Detection or quantification of desirable target molecules, novel dyes, composite dyes, and oligonucleotides or polynucleotides comprising such dyes

A dye having the formula:

• wherein X and Y independently comprise CR11R12, NR11, O, S or Se, wherein 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 at least one of R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11, or R12 comprises Q, wherein Q comprises a sulfoxide (SOR13), a sulfone (SO2CR13R14R15, a sulfonamide (SO2NR13R14), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), 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 independently comprises O or S;
• wherein Q is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, or any combinations thereof, wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted or any combinations thereof, and wherein when Q is a sulfonamide, Q does not have a terminal reactive group or a linker arm joining the dye to a target molecule;
• wherein R13, R14, R15, R16, R17, R18, R19, R20 and the remaining R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11, and R12, independently comprise hydrogen, Z, 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 R2 and R3, R3 and R4, R4 and R5, R7 and R8, R8 and R9, R9 and R10, R1 and R16, R6 and R18, R11 and R16, R16 and R17, R18 and R11, R13 and R14, R14 and R15, R19 and R20 independently comprise 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 (PSO2=), a thiophosphonate monoester (PSO−ER13), a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14), or its thioanalogue (POSR19NR13R14), wherein any of E independently comprises 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 is saturated or unsaturated, linear or branched, substituted or unsubstituted, or any combinations thereof;
• wherein any of R1, R2, R3, R4, R5, R6, R7, R8, R9R10, 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, 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 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 R1, 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.