Dyes for the detection or quantification of desirable target molecules

A dye having the formula:

• wherein X comprises CR11R12, NR11, O, S or Se where R11 and R12 independently comprise hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R11 and R12 form a five- or six-membered ring;
• wherein n can be 0, 1, 2 or 3;
• wherein Y is —CR9=CR10—;
• wherein m and p can have values of 0 or 1 and m+p=1;
• wherein at least one of R1, R2, R3, R4, R5, R11 or R12 comprises Q(1) or at least one of R6, R7, R8, R9 or R10 comprises Q(2);
• wherein Q(1) comprises, a sulfonate ester (SO2ER13), a sulfoxide (SOR13, a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER—ER14) , a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanafogue (PSNR13R14 NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S;
• wherein Q(1) is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, or any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted, or any combinations thereof and wherein when Q(1) is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
• wherein Q(2) comprises a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphonate (PO3=), a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3═), a thiophosphate 13 monoester (PSO2−ER ) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20) its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20) its thtoanalogue (PSNR13R14NR15NR19R20), or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S;
• wherein Q(2) is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, or any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted or any combinations thereof and wherein when Q(2) is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
• wherein R13, R14, R15, R19 and R20 can be hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together R13 and R14 form a five- or six-membered ring;
• wherein R16, R17, R18 and the remaining R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11 and R12 can independently be hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated1 branched or l(near, substituted or unsubstituted, or when taken together, R2 and R3, R3 and R4, R4 and R5, R6 and R7, and R7 and R8 may form a five- or six-membered ring;
• or when taken together R1 and R16, R11 and R16, R16 and R17, R17 and R18, and R18 and R9 may form a five- or six-membered ring;
• wherein Z comprises a carboxyl group (CO2—), a carbonate ester (COER13), a sulfonate (S03), a sulfonate ester (SO2ER13), a sulfoxide (SO3—), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14) ,a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20) its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20) , its thioanalog (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) where E can be independently O or S and the structures are as described previously;
• wherein Z is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, or any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, suWtituted or unsubstituted or any combinations thereof;
• wherein any of R1, R2, R3, R4, R5, R6, R7, R8, R9 or R10, R11 or R12 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25) or an amine linkage (—NR25R26 or —N+R25R26R27), and wherein R25, R26 and R27 independently comprise hydrogen, Z an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five- or six-membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain;
• and wherein at least one of R2, R3, R4, R5, R6, R7, R8, R9, R10, R13, R14, or R15 further comprises a nucleophilic reactive group, an electrophilic reactive group, a terminal alkene, a terminal alkyne, a coordinate group or an alkylating agent.

A dye having the formula:

• wherein X comprises CR11R12, NR11, O, S or Se where R11 and R12 independently comprise hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R11 and R12 form a five- or six-membered ring;
• wherein n can be 0, 1, 2 or 3;
• wherein Y is —CR9=CR10—;
• wherein m and p can have values of 0 or 1 and m+p=1;
• wherein at least one of R2, R3, R4, R5, R11 or R12 comprises Q(1) or at least one of R6, R7, R8, R9 or R10 comprises Q(2);
• wherein Q(1) comprises a sulfonate (SO3—), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15) a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14) , a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER3ER14) , a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER3ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20)1 a phosphoramide (PONR13R14NR15NR19R20),its thioanalogue (PSNR13R14NR15NR19R20) , a phosphoramidite (PO2R19NR13R14) or its thicanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S;
• wherein Q(1) is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, or any combinations thereot wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted, or any combinations thereof and wherein when Q(1) is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
• wherein Q(2) comprises a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphonate (PO3=), a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20) , a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S;
• wherein Q(2) is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, or any combinations thereof and wherein said linker arm may be saturated or unsaturated1 linear or branched, substituted or unsubstituted or any combinations thereof, and wherein when Q(2) is a sulfonamide1 it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
• wherein R13, R14, R 15, R19 and R20 can be hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together R13 and R14 form a five- or six-membered ring;
• wherein R1 is hydrogen or alkyl, and wherein R16, R17, R18 and the remaining R2, R3, R4, R5, R6, R7, R8, R9, R10, R11 and R12 independently be hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R2 and R3, R3 and R4, R4 and R5, R6 and R7, and R7 and R8 may form a five- or six-membered ring;
• or when taken together R1 and R16, R11 and R16 , R16 and R17, R17 and R18 and R18 and R9may form a five- or six-membered ring;
• wherein Z comprises a carboxyl group (CO2−), a carbonate ester (COER13), a sulfonate (SO3−), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14) , a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO250 ), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20),its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) where E can be independently O or S;
• wherein Z is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, or any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted or any combinations thereof;
• and wherein any of R2, R3, R4, R5, R6, R7, R8, R9 or R10, R11 or R12 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25) or an amine linkage (—NR25R26 or —N+R25R26R27), and wherein R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five- or six-membered ring, and wherein any of R25, R26 or may further comprise said heteroatom containing side chain.

A dye having the formula:

• wherein X comprises CR11R12, NR11, O, S or Se where R11 and R12 independently comprise hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R11 and R12 form a five- or six-membered ring;
• wherein n can be 0, 1, 2 or 3;
• wherein Y is —CR9=CR10—;
• wherein m and p can have values of 0 or 1 and m+p=1;
• wherein at least one of R2, R3, R4, R5, R11 or R12 comprises Q(1) or at least one of R6, R7, R8, R9 or R10 comprises Q(2);
• wherein Q(1) comprises a sulfonate (SO3—), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13)S a phosphate diester (PO2ER13ER14) , a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20) , a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S;
• wherein Q(1) is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, or any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted, or any combinations thereof and wherein when Q(1) is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
• wherein Q(2) comprises a sulfoxide SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphonate (PO3=), a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3═), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13), a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20, its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20) ,a phosphoramidite (PO2R19NR13R14) or its thioanalogue 19 13 14 (POSR19NR13R14) wherein any of E can independently comprise O or S;
• wherein Q(2) is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, or any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted or any combinations thereof and wherein when Q(2) is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
• wherein R13, R14, R15, R19 and R20 can be hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together R13 and R14 form a five- or six-membered ring;
• wherein R1, R16, R17 and R18 is hydrogen, and the remaining R2, R3, R4, R5, R6, R7, R8, R9, R10, R11 and R12 can independently be hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R2 and R3, R3 and R4, R4 and R5, R6 and R7, and R7 and N8 may form a five- or six-membered ring;
• or when taken together R1 and R16, R11 and R16, R16 and R17, R17 and R18, and R18 and R19 may form a five- or six-membered ring;
• wherein Z comprises a carboxyl group (CO2—), a carbonate ester (COER13), a sulfonate (SO3—), a sultonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14) , a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20) , its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) where E can be independently O or S and the structures are as described previously;
• wherein Z is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, or any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted or any combinations thereof;
• wherein any of R2, R3, R4, R5, R6, R7, R8, R9 or R10, R11 or R12 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR26). a thioether rinkage (—SR25), or an amine linkage (—NR26R26 or —N+R25R26R27), and wherein R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five- or six-membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain;
• and wherein at least one of R2, R3, R4, R5, R6, R7, R8, R9, R10, R13, R14, or R15 further comprises a nucleophilic reactive group, an electrophilic reactive group, a terminal alkene, a terminal alkyne, a coordinate group or an alkylating agent.