Fluorinated xanthene derivatives
DCFirst Claim
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1. A compound having the formula ##STR10## or the formula ##STR11## wherein R1 and R6 are independently H, F, Cl, Br, I, C1 -C18 alkyl or C1 -C18 alkoxy;
- R2, R3, R4 and R5 are independently H, F, Cl, Br, I, CN;
or C1 -C18 alkyl, C1 -C18 alkoxy or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 where R18 is a C1 -C4 alkyl;
or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
or one or both of R3 and R4 are --CH2 N(CH2 COOR17)2, where R17 is H, a biologically compatible counterion, a linear or branched alkyl having 1-6 carbons, or --CH2 --O--(C═
O)--R18 ;
A is OR7 or NR8 R9,where each R7 is independently H, C1 -C18 alkyl, a C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or a trialkylsilyl wherein each alkyl group independently has 1-6 carbons;
R8 and R9 are independently H, C1 -C6 alkyl, C1 -C6 carboxyalkyl, C1 -C6 sulfoalkyl, a salt of C1 -C6 carboxyalkyl, a salt of C1 -C6 sulfoalkyl, or C1 -C18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R8 in combination with R2, or R9 in combination with R3, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
or R8 in combination with R9 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 C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
R10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R10 is C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
or R10 has the formula ##STR12## where R12, R13, R14, R15 and R16 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, CN, nitro, hydroxy, azido, amino, hydrazino;
or C1 -C18 alkyl, C1 -C18 alkoxy, C1 -C18 alkylthio, C1 -C18 alkylamino, C1 -C18 alkylester, C1 -C18 alkylamido or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, 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 R13 and R14, R14 and R15 or R15 and R16, 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ; and
R11 is H, hydroxy, CN or a C1 -C6 alkoxy;
or R10 in combination with R11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
or R11 in combination with R12 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 CH3 ;
or R10 when taken in combination with R11 is a carbonyl oxygen;
provided that at least one of R1, R2, R3, R4, R5, R6, and R10 is F, or at least three of R12, R13, R14, R15 and R16 are F.
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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.
221 Citations
107 Claims
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1. A compound having the formula ##STR10## or the formula ##STR11## wherein R1 and R6 are independently H, F, Cl, Br, I, C1 -C18 alkyl or C1 -C18 alkoxy;
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R2, R3, R4 and R5 are independently H, F, Cl, Br, I, CN;
or C1 -C18 alkyl, C1 -C18 alkoxy or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 where R18 is a C1 -C4 alkyl;
or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
or one or both of R3 and R4 are --CH2 N(CH2 COOR17)2, where R17 is H, a biologically compatible counterion, a linear or branched alkyl having 1-6 carbons, or --CH2 --O--(C═
O)--R18 ;A is OR7 or NR8 R9, where each R7 is independently H, C1 -C18 alkyl, a C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or a trialkylsilyl wherein each alkyl group independently has 1-6 carbons;R8 and R9 are independently H, C1 -C6 alkyl, C1 -C6 carboxyalkyl, C1 -C6 sulfoalkyl, a salt of C1 -C6 carboxyalkyl, a salt of C1 -C6 sulfoalkyl, or C1 -C18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R8 in combination with R2, or R9 in combination with R3, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
or R8 in combination with R9 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 C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;R10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R10 is C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
or R10 has the formula ##STR12## where R12, R13, R14, R15 and R16 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, CN, nitro, hydroxy, azido, amino, hydrazino;
or C1 -C18 alkyl, C1 -C18 alkoxy, C1 -C18 alkylthio, C1 -C18 alkylamino, C1 -C18 alkylester, C1 -C18 alkylamido or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, 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 R13 and R14, R14 and R15 or R15 and R16, 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ; andR11 is H, hydroxy, CN or a C1 -C6 alkoxy;
or R10 in combination with R11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
or R11 in combination with R12 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 CH3 ;
or R10 when taken in combination with R11 is a carbonyl oxygen;provided that at least one of R1, R2, R3, R4, R5, R6, and R10 is F, or at least three of R12, R13, R14, R15 and R16 are F. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22)
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23. A compound having the formula ##STR14## or the formula ##STR15## wherein R1 and R6 are independently H, F, Cl, Br, I, C1 -C18 alkyl or C1 -C18 alkoxy;
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R2, R3, R4 and R5 are independently H, F, Cl, Br, I, CN;
or C1 -C18 alkyl, C1 -C18 alkoxy or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 where R18 is a C1 -C4 alkyl;
or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
or one or more of R2, R3, R4, and R5 is --L--Rx ;A is OR7 or NR8 R9, where each R7 is independently H, C1 -C18 alkyl, a C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or a trialkylsilyl wherein each alkyl group independently has 1-6 carbons;
or R7 is an --L--Rx ;R8 and R9 are independently H, C1 -C6 alkyl, C1 -C6 carboxyalkyl, C1 -C6 sulfoalkyl, a salt of C1-C6 carboxyalkyl, a salt of C1 -C6 sulfoalkyl, or C1 -C18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R8 in combination with R2, or R9 in combination with R8, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
or R8 in combination with R9 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 C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or one of R8 and R9 is --L--Rx ; andR10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R10 is C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
or R10 is an --L--Rx ;
or R10 has the formula ##STR16## where R12, R13, R14, R15 and R16 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, CN, nitro, hydroxy, azido, amino, hydrazino;
or C1 -C18 alkyl, C1 -C18 alkoxy, C1 -C18 alkylthio, C1 -C18 alkylamino, C1 -C18 alkylester, C1 -C18 alkylamido or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, 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 R13 and R14, R14 and R15 or R15 and R16, 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or one or more of R12, R13, R14, R15 and R16 is --L--Rx ;R11 is H, hydroxy, CN or a C1 -C6 alkoxy;
or R10 in combination with R11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
or R11 in combination with R12 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 CH3 ;
or R10 when taken in combination with R11 is a carbonyl oxygen;provided that at least one of R1, R2, R3, R4, R5, R6, and R10 is F, or at least three of R12, R13, R14, R15 and R16 are F; and further provided that at least one of R2, R3, R4, R5, R7, R8, R9, R10, R12, R13, R14, R15 and R16 is --L--Rx, where each --L--Rx 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 Rx is a reactive site. - View Dependent Claims (24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45)
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46. A compound having the formula ##STR17## or the formula ##STR18## wherein R1 and R6 are independently H, F, Cl, Br, I, C1 -C18 alkyl or C1 -C18 alkoxy;
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R2, R3, R4 and R5 are independently H, F, Cl, Br, I, CN;
or C1 -C18 alkyl, C1 -C18 alkoxy or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 where R18 is a C1 -C4 alkyl;
or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
or one or more of R2, R3, R4, and R5 is --L--Sc ;A is OR7 or NR8 R9, where each R7 is independently H, C1 -C18 alkyl, a C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R7 is --L--Sc ;R8 and R9 are independently H, C1 -C6 alkyl, C1 -C6 carboxyalkyl, C1 -C6 sulfoalkyl, a salt of C1 -C6 carboxyalkyl, a salt of C1 -C6 sulfoalkyl, or C1 -C18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R8 in combination with R2, or R9 in combination with R3, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
or R8 in combination with R9 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 C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or one of R8 and R9 is --L--Sc ; andR10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R10 is C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
or R10 is --L--Sc ;
or R10 has the formula ##STR19## where R12, R13, R14, R15 and R16 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, CN, nitro, hydroxy, azido, amino, hydrazino;
or C1 -C18 alkyl, C1 -C18 alkoxy, C1 -C18 alkylthio, C1 -C18 alkylamino, C1 -C18 alkylester, C1 -C18 alkylamido or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, 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 R13 and R14, R14 and R15 or R15 and R16, 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or one or more of R12, R13, R14, R15 and R16 is --L--Sc ;R11 is H, hydroxy, CN or a C1 -C6 alkoxy;
or R10 in combination with R11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
or R11 in combination with R12 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 CH3 ;
or R10 in combination with R11 is a carbonyl oxygen;provided that at least one of R1, R2, R3, R4, R5, R6 and R10 is F, or at least three of R12, R13, R14, R15 and R16 are F; and further provided that at least one of R2, R3, R4, R5, R7, R8, R9, R10, R12, R13, R14, R15 and R16 is an --L--Sc ; 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 Sc is a conjugated substance. - View Dependent Claims (47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 104, 105, 106, 107)
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67. A compound having the formula ##STR20## or the formula ##STR21## wherein R1 and R6 are independently H, F, Cl, Br, I, C1 -C18 alkyl or C1 -C18 alkoxy;
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R2, R3, R4 and R5 are independently H, F, Cl, Br, I, CN;
or C1 -C18 alkyl, C1 -C18 alkoxy or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 where R18 is a C1 -C4 alkyl;
or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
or one or both of R3 and R4 are --CH2 N(CH2 COOR17)2, where R17 is H, a biologically compatible counterion, a linear or branched alkyl having 1-6 carbons, or --CH2 --O--(C═
O)--R18 ;
or one or more of R2, R3, R4, and R5 is --L--Rx ;
or one or more of R2, R3, R4, and R5 is --L--Sc ;A is OR7 or NR8 R9, where each R7 is independently a BLOCK, or R7 is --L--Rx, or R7 is --L--Sc ; R8 and R9 are independently H, C1 -C6 alkyl, C1 -C6 carboxyalkyl, C1 -C6 sulfoalkyl, a salt of C1 -C6 carboxyalkyl, a salt of C1 -C6 sulfoalkyl, or C1 -C18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R8 in combination with R2, or R9 in combination with R3, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
or R8 in combination with R9 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 C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or one of R8 and R9 is a BLOCK;
or one of R8 and R9 is --L--Rx ;
or one of R8 and R9 is --L--Sc ; andR10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R10 is C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
or R10 is --L--Rx ;
or R10 is --L--Sc ;
or R10 has the formula ##STR22## where R12, R13, R14, R15 and R16 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, CN, nitro, hydroxy, azido, amino, hydrazino;
or C1 -C18 alkyl, C1 -C18 alkoxy, C1 -C18 alkylthio, C1 -C18 alkylamino, C1 -C18 alkylester, C1 -C18 alkylamido or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, 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 R13 and R14, R14 and R15 or R15 and R16, 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or one or more of R12, R13, R14, R15 and R16 is --L--Rx ;
or one or more of R12, R13, R14, R15 and R16 is --L--Sc ;R11 is H, hydroxy, CN or a C1 -C6 alkoxy;
or R10 in combination with R11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
or R11 in combination with R12 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 CH3 ;
or R10 in combination with R11 is a carbonyl oxygen;provided that at least one of R1, R2, R3, R4, R5, R6, and R10 is F, or at least three of R12, R13, R14, R15 and R16 are F; and further provided at least one of R7, R8 or R9 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 Rx is a reactive site; Sc 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. - View Dependent Claims (68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86)
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87. A method of staining a biological sample, comprising the steps of:
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a) preparing a dye solution comprising a dye compound of the formula;
##STR23## or the formula ##STR24## wherein R1 and R6 are independently H, F, Cl, Br, I, C1 -C18 alkyl or C1 -C18 alkoxy;R2, R3, R4 and R5 are independently H, F, Cl, Br, I, CN;
or C1 -C18 alkyl, C1 -C18 alkoxy or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 where R18 is a C1 -C4 alkyl;
or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;
or one or both of R3 and R4 are --CH2 N(CH2 COOR17)2, where R17 is H, a biologically compatible counterion, a linear or branched alkyl having 1-6 carbons, or --CH2 --O--(C═
O)--R18 ;
or one or more of R2, R3, R4, and R5 is --L--Rx ;
or one or more of R2, R3, R4, and R5 is --L--Sc ;A is OR7 or NR8 R9, where each R7 is independently a BLOCK, or R7 is --L--Rx, or R7 is --L--Sc ; R8 and R9 are independently H, C1 -C6 alkyl, C1 -C6 carboxyalkyl, C1 -C6 sulfoalkyl, a salt of C1 -C6 carboxyalkyl, a salt of C1 -C6 sulfoalkyl, or C1 -C18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R8 in combination with R2, or R9 in combination with R3, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
or R8 in combination with R9 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 C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or one of R8 and R9 is a BLOCK;
or one of R8 and R9 is --L--Rx ;
or one of R8 and R9 is --L--Sc ; andR10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R10 is C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
or R10 is --L--Rx ;
or R10 is --L--Sc ;
or R10 has the formula ##STR25## where R12, R13, R14, R15 and R16 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, CN, nitro, hydroxy, azido, amino, hydrazino;
or C1 -C18 alkyl, C1 -C18 alkoxy, C1 -C18 alkylthio, C1 -C18 alkylamino, C1 -C18 alkylester, C1 -C18 alkylamido or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, 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 R13 and R14, R14 and R15 or R15 and R16, 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or one or more of R12, R13, R14, R15 and R16 is --L--Rx ;
or one or more of R12, R13, R14, R15 and R16 is --L--Sc ;R11 is H, hydroxy, CN or a C1 -C6 alkoxy;
or R10 in combination with R11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
or R11 in combination with R12 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 CH3 ;
or R10 in combination with R11 is a carbonyl oxygen;provided that at least one of R1, R2, R3, R4, R5, R6, and R10 is F, or at least three of R12, R13, R4, R15 and R16 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 Rx is a reactive site; Sc 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. - View Dependent Claims (88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102)
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103. One or more dye compounds of the formula ##STR27## or the formula ##STR28## wherein R1 and R6 are independently H, F, Cl, Br, I, C1 -C18 alkyl or C1 -C18 alkoxy;
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R2, R3, R4 and R5 are independently H, F, Cl, Br, I, CN;
or C1 -C18 alkyl, C1 -C18 alkoxy or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 where R18 is a C1 -C4 alkyl;
or amino, alkylamino, dialkylamino, or alkoxy, the alkyl portions of which independently have 1-6 carbons;A is OR7 or NR8 R9, where each R7 is independently H, C1 -C18 alkyl, a C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;R8 and R9 are independently H, C1 -C6 alkyl, C1 -C6 carboxyalkyl, C1 -C6 sulfoalkyl, a salt of C1 -C6 carboxyalkyl, a salt of C1 -C6 sulfoalkyl, or C1 -C18 acyl wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R8 in combination with R2, or R9 in combination with R3, or both, form a saturated 5- or 6-membered ring that is optionally substituted by one or more methyls;
or R8 in combination with R9 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 C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;R10 is F, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C1 -C6 alkyl, or a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;
or R10 is C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, sulfonic acid, salt of sulfonic acid, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;
or R10 is --L--;
or R10 has the formula ##STR29## where R12, R13, R14, R15 and R16 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, CN, nitro, hydroxy, azido, amino, hydrazino;
or C1 -C18 alkyl, C1 -C18 alkoxy, C1 -C18 alkylthio, C1 -C18 alkylamino, C1 -C18 alkylester, C1 -C18 alkylamido or C1 -C18 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18, 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 R13 and R14, R14 and R15 or R15 and R16, 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 C1 -C6 alkyl, a carboxylic acid ester of --CH2 --O--(C═
O)--R18 ;R11 is H, hydroxy, CN or a C1 -C6 alkoxy;
or R10 in combination with R11 forms a 5-membered spirolactone ring or a 5-membered spirosultone ring;
or R11 in combination with R12 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 CH3 ;
or R10 in combination with R11 is a carbonyl oxygen;provided that at least one of R1, R2, R3, R4, R5, R6, and R10 is F, or at least three of R12, R13, R14, R15 and R16 are F; and further provided that one of R2, R3, R4, R5, R7, R8, R9, R10, R12, R13, R14, R15 or R16 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 Sc that is a conjugated substance.
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Specification