein
- L is a single covalent bond, or L is a covalent linkage having 1-24 nonhydrogen atoms selected from the group consisting of C, N, O and S and is composed of any combination of single, double, triple or aromatic carbon-carbon bonds, carbon-nitrogen bonds, nitrogen-nitrogen bonds, carbon-oxygen bonds and carbon-sulfur bonds;
- and
- R.sub.x is a reactive site.
A compound having the formula ##STR17## or the formula ##STR18## wherein R.sup.1 and R.sup.6 are independently H, F, Cl, Br, I, C.sub.1 -C.sub.18 alkyl or C.sub.1 -C.sub.18 alkoxy;
- R.sup.2, R.sup.3, R.sup.4 and R.sup.5 are independently H, F, Cl, Br, I, CN;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy or C.sub.1 -C.sub.18 alkylthio, where each alkyl, alkoxy or alkylthio is optionally further substituted by F, Cl, Br, I, sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 where R.sup.18 is a C.sub.1 -C.sub.4 alkyl;
- or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
- or one or more of R.sup.2, R.sup.3, R.sup.4, and R.sup.5 is --L--S.sub.c ;
- A is OR.sup.7 or NR.sup.8 R.sup.9,
- where each R.sup.7 is independently H, C.sub.1 -C.sub.18 alkyl, a C.sub.1 -C.sub.18 acyl wherein each alkyl group independently has 1-6 carbons and is optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.7 is --L--S.sub.c ;
- R.sup.8 and R.sup.9 are independently H, C.sub.1 -C.sub.6 alkyl, C.sub.1 -C.sub.6 carboxyalkyl, C.sub.1 -C.sub.6 sulfoalkyl, a salt of C.sub.1 -C.sub.6 carboxyalkyl, a salt of C.sub.1 -C.sub.6 sulfoalkyl, or C.sub.1 -C.sub.18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.8 in combination with R.sup.2, or R.sup.9 in combination with R.sup.3, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
- or R.sup.8 in combination with R.sup.9 forms a saturated 5- or 6-membered heterocycle that is a piperidine, a morpholine, a pyrrolidine or a piperazine, each of which is optionally substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or one of R.sup.8 and R.sup.9 is --L--S.sub.c ;
- and
- R.sup.10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.10 is C.sub.1 -C.sub.18 alkyl, alkenyl or alkynyl that is optionally substituted one or more times by F, Cl, Br, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
- or R.sup.10 is --L--S.sub.c ;
- or R.sup.10 has the formula ##STR19## where R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 are independently H, F, Cl, Br, I;
- or sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, CN, nitro, hydroxy, azido, amino, hydrazino;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy, C.sub.1 -C.sub.18 alkylthio, C.sub.1 -C.sub.18 alkylamino, C.sub.1 -C.sub.18 alkylester, C.sub.1 -C.sub.18 alkylamido or C.sub.1 -C.sub.18 arylamido, the alkyl or aryl portions of which are optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, dialkylamino or alkoxy, the alkyl portions of each having 1-6 carbons;
- or one pair of adjacent substituents R.sup.13 and R.sup.14, R.sup.14 and R.sup.15 or R.sup.15 and R.sup.16, when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or one or more of R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 is --L--S.sub.c ;
- R.sup.11 is H, hydroxy, CN or a C.sub.1 -C.sub.6 alkoxy;
- or R.sup.10 in combination with R.sup.11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
- or R.sup.11 in combination with R.sup.12 forms a 5- or 6-membered spirolactone ring or a 5- or 6-membered spirosultone ring that is optionally and independently substituted by H, F or CH.sub.3 ;
- or R.sup.10 in combination with R.sup.11 is a carbonyl oxygen;
- provided that at least one of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.6 and R.sup.10 is F, or at least three of R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 are F;
- and
- further provided that at least one of R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.7, R.sup.8, R.sup.9, R.sup.10, R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 is an --L--S.sub.c ;
- L is a single covalent bond, or L is a covalent linkage having 1-24 nonhydrogen atoms selected from the group consisting of C, N, O and S and is composed of any combination of single, double, triple or aromatic carbon-carbon bonds, carbon-nitrogen bonds, nitrogen-nitrogen bonds, carbon-oxygen bonds and carbon-sulfur bonds;
- and
- S.sub.c is a conjugated substance.
A compound having the formula ##STR20## or the formula ##STR21## wherein R.sup.1 and R.sup.6 are independently H, F, Cl, Br, I, C.sub.1 -C.sub.18 alkyl or C.sub.1 -C.sub.18 alkoxy;
- R.sup.2, R.sup.3, R.sup.4 and R.sup.5 are independently H, F, Cl, Br, I, CN;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy or C.sub.1 -C.sub.18 alkylthio, where each alkyl, alkoxy or alkylthio is optionally further substituted by F, Cl, Br, I, sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 where R.sup.18 is a C.sub.1 -C.sub.4 alkyl;
- or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
- or one or both of R.sup.3 and R.sup.4 are --CH.sub.2 N(CH.sub.2 COOR.sup.17).sub.2, where R.sup.17 is H, a biologically compatible counterion, a linear or branched alkyl having 1-6 carbons, or --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or one or more of R.sup.2, R.sup.3, R.sup.4, and R.sup.5 is --L--R.sub.x ;
- or one or more of R.sup.2, R.sup.3, R.sup.4, and R.sup.5 is --L--S.sub.c ;
- A is OR.sup.7 or NR.sup.8 R.sup.9,
- where each R.sup.7 is independently a BLOCK, or R.sup.7 is --L--R.sub.x, or R.sup.7 is --L--S.sub.c ;
- R.sup.8 and R.sup.9 are independently H, C.sub.1 -C.sub.6 alkyl, C.sub.1 -C.sub.6 carboxyalkyl, C.sub.1 -C.sub.6 sulfoalkyl, a salt of C.sub.1 -C.sub.6 carboxyalkyl, a salt of C.sub.1 -C.sub.6 sulfoalkyl, or C.sub.1 -C.sub.18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.8 in combination with R.sup.2, or R.sup.9 in combination with R.sup.3, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
- or R.sup.8 in combination with R.sup.9 forms a saturated 5- or 6-membered heterocycle that is a piperidine, a morpholine, a pyrrolidine or a piperazine, each of which is optionally substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or one of R.sup.8 and R.sup.9 is a BLOCK;
- or one of R.sup.8 and R.sup.9 is --L--R.sub.x ;
- or one of R.sup.8 and R.sup.9 is --L--S.sub.c ;
- and
- R.sup.10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.10 is C.sub.1 -C.sub.18 alkyl, alkenyl or alkynyl that is optionally substituted one or more times by F, Cl, Br, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
- or R.sup.10 is --L--R.sub.x ;
- or R.sup.10 is --L--S.sub.c ;
- or R.sup.10 has the formula ##STR22## where R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 are independently H, F, Cl, Br, I;
- or sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, CN, nitro, hydroxy, azido, amino, hydrazino;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy, C.sub.1 -C.sub.18 alkylthio, C.sub.1 -C.sub.18 alkylamino, C.sub.1 -C.sub.18 alkylester, C.sub.1 -C.sub.18 alkylamido or C.sub.1 -C.sub.18 arylamido, the alkyl or aryl portions of which are optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, dialkylamino or alkoxy, the alkyl portions of each having 1-6 carbons;
- or one pair of adjacent substituents R.sup.13 and R.sup.14, R.sup.14 and R.sup.15 or R.sup.15 and R.sup.16, when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or one or more of R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 is --L--R.sub.x ;
- or one or more of R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 is --L--S.sub.c ;
- R.sup.11 is H, hydroxy, CN or a C.sub.1 -C.sub.6 alkoxy;
- or R.sup.10 in combination with R.sup.11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
- or R.sup.11 in combination with R.sup.12 forms a 5- or 6-membered spirolactone ring or a 5- or 6-membered spirosultone ring that is optionally and independently substituted by H, F or CH.sub.3 ;
- or R.sup.10 in combination with R.sup.11 is a carbonyl oxygen;
- provided that at least one of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.6, and R.sup.10 is F, or at least three of R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 are F;
- and
- further provided at least one of R.sup.7, R.sup.8 or R.sup.9 is a BLOCK;
- each L is a single covalent bond, or L is a covalent linkage having 1-24 nonhydrogen atoms selected from the group consisting of C, N, O and S and is composed of any combination of single, double, triple or aromatic carbon-carbon bonds, carbon-nitrogen bonds, nitrogen-nitrogen bonds, carbon-oxygen bonds and carbon-sulfur bonds;
- and
- R.sub.x is a reactive site;
- S.sub.c is a conjugated substance;
- and
- each BLOCK moiety is independently a monovalent moiety derived by removal of a hydroxy group from phosphate or from sulfate, or a biologically compatible salt thereof;
- or a monovalent moiety derived by removal of a hydroxy group from a carboxy group of an aliphatic or aromatic carboxylic acid or of an amino acid, protected amino acid, peptide, or protected peptide;
- or a monovalent moiety derived by removal of a hydroxy group from an alcohol or from a mono- or polysaccharide, where said BLOCK is selected to be removable from said compound by action of an enzyme;
- or
- BLOCK is a photolabile caging group.
A method of staining a biological sample, comprising the steps of:
- a) preparing a dye solution comprising a dye compound of the formula:
- ##STR23## or the formula ##STR24## wherein R.sup.1 and R.sup.6 are independently H, F, Cl, Br, I, C.sub.1 -C.sub.18 alkyl or C.sub.1 -C.sub.18 alkoxy;
- R.sup.2, R.sup.3, R.sup.4 and R.sup.5 are independently H, F, Cl, Br, I, CN;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy or C.sub.1 -C.sub.18 alkylthio, where each alkyl, alkoxy or alkylthio is optionally further substituted by F, Cl, Br, I, sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 where R.sup.18 is a C.sub.1 -C.sub.4 alkyl;
- or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
- or one or both of R.sup.3 and R.sup.4 are --CH.sub.2 N(CH.sub.2 COOR.sup.17).sub.2, where R.sup.17 is H, a biologically compatible counterion, a linear or branched alkyl having 1-6 carbons, or --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or one or more of R.sup.2, R.sup.3, R.sup.4, and R.sup.5 is --L--R.sub.x ;
- or one or more of R.sup.2, R.sup.3, R.sup.4, and R.sup.5 is --L--S.sub.c ;
- A is OR.sup.7 or NR.sup.8 R.sup.9,
- where each R.sup.7 is independently a BLOCK, or R.sup.7 is --L--R.sub.x, or R.sup.7 is --L--S.sub.c ;
- R.sup.8 and R.sup.9 are independently H, C.sub.1 -C.sub.6 alkyl, C.sub.1 -C.sub.6 carboxyalkyl, C.sub.1 -C.sub.6 sulfoalkyl, a salt of C.sub.1 -C.sub.6 carboxyalkyl, a salt of C.sub.1 -C.sub.6 sulfoalkyl, or C.sub.1 -C.sub.18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.8 in combination with R.sup.2, or R.sup.9 in combination with R.sup.3, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
- or R.sup.8 in combination with R.sup.9 forms a saturated 5- or 6-membered heterocycle that is a piperidine, a morpholine, a pyrrolidine or a piperazine, each of which is optionally substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or one of R.sup.8 and R.sup.9 is a BLOCK;
- or one of R.sup.8 and R.sup.9 is --L--R.sub.x ;
- or one of R.sup.8 and R.sup.9 is --L--S.sub.c ;
- and
- R.sup.10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.10 is C.sub.1 -C.sub.18 alkyl, alkenyl or alkynyl that is optionally substituted one or more times by F, Cl, Br, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
- or R.sup.10 is --L--R.sub.x ;
- or R.sup.10 is --L--S.sub.c ;
- or R.sup.10 has the formula ##STR25## where R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 are independently H, F, Cl, Br, I;
- or sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, CN, nitro, hydroxy, azido, amino, hydrazino;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy, C.sub.1 -C.sub.18 alkylthio, C.sub.1 -C.sub.18 alkylamino, C.sub.1 -C.sub.18 alkylester, C.sub.1 -C.sub.18 alkylamido or C.sub.1 -C.sub.18 arylamido, the alkyl or aryl portions of which are optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, dialkylamino or alkoxy, the alkyl portions of each having 1-6 carbons;
- or one pair of adjacent substituents R.sup.13 and R.sup.14, R.sup.14 and R.sup.15 or R.sup.15 and R.sup.16, when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or one or more of R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 is --L--R.sub.x ;
- or one or more of R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 is --L--S.sub.c ;
- R.sup.11 is H, hydroxy, CN or a C.sub.1 -C.sub.6 alkoxy;
- or R.sup.10 in combination with R.sup.11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
- or R.sup.11 in combination with R.sup.12 forms a 5- or 6-membered spirolactone ring or a 5- or 6-membered spirosultone ring that is optionally and independently substituted by H, F or CH.sub.3 ;
- or R.sup.10 in combination with R.sup.11 is a carbonyl oxygen;
- provided that at least one of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.6, and R.sup.10 is F, or at least three of R.sup.12, R.sup.13, R.sup.4, R.sup.15 and R.sup.16 are F;
- each L is a single covalent bond, or L is a covalent linkage having 1-24 nonhydrogen atoms selected from the group consisting of C, N, O and S and is composed of any combination of single, double, triple or aromatic carbon-carbon bonds, carbon-nitrogen bonds, nitrogen-nitrogen bonds, carbon-oxygen bonds and carbon-sulfur bonds;
- and
- R.sub.x is a reactive site;
- S.sub.c is a conjugated substance;
- and
- each BLOCK moiety is independently a monovalent moiety derived by removal of a hydroxy group from phosphate or from sulfate, or a biologically compatible salt thereof;
- or a monovalent moiety derived by removal of a hydroxy group from a carboxy group of an aliphatic or aromatic carboxylic acid or of an amino acid, protected amino acid, peptide, or protected peptide;
- or a monovalent moiety derived by removal of a hydroxy group from an alcohol or from a mono- or polysaccharide, where said BLOCK is selected to be removable from said compound by action of an enzyme;
- or
- BLOCK is a photolabile caging group;
- in a concentration sufficient to yield a detectable optical response under the desired conditions;
- b) combining the sample of interest with the dye solution for a period of time sufficient for the dye compound to yield a detectable optical response upon illumination;
- and
- c) illuminating said sample at a wavelength selected to elicit said optical response.
One or more dye compounds of the formula ##STR27## or the formula ##STR28## wherein R.sup.1 and R.sup.6 are independently H, F, Cl, Br, I, C.sub.1 -C.sub.18 alkyl or C.sub.1 -C.sub.18 alkoxy;
- R.sup.2, R.sup.3, R.sup.4 and R.sup.5 are independently H, F, Cl, Br, I, CN;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy or C.sub.1 -C.sub.18 alkylthio, where each alkyl, alkoxy or alkylthio is optionally further substituted by F, Cl, Br, I, sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 where R.sup.18 is a C.sub.1 -C.sub.4 alkyl;
- or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
- A is OR.sup.7 or NR.sup.8 R.sup.9,
- where each R.sup.7 is independently H, C.sub.1 -C.sub.18 alkyl, a C.sub.1 -C.sub.18 acyl wherein each alkyl group independently has 1-6 carbons and is optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- R.sup.8 and R.sup.9 are independently H, C.sub.1 -C.sub.6 alkyl, C.sub.1 -C.sub.6 carboxyalkyl, C.sub.1 -C.sub.6 sulfoalkyl, a salt of C.sub.1 -C.sub.6 carboxyalkyl, a salt of C.sub.1 -C.sub.6 sulfoalkyl, or C.sub.1 -C.sub.18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sup.8 in combination with R.sup.2, or R.sup.9 in combination with R.sup.3, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
- or R.sup.8 in combination with R.sup.9 forms a saturated 5- or 6-membered heterocycle that is a piperidine, a morpholine, a pyrrolidine or a piperazine, each of which is optionally substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- R.sup.10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, or a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- or R.sub.10 is C.sub.1 -C.sub.18 alkyl, alkenyl or alkynyl that is optionally substituted one or more times by F, Cl, Br, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
- or R.sup.10 is --L--;
- or R.sup.10 has the formula ##STR29## where R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 are independently H, F, Cl, Br, I;
- or sulfonic acid, salt of sulfonic acid, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, CN, nitro, hydroxy, azido, amino, hydrazino;
- or C.sub.1 -C.sub.18 alkyl, C.sub.1 -C.sub.18 alkoxy, C.sub.1 -C.sub.18 alkylthio, C.sub.1 -C.sub.18 alkylamino, C.sub.1 -C.sub.18 alkylester, C.sub.1 -C.sub.18 alkylamido or C.sub.1 -C.sub.18 arylamido, the alkyl or aryl portions of which are optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, dialkylamino or alkoxy, the alkyl portions of each having 1-6 carbons;
- or one pair of adjacent substituents R.sup.13 and R.sup.14, R.sup.14 and R.sup.15 or R.sup.15 and R.sup.16, when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C.sub.1 -C.sub.6 alkyl, a carboxylic acid ester of --CH.sub.2 --O--(C.dbd.O)--R.sup.18 ;
- R.sup.11 is H, hydroxy, CN or a C.sub.1 -C.sub.6 alkoxy;
- or R.sup.10 in combination with R.sup.11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
- or R.sup.11 in combination with R.sup.12 forms a 5- or 6-membered spirolactone ring or a 5- or 6-membered spirosultone ring that is optionally and independently substituted by H, F or CH.sub.3 ;
- or R.sup.10 in combination with R.sup.11 is a carbonyl oxygen;
- provided that at least one of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.6, and R.sup.10 is F, or at least three of R.sup.12, R.sup.13, R.sup.14, R.sup.15 and R.sup.16 are F;
- and
- further provided that one of R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.7, R.sup.8, R.sup.9, R.sup.10, R.sup.12, R.sup.13, R.sup.14, R.sup.15 or R.sup.16 on each dye is --L--;
- where each L is a single covalent bond, or L is a covalent linkage having 1-24 nonhydrogen atoms selected from the group consisting of C, N, O and S and is composed of any combination of single, double, triple or aromatic carbon-carbon bonds, carbon-nitrogen bonds, nitrogen-nitrogen bonds, carbon-oxygen bonds and carbon-sulfur bonds;
- and
- each --L-- is bound to a S.sub.c that is a conjugated substance.
Dependencies are inferred from the claim text.