US5863753A — Chemically reactive unsymmetrical cyanine dyes an…

Claim 1

Independent Claim 869 words

A compound of the formula ##STR41## wherein each R 1 is independently H; or an alkyl group having from 1-6 carbons; an alkoxy group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or -L-R x ; R 2 is an alkyl group having 1-6 carbons; or -L-R x ; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons; n=0, 1 or 2; ψ - is a compatible counterion; Y is --CR 3 ═CR 4 --; p and m=0 or 1, such that p+m=1; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl; or R 5 is a TAIL; or R 5 is -L-R x ; R 4 is H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or a halogen; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or a TAIL; or -L-R x ; where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or -L-R x ; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR42## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ); or a TAIL; or -L-R x ; L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; R x is a reactive group; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR43## where R 21 , R 22 , R 23 , and ψ - are as defined previously; such that at least one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x ; and where more than one of R 1 R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x , each -L-R x is optionally the same or different; provided that when R 5 is -L-R x and m=1, R 4 is not hydrogen.

Claim 2

Dependent Claim 869 words

A compound of the formula ##STR41## wherein each R 1 is independently H; or an alkyl group having from 1-6 carbons; an alkoxy group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or -L-R x ; R 2 is an alkyl group having 1-6 carbons; or -L-R x ; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons; n=0, 1 or 2; ψ - is a compatible counterion; Y is --CR 3 ═CR 4 --; p and m=0 or 1, such that p+m=1; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl; or R 5 is a TAIL; or R 5 is -L-R x ; R 4 is H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or a halogen; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or a TAIL; or -L-R x ; where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or -L-R x ; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR42## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ); or a TAIL; or -L-R x ; L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; R x is a reactive group; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR43## where R 21 , R 22 , R 23 , and ψ - are as defined previously; such that at least one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x ; and where more than one of R 1 R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x , each -L-R x is optionally the same or different; provided that when R 5 is -L-R x and m=1, R 4 is not hydrogen.

Claim 3

Dependent Claim 97 words

A compound, as claimed in claim 1, wherein R x is a reactive group that is a carboxylic acid, an activated ester of a carboxylic acid, an acyl azide, an acyl halide, an acyl nitrile, an aldehyde, an anhydride, an acrylamide, an alkyl halide, a sulfonate, an aniline, an aryl halide, a thiol, an azide, an aziridine, a boronate, a carbodiimide, a diazoalkane, an epoxide, a glycol, a haloacetamide, a halotriazine, a hydrazine, a hydroxylamine, an imido ester, an isocyanate, an isothiocyanate, a ketone, an aldehyde, a maleimide, a phosphoramidite, a silyl halide, or a sulfonyl halide.

Claim 4

Dependent Claim 38 words

A compound, as claimed in claim 1, wherein R x is an activated ester of a carboxylic acid, an aldehyde, an alkyl halide, a haloacetamide, a halotriazine, a hydrazine, an isothiocyanate, a maleimide, a thiol, or an azide.

Claim 5

Dependent Claim 13 words

A compound, as claimed in claim 1, wherein R 4 is not hydrogen.

Claim 6

Dependent Claim 9 words

A compound, as claimed in claim 1, wherein m=1.

Claim 7

Dependent Claim 36 words

A compound, as claimed in claim 1 wherein R 6 and R 7 form a fused aromatic ring; and at least three of R 11 , R 12 , R 13 and R 14 are H.

Claim 8

Dependent Claim 26 words

A compound, as claimed in claim 1, wherein R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons.

Claim 9

Dependent Claim 14 words

A compound, as claimed in claim 1, wherein R 5 is -L-R x .

Claim 10

Dependent Claim 16 words

A compound, as claimed in claim 8, wherein R 4 is -L-R x , and m=1.

Claim 11

Dependent Claim 77 words

A compound, as claimed in claim 9, wherein R 1 and R 3 are H; R 2 is methyl or ethyl; X is O or S; R 5 is an alkyl having 1-6 carbons, or an aryl or heteroaryl; or R 5 is a TAIL; R 6 and R 7 form a fused aromatic ring; at least three of R 11 , R 12 , R 13 , and R 14 are H; and n=0 or 1.

Claim 12

Dependent Claim 53 words

A compound, as claimed in claim 8, wherein R 4 is an alkyl that is saturated or unsaturated, linear or branched having 1-6 carbons; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or R 4 is a TAIL.

Claim 13

Dependent Claim 84 words

A compound, as claimed in claim 1, wherein R 1 and R 3 are H; R 2 is methyl or ethyl; X is O or S; R 5 is an alkyl having 1-6 carbons, or an aryl or heteroaryl; or R 5 is a TAIL; or R 5 is -L-R x ; R 6 and R 7 form a fused aromatic ring; at least three of R 11 , R 12 , R 13 , and R 14 are H; and n=0 or 1.

Claim 14

Dependent Claim 14 words

A compound, as claimed in claim 12, wherein R 5 is aryl or heteroaryl.

Claim 15

Dependent Claim 19 words

A compound, as claimed in claim 12, wherein one of R 4 and R 5 is -L-R x .

Claim 16

Dependent Claim 870 words

A compound of the formula ##STR44## wherein each R 1 is independently H; or an alkyl group having from 1-6 carbons; an alkoxy group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or -L-S c ; R 2 is an alkyl group having 1-6 carbons; or -L-S c ; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-6 carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons; n=0, 1 or 2; ψ - is a compatible counterion; Y is --CR 3 ═CR 4 --; p and m=0 or 1, such that p+m=1; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl; or R 5 is a TAIL; or R 5 is -L-S c ; R 4 is H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or a halogen; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or a TAIL; or -L-S c ; where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or -L-S c ; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR45## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ); or a TAIL; or -L-S c ; L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; S c is a conjugated substance; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR46## where R 21 , R 22 , R 23 , and ψ - are as defined previously; such that at least one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-S c ; and where more than one of R 1 R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-S c , each -L-S c is optionally the same or different; provided that when R 5 is -L-S c and m=1, R 4 is not hydrogen.

Claim 17

Dependent Claim 870 words

A compound of the formula ##STR44## wherein each R 1 is independently H; or an alkyl group having from 1-6 carbons; an alkoxy group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or -L-S c ; R 2 is an alkyl group having 1-6 carbons; or -L-S c ; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-6 carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons; n=0, 1 or 2; ψ - is a compatible counterion; Y is --CR 3 ═CR 4 --; p and m=0 or 1, such that p+m=1; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl; or R 5 is a TAIL; or R 5 is -L-S c ; R 4 is H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or a halogen; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or a TAIL; or -L-S c ; where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or -L-S c ; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR45## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ); or a TAIL; or -L-S c ; L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; S c is a conjugated substance; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR46## where R 21 , R 22 , R 23 , and ψ - are as defined previously; such that at least one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-S c ; and where more than one of R 1 R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-S c , each -L-S c is optionally the same or different; provided that when R 5 is -L-S c and m=1, R 4 is not hydrogen.

Claim 18

Dependent Claim 18 words

A compound, as claimed in claim 15, wherein S c is a member of a specific binding pair.

Claim 19

Dependent Claim 16 words

A compound, as claimed in claim 16, wherein S c is a drug or a hapten.

Claim 20

Dependent Claim 43 words

A compound, as in claim 15, wherein S c is an amino acid, peptide, protein, polysaccharide, a nucleic acid base, nucleoside, nucleotide or a nucleic acid polymer, lipid, lipophilic polymer, non-biological organic polymer, polymeric microparticle, animal cell, plant cell, bacterium, yeast, or virus.

Claim 21

Dependent Claim 30 words

A compound, as in claim 18, wherein S c is an amino acid, peptide, protein, nucleotide, a nucleic acid polymer, a polysaccharide, or a non-biological organic polymer or polymeric microparticle.

Claim 22

Dependent Claim 17 words

A compound, as in claim 19, wherein S c is a protein, or a nucleic acid polymer.

Claim 23

Dependent Claim 17 words

A compound, as claimed in claim 15, wherein S c is an enzyme, or an enzyme substrate.

Claim 24

Dependent Claim 18 words

A compound, as claimed in claim 15, wherein neither R 1 nor R 2 is -L-S c .

Claim 25

Dependent Claim 13 words

A compound, as claimed in claim 15, wherein R 4 is not hydrogen.

Claim 26

Dependent Claim 9 words

A compound, as claimed in claim 15, wherein m=1.

Claim 27

Dependent Claim 36 words

A compound, as claimed in claim 15 wherein R 6 and R 7 form a fused aromatic ring; and at least three of R 11 , R 12 , R 13 and R 14 are H.

Claim 28

Dependent Claim 26 words

A compound, as claimed in claim 15 wherein R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons.

Claim 29

Dependent Claim 14 words

A compound, as claimed in claim 15, wherein R 5 is -L-S c .

Claim 30

Dependent Claim 15 words

A compound, as claimed in claim 15, wherein R 4 is -L-S c and m=1.

Claim 31

Dependent Claim 77 words

A compound, as claimed in claim 15, wherein R 1 and R 3 are H; R 2 is methyl or ethyl; X is O or S; R 5 is an alkyl having 1-6 carbons, or an aryl or heteroaryl; or R 5 is a TAIL; R 6 and R 7 form a fused aromatic ring; at least three of R 11 , R 12 , R 13 , and R 14 are H; and n=0 or 1.

Claim 32

Dependent Claim 53 words

A compound, as claimed in claim 15, wherein R 4 is an alkyl that is saturated or unsaturated, linear or branched having 1-6 carbons; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or R 4 is a TAIL.

Claim 33

Dependent Claim 77 words

A compound, as claimed in claim 15 wherein R 1 and R 3 are H; R 2 is methyl or ethyl; X is O or S; R 5 is an alkyl having 1-6 carbons, or an aryl or heteroaryl; or R 5 is a TAIL; R 6 and R 7 form a fused aromatic ring; at least three of R 11 , R 12 , R 13 , and R 14 are H; and n=0 or 1.

Claim 34

Dependent Claim 14 words

A compound, as claimed in claim 31, wherein R 5 is aryl or heteroaryl.

Claim 35

Dependent Claim 927 words

A complex comprising a nucleic acid polymer non-covalently bound to a dye of the formula ##STR47## wherein each R 1 is independently H; or an alkyl group having from 1-6 carbons; an alkoxy group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or -L-R x ; or -L-S c ; R 2 is an alkyl group having 1-6 carbons; or -L-R x ; or -L-S c ; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-6 carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons; n=0, 1 or 2; ψ - is a compatible counterion; Y is --CR 3 ═CR 4 --; p and m=0 or 1, such that p+m=1; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl; or R 5 is a TAIL; or R 5 is -L-R x ; or R 5 is -L-S c ; R 4 is H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or a halogen; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or a TAIL; or -L-R x ; or -L-S c ; where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or -L-R x ; or -L-S c ; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR48## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ); or a TAIL; or -L-R x ; or -L-S c ; each L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; R x is a reactive group; S c is a conjugated substance; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR49## ; where R 21 , R 22 , R 23 , and ψ - are as defined previously; such that at least one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x or -L-S c ; and where more than one of R 1 R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x or -L-S c , each -L-R x and -L-S c is optionally the same or different; provided that when R 5 is -L-R x or -L-S c and m=1, R 4 is not hydrogen.

Claim 36

Dependent Claim 927 words

A complex comprising a nucleic acid polymer non-covalently bound to a dye of the formula ##STR47## wherein each R 1 is independently H; or an alkyl group having from 1-6 carbons; an alkoxy group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or -L-R x ; or -L-S c ; R 2 is an alkyl group having 1-6 carbons; or -L-R x ; or -L-S c ; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-6 carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons; n=0, 1 or 2; ψ - is a compatible counterion; Y is --CR 3 ═CR 4 --; p and m=0 or 1, such that p+m=1; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl; or R 5 is a TAIL; or R 5 is -L-R x ; or R 5 is -L-S c ; R 4 is H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or a halogen; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or a TAIL; or -L-R x ; or -L-S c ; where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or -L-R x ; or -L-S c ; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR48## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ); or a TAIL; or -L-R x ; or -L-S c ; each L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; R x is a reactive group; S c is a conjugated substance; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR49## ; where R 21 , R 22 , R 23 , and ψ - are as defined previously; such that at least one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x or -L-S c ; and where more than one of R 1 R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x or -L-S c , each -L-R x and -L-S c is optionally the same or different; provided that when R 5 is -L-R x or -L-S c and m=1, R 4 is not hydrogen.

Claim 37

Dependent Claim 58 words

A complex, as claimed in claim 33, wherein one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-S c , and S c is a member of a specific binding pair.

Claim 38

Dependent Claim 28 words

A complex, as claimed in claim 34, wherein the specific binding pair member is a drug, a hapten, an enzyme, an enzyme substrate, an oligonucleotide, or a peptide.

Claim 39

Dependent Claim 14 words

A complex, as claimed in claim 33, wherein S c is an organic polymer.

Claim 40

Dependent Claim 18 words

A complex, as claimed in claim 36, wherein S c is a polymeric microparticle, or a polymeric membrane.

Claim 41

Dependent Claim 16 words

A complex, as claimed in claim 36, wherein S c is poly(ethylene glycol) or a polysaccharide.

Claim 42

Dependent Claim 42 words

A complex, as claimed in claim 33, wherein R 4 is not hydrogen, m=1, R 6 and R 7 form a fused aromatic ring; and at least three of R 11 , R 12 , R 13 and R 14 are H.

Claim 43

Dependent Claim 53 words

A compound, as claimed in claim 39, wherein R 4 is an alkyl that is saturated or unsaturated, linear or branched having 1-6 carbons; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or R 4 is a TAIL.

Claim 44

Dependent Claim 36 words

A complex, as claimed in claim 33, wherein R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons and R 4 is -L-R x or -L-S c .

Claim 45

Dependent Claim 17 words

A complex, as claimed in claim 33, wherein R 5 is -L-R x or -L-S c .

Claim 46

Dependent Claim 17 words

A complex, as claimed in claim 33, wherein R 4 is -L-R x or -L-S c .

Claim 47

Independent Claim 976 words

A method of forming a nucleic acid complex, comprising a) combining a sample that contains or is thought to contain a nucleic acid, with a mixture containing a compound of the formula ##STR50## wherein each R 1 is independently H; or an alkyl group having from 1-6 carbons; an alkoxy group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or -L-R x ; or -L-S c ; R 2 is an alkyl group having 1-6 carbons; or -L-R x ; or -L-S c ; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-6 carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons; n=0, 1 or 2; ψ - is a compatible counterion; Y is --CR 3 ═CR 4 --; p and m=0 or 1, such that p+n=1; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl; or R 5 is a TAIL; or R 5 is -L-R x ; or R 5 is -L-S c ; R 4 is H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or a halogen; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or a TAIL; or -L-R x ; or -L-S c ; where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or -L-R x ; or -L-S c ; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR51## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ); or a TAIL; or -L-R x ; or -L-S c ; each L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; R x is a reactive group; S c is a conjugated substance; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR52## ; where R 21 , R 22 , R 23 , and ψ - are as defined previously; such that at least one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x or -L-S c ; and where more than one of R 1 R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x or -L-S c , each -L-R x and -L-S c is optionally the same or different; provided that when R 5 is -L-R x or -L-S c and m=1, R 4 is not hydrogen; and b) incubating the sample and mixture for a time sufficient for the compound to associate non-covalently with the nucleic acid in the sample to form one or more nucleic acid complexes.

Claim 48

Independent Claim 976 words

A method of forming a nucleic acid complex, comprising a) combining a sample that contains or is thought to contain a nucleic acid, with a mixture containing a compound of the formula ##STR50## wherein each R 1 is independently H; or an alkyl group having from 1-6 carbons; an alkoxy group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or -L-R x ; or -L-S c ; R 2 is an alkyl group having 1-6 carbons; or -L-R x ; or -L-S c ; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-6 carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons; n=0, 1 or 2; ψ - is a compatible counterion; Y is --CR 3 ═CR 4 --; p and m=0 or 1, such that p+n=1; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl; or R 5 is a TAIL; or R 5 is -L-R x ; or R 5 is -L-S c ; R 4 is H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or a halogen; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or a TAIL; or -L-R x ; or -L-S c ; where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or -L-R x ; or -L-S c ; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR51## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ); or a TAIL; or -L-R x ; or -L-S c ; each L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; R x is a reactive group; S c is a conjugated substance; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR52## ; where R 21 , R 22 , R 23 , and ψ - are as defined previously; such that at least one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x or -L-S c ; and where more than one of R 1 R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-R x or -L-S c , each -L-R x and -L-S c is optionally the same or different; provided that when R 5 is -L-R x or -L-S c and m=1, R 4 is not hydrogen; and b) incubating the sample and mixture for a time sufficient for the compound to associate non-covalently with the nucleic acid in the sample to form one or more nucleic acid complexes.

Claim 49

Dependent Claim 17 words

A method, as claimed in claim 44, wherein said nucleic acid complex exhibits a detectable optical response.

Claim 50

Dependent Claim 16 words

A method, as claimed in claim 45, wherein the detectable optical response is a fluorescence response.

Claim 51

Dependent Claim 47 words

A method, as claimed in claim 45, wherein one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 11 , R 12 , R 13 , and R 14 is -L-S c .

Claim 52

Dependent Claim 17 words

A method, as claimed in claim 47, further comprising separating the nucleic acid complex from the sample.

Claim 53

Dependent Claim 14 words

A method, as claimed in claim 47, wherein S c is an organic polymer.

Claim 54

Dependent Claim 16 words

A method, as claimed in claim 49, wherein S c is poly(ethylene glycol) or a polysaccharide.

Claim 55

Dependent Claim 18 words

A method, as claimed in claim 47, wherein S c is a polymeric microparticle, or a polymeric membrane.

Claim 56

Dependent Claim 34 words

A method, as claimed in claim 51, wherein the polymeric microparticle is a magnetic microparticle and, further comprising separating the nucleic acid complex from the sample by removing the magnetic microparticle from the sample.

Claim 57

Dependent Claim 25 words

A method, as claimed in claim 47, wherein S c is a first member of a specific binding pair having a first and second member.

Claim 58

Dependent Claim 28 words

A method, as claimed in claim 53, wherein the formation of said complex indicates the location of the second member of the specific binding pair in the sample.

Claim 59

Dependent Claim 28 words

A method, as claimed in claim 53, wherein the first member is a drug, a hapten, an enzyme substrate, a nucleic acid polymer, a peptide, or a protein.

Claim 60

Dependent Claim 23 words

A method, as claimed in claim 53, wherein the first member is a biotin, a digoxigenin, an avidin, a streptavidin, or an antibody.

Claim 61

Dependent Claim 26 words

A method, as claimed in claim 54, wherein the sample comprises one or more cells, bacteria, virus, yeast cells, or a polymeric membrane or polymeric microparticles.

Claim 62

Dependent Claim 42 words

A method, as claimed in claim 44, wherein R 4 is not hydrogen, m=1, R 6 and R 7 form a fused aromatic ring; and at least three of R 11 , R 12 , R 13 and R 14 are H.

Claim 63

Dependent Claim 53 words

A method, as claimed in claim 44, wherein R 4 is an alkyl that is saturated or unsaturated, linear or branched having 1-6 carbons; or an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons; or --OR 8 , --SR 8 , --(NR 8 R 9 ); or R 4 is a TAIL.

Claim 64

Dependent Claim 36 words

A method, as claimed in claim 44, wherein R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl having 3-10 carbons and R 4 is -L-R x or -L-S c .

Claim 65

Dependent Claim 17 words

A method, as claimed in claim 44, wherein R 5 is -L-R x or -L-S c .

Claim 66

Dependent Claim 17 words

A method, as claimed in claim 44, wherein R 4 is -L-R x or -L-S c .

Claim 67

Dependent Claim 639 words

A compound of the formula ##STR53## wherein X is O or S; R 2 is an alkyl group having 1-6 carbons; n=0, 1 or2; ψ - is a compatible counterion; R 4 is an aryl or heteroaryl that is optionally substituted by halogen, alkyl, perfluoroalkyl, amino, alkylamino, dialkylamino, alkoxy or carboxyalkyl, each alkyl group having 1-6 carbons; or is substituted by TAIL; or is substituted by -L-R x ; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; an aryl or heteroaryl; or R 5 is a TAIL; or R 5 is -L-R x ; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR54## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or an alkoxy having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ) where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; or a TAIL; L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; R x is a reactive group; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N, S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR55## where R 21 , R 22 , R 23 , and ψ - are as defined previously.

Claim 68

Dependent Claim 639 words

A compound of the formula ##STR53## wherein X is O or S; R 2 is an alkyl group having 1-6 carbons; n=0, 1 or2; ψ - is a compatible counterion; R 4 is an aryl or heteroaryl that is optionally substituted by halogen, alkyl, perfluoroalkyl, amino, alkylamino, dialkylamino, alkoxy or carboxyalkyl, each alkyl group having 1-6 carbons; or is substituted by TAIL; or is substituted by -L-R x ; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; an aryl or heteroaryl; or R 5 is a TAIL; or R 5 is -L-R x ; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR54## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or an alkoxy having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ) where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; or a TAIL; L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; R x is a reactive group; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N, S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR55## where R 21 , R 22 , R 23 , and ψ - are as defined previously.

Claim 69

Dependent Claim 55 words

A compound, as claimed in claim 63, wherein R 4 is a naphthyl, a phenyl, a thienyl, a benzothiazolyl, a furanyl, an oxazolyl, a benzoxazolyl, or a pyridinyl that is optionally substituted by halogen, alkyl, perfluoroalkyl, amino, alkylamino, dialkylamino, alkoxy or carboxyalkyl, each alkyl group having 1-6 carbons; or by TAIL; or -L-R x .

Claim 70

Dependent Claim 18 words

A compound, as claimed in claim 64, wherein R 4 is substituted by TAIL or -L-R x .

Claim 71

Dependent Claim 105 words

A compound, as claimed in claim 65, wherein R 4 is substituted by TAIL having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER' independently have the formula --(CH 2 ) k --, where k=1-8, CAP and CAP', which may be the same or different, are --NR 21 R 22 or --N + R 21 R 22 R 23 ψ - ; where R 21 , R 22 , and R 23 are independently methyl or ethyl.

Claim 72

Dependent Claim 16 words

A compound, as claimed in claim 64, wherein R 5 is an alkyl having 1-6 carbons.

Claim 73

Dependent Claim 732 words

A compound of the formula ##STR56## or of the formula ##STR57## wherein each R 1 is independently H; or an alkyl group having from 1-6 carbons; an alkoxy group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or -L-R x ; R 2 is an alkyl group having 1-6 carbons; or -L-R x ; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-6 carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons; n=0, 1 or 2; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl; or R 5 is a TAIL; or R 5 is -L-R x ; R 4 is NR 19 ; where R 19 is an alkyl group having 1-6 carbons; or an alicyclic or aromatic ring; or R 19 is -SPACER-CAP; or R 19 is -L-R x ; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or -L-R x ; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR58## or the formula ##STR59## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ), where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; or a TAIL; or -L-R x ; L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; R x is a reactive group; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR60## where R 21 , R 22 , R 23 , and ψ - are as defined previously.

Claim 74

Dependent Claim 732 words

A compound of the formula ##STR56## or of the formula ##STR57## wherein each R 1 is independently H; or an alkyl group having from 1-6 carbons; an alkoxy group having from 1-6 carbons; or a trifluoromethyl; or a halogen; or -L-R x ; R 2 is an alkyl group having 1-6 carbons; or -L-R x ; X is O, S, Se or NR 15 , where R 15 is H or an alkyl group having 1-6 carbons; or X is CR 16 R 17 where R 16 and R 17 , which may be the same or different, are independently alkyl groups having 1-6 carbons; n=0, 1 or 2; R 5 is an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or R 5 is a cyclic substituent that is an aryl or heteroaryl; or a cycloalkyl; or R 5 is a TAIL; or R 5 is -L-R x ; R 4 is NR 19 ; where R 19 is an alkyl group having 1-6 carbons; or an alicyclic or aromatic ring; or R 19 is -SPACER-CAP; or R 19 is -L-R x ; R 3 , R 6 and R 7 are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or -L-R x ; or R 6 and R 7 form a fused aromatic ring such that said compound has the formula ##STR58## or the formula ##STR59## wherein R 11 , R 12 , R 13 , and R 14 , which may be the same or different, are independently H; or an alkyl that is saturated or unsaturated, linear or branched, having 1-6 carbons; or --OR 8 , --SR 8 , or --(NR 8 R 9 ), where R 8 and R 9 , which can be the same or different, are independently alkyl groups having 1-6 carbons; or 1-2 alicyclic or aromatic rings; or R 8 and R 9 taken in combination are --(CH 2 ) 2 --V--(CH 2 ) 2 -- where V is a single bond, --O--, --CH 2 --, or --NR 10 --, where R 10 is H or an alkyl having 1-6 carbons; or a TAIL; or -L-R x ; L is a single covalent bond, or L is a covalent linkage that is linear or branched, cyclic or heterocyclic, saturated or unsaturated, having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; R x is a reactive group; TAIL is a heteroatom-containing moiety having the formula LINK-SPACER-CAP; wherein LINK is a single covalent bond, --O--, --S--, or --NR 20 --; where R 20 is H, a linear or branched alkyl having 1-8 carbons, or R 20 is -SPACER'-CAP'; SPACER and SPACER', which may be the same or different, are covalent linkages, linear or branched, cyclic or heterocyclic, saturated or unsaturated, each having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds; or single, double, triple or aromatic carbon--carbon bonds; or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen--nitrogen or nitrogen-oxygen bonds; or aromatic or heteroaromatic bonds; CAP and CAP', which may be the same or different, are --O--R 21 , --S--R 21 , --NR 21 R 22 , or --N + R 21 R 22 R 23 ψ - ; wherein R 21 , R 22 , and R 23 are independently H, or a linear or branched alkyl or cycloalkyl having 1-8 carbons, optionally further substituted by hydroxy, alkoxy having 1-8 carbons, carboxyalkyl having 1-8 carbons, or phenyl, where phenyl is optionally further substituted by halogen, hydroxy, alkoxy having 1-8 carbons, aminoalkyl having 1-8 carbons, or carboxyalkyl having 1-8 carbons; or, one or more of R 21 , R 22 and R 23 , taken in combination with SPACER or SPACER' or R 20 forms a 5- or 6-membered aromatic, heteroaromatic, alicyclic or heteroalicyclic ring, the heteroatoms selected from O, N or S; where ψ - is a compatible counterion; or CAP and CAP' are independently ##STR60## where R 21 , R 22 , R 23 , and ψ - are as defined previously.

Claim 75

Dependent Claim 41 words

A compound, as claimed in claim 68, wherein R 5 is aryl or heteroaryl; X is O or S; n is 0 or 1; and R 6 and R 7 are H; or taken in combination, form a fused aromatic ring.

Claim 76

Dependent Claim 67 words

A compound, as claimed in claim 69, wherein R 5 is phenyl; and R 19 is -SPACER-CAP; wherein SPACER and has the formula --(CH 2 ) k --, where k=1-8; CAP is --NR 21 R 22 or --N + R 21 R 22 R 23 ψ - ; where R 21 , R 22 , and R 23 are independently methyl or ethyl, or CAP is ##STR61##

Annuity Stage	Window Opens	Payment Deadline	Surcharge Period Until	Estimated Fee	Status
3.5 Years (Year 4)	2002-01-25	2002-07-27	2003-01-26	$2000.00	Window Closed / Lapsed
7.5 Years (Year 8)	2006-01-25	2006-07-27	2007-01-26	$3760.00	Window Closed / Lapsed
11.5 Years (Year 12)	2010-01-25	2010-07-27	2011-01-26	$7700.00	Window Closed / Lapsed

Chemically reactive unsymmetrical cyanine dyes and their conjugates

Abstract

Inventors

Bibliographic Details

Claims Analysis

References Cited (Backward Citations)

USPTO Annuity & Maintenance Windows

Assigned Categories & Tags

Assign Category Tag