Phenyl Xanthene Dyes

Abstract

Fluorescent phenyl xanthene dyes are described that comprise any fluorescein, rhodamine or rhodol comprising a particular C9 phenyl ring. One or both of the ortho groups on the lower C9 phenyl ring is ortho substituted with a group selected from alkyl, heteroalkyl, alkoxy, halo, haloalkyl, amino, mercapto, alkylthio, cyano, isocyano, cyanato, mercaptocyanato, nitroso, nitro, azido, sulfeno, sulfinyl, and sulfino. In one embodiment, halo and/or hydroxy groups are used. Optimal dyes contain a lower C9 phenyl ring in which both ortho groups are the same and the lower ring exhibits some form a symmetry relative to an imaginary axis running from the phenyl rings point of attachment to the remainder of the xanthene dye through a point para to the point of attachment. The phenyl xanthene dyes may be activated. Furthermore, the phenyl xanthene dyes may be conjugated to one or more substances including other dyes. The phenyl xanthene dyes are useful for a number of purposes, including labels for use in automated DNA sequencing as well the formation of fluorescent “bar codes” for polymeric particles used in the multiplexed analysis of analytes.

1 .- 24 . (canceled) 
     
     
         25 . A lipid soluble fluorescent phenyl xanthene dye comprising a fluorescein, rhodol or rhodamine that comprises a C9 phenyl ring comprising the following structure: 
       
         
           
           
               
               
           
         
       
       where R 11  and/or R 15  are selected from alkyl, heteroalkyl, alkoxy, halo, haloalkyl, amino, alkylthio, cyano, isocyano, mercaptocyanato, nitro, and sulfinyl, and R 12 , R 13 , and R 14  are, independently, selected from hydrogen, alkyl, heteroalkyl, aryl, heteroaryl, alkoxy, halo, haloalkyl, amino, alkylthio, cyano, isocyano, cyanato, mercaptocyanato, nitro, sulfinyl, sulfonyl, sulfonamide, carboxyl, and carboxyamide. 
     
     
         26 .- 29 . (canceled) 
     
     
         30 . The lipid soluble phenyl xanthene dye of  claim 25  wherein the phenyl ring is only substituted with hydrogen, alkoxy, halo, and haloalkyl groups. 
     
     
         31 . The lipid soluble phenyl xanthene dye of  claim 25  wherein R 11  and R 15  are identical. 
     
     
         32 .- 36 . (canceled) 
     
     
         37 . The lipid soluble phenyl xanthene dye of  claim 25  wherein said dye is a fluorescein. 
     
     
         38 .- 39 . (canceled) 
     
     
         40 . The lipid soluble phenyl xanthene dye of  claim 25  further comprising one or more lipophilic groups selected from (C4-C20) alkyls, (C5-C40) aryls, and/or (C6-C40) arylalkyls. 
     
     
         41 .- 42 . (canceled) 
     
     
         43 . The lipid soluble phenyl xanthene dye of  claim 40  wherein said dye contains one or more linkers that contain a linking group capable of forming a covalent or non-covalent linkage to a second substance. 
     
     
         44 . The lipid soluble phenyl xanthene dye of  claim 43  wherein said second substance is selected from a biomolecule, a glass substrate, a metal substrate and a polymer substrate. 
     
     
         45 . The lipid soluble phenyl xanthene dye of  claim 43  wherein said second substance is another dye and the phenyl xanthene dye is part of an energy transfer network. 
     
     
         46 - 84 . (canceled) 
     
     
         85 . A fluorescent phenyl xanthene dye comprising one of the following core structures: 
       
         
           
           
               
               
           
         
         where A is —OH or NR 3′ R 3″ , 
         where B is a ═O or ═N + R 6′ R 6″ ; 
         where at least one of R 11  and R 15  is selected from alkyl, heteroalkyl, alkoxy, halo, haloalkyl, amino, alkylthio, cyano, isocyano, cyanato, mercaptocyanato, nitro, and sulfinyl, 
         wherein one or more of R 2 , R 2′ , R 3′ , R 3″ , R 4 , R 4′ , R 5 , R 5′ , R 6′ , R 6″ , R 7 , R 7′ , R 12 , R 13 , and R 14  are optionally —S-LG or S 1 -LK-S 2 —CS, where S is a direct bond or a spacing moiety, LG is a linking group, S 1  and S 2  are, independently, a direct bond or a spacing moiety, LK is a linkage formed from a reacted linking group, and CS is a conjugated substance; 
         and the remainder of R 1′ , R 2 , R 2′ , R 3′ , R 3″ , R 4 , R 4′ , R 5 , R 5′ , R 6′ , R 6″ , R 7 , R 7′ , R 8 , R 12 , R 13 , and R 14  are, independently, selected from hydrogen and a substituent having less than 40 atoms. 
       
     
     
         86 . The phenyl xanthene dye of  claim 85 , wherein the dye comprises core structure (I) and the substituents therein are further defined as follows:
 R 1  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 1  may be taken together with R 2  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 2  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 2  may be taken together with R 1 , to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, when A is —NR 3′ R 3″ , R 2  may be taken together with R 3′  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 3′ , when present, is selected from hydrogen, (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 3′  may be taken together with R 2  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 3″ , when present, is selected from (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 3″  may be taken together with R 4  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 4  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, when B is —NR 3′ R 3″ , R 4  may be taken together with R 3″  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 5  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, when B is —NR 6′ R 6″+ , R 5  may be taken together with R 6″  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 6″ , when present, is selected from (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively R 6″  may be taken together with R 5  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 6′ , when present, is selected from hydrogen, (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 6′  may be taken together with R 7  to form a 5- or 6-membered ring optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 7  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 7  may be taken together with R 8  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, when B is —NR 6′ R 6″+ , R 7  may be taken together with R 6′  to form a 5- or 6-membered ring optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 8  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 8  together with R 7  may form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 11  and R 15  are each, independently of one another, selected from halo, (C1-C20) alkyl, haloalkyl, —OR y , —SR y , —SOR y , —SO 2 R y , and nitrile;   R 12 , R 13  and R 14  are each, independently of one another, selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R x  is selected from —NR c R c , —OR d , —SR d , halo, haloalkyl, —CN, —NC, —OCN, —SCN, —NO, —NO 2 , —N 3 , —S(O)R d , —S(O) 2 R d , —S(O) 2 OR d , —S(O)NR c R c , —S(O) 2 NR c R c , —OS(O)R d , —OS(O) 2 R d , —OS(O) 2 NR c R c , —C(O)R d , —C(O)OR d , —C(O)NR c R c , —C(NH)NR c R c , —OC(O)R d , —OC(O)OR d , —OC(O)NR c R c  and —OC(NH)NR c R c ;   R y  is selected from (C1-C20) alkyls or heteroalkyls optionally substituted with lipophilic substituents, (C5-C20) aryls or heteroaryls optionally substituted with lipophilic substituents and (C2-C26) arylalkyl or heteroarylalkyls optionally substituted with lipophilic substituents;   R a  is selected from hydrogen, (C1-C8) alkyl or heteroalkyl, (C5-C20) aryl or heteroaryl and (C6-C28) arylalkyl or heteroarylalkyl;   R b  is selected from —NR c R c , ═O, —OR d , ═S, —SR d , ═NR d , ═NOR d , halo, haloalkyl, —CN, —NC, —OCN, —SCN, —NO, —NO 2 , ═N2, —N 3 , —S(O)R d , —S(O) 2 R d , —S(O) 2 OR d , —S(O)NR c R c , —S(O) 2 NR c R c , —OS(O)R d , —OS(O) 2 R d , —OS(O) 2 NR c R c , —OS(O) 2 OR d , —OS(O) 2 NR c R c , —C(O)R d , —C(O)OR d , —C(O)NR c R c , —C(NH)NR c R c , —OC(O)R d , —OC(O)OR d , —OC(O)NR c R c  and —OC(NH)NR c R c ;   each R c  is independently hydrogen or R d , or alternatively, each R c  is taken together with the nitrogen atom to which it is bonded to form a 5- to 8-membered saturated or unsaturated ring which may optionally include one or more of the same or different additional heteroatoms and which may optionally be substituted with one or more of the same or different R a  or R d  groups;   each R d  is independently R a  or R a  substituted with one or more of the same or different R a  or R e  groups; and   each R e  is selected from —NR a R a , ═O, —OR a , ═S, —SR a , ═NR a , ═NOR a , halo, haloalkyl, —CN, —NC, —OCN, —SCN, —NO, —NO 2 , ═N 2 , —N 3 , —S(O)R a , —S(O) 2 R a , —S(O) 2 OR a , —S(O)NR a R a , —S(O) 2 NR a R a , —OS(O)R a , —OS(O) 2 R a , —OS(O) 2 NR a R a , —OS(O) 2 OR d , —OS(O) 2 NR a R a , —C(O)R a , —C(O)OR a , —C(O)NR a R a , —C(NH)NR c R a , —OC(O)R a , —OC(O)OR a , —OC(O)NR a R a  and —OC(NH)NR a R a      or, alternatively, one or more of R 2 , R 3′ , R 3″ , R 4 , R 5 , R 6′ , R 6″ , R 7 , R 12 , R 13  and R 14  are each, independently of one another, selected from the group consisting of —S-LG and —S 1 -LK-S 2 —CS, wherein   each S, which may be the same or different, is a direct bond or linker;   each LG, which may be the same or different, is a linking group;   each S 1  and S 2 , independently, is a direct bond or linker;   each LK is a linkage formed from a reacted linking group; and   each CS, which may be the same or different, is a conjugated substance.   
     
     
         87 . The phenyl xanthene dye of  claim 85 , wherein the dye comprises core structure (II) and the substituents therein are further defined as follows:
 R 1  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 1  may be taken together with R 2  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 2  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 2  may be taken together with R 1  or R 2′  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 2′  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 2′  may be taken together with R 2  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, when A is —NR 3′ R 3″ , R 2′  may be taken together with R 3′  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 3′ , when present, is selected from hydrogen, (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 3′  may be taken together with R 2′  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 3″ , when present, is selected from (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 3″  may be taken together with R 4  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 4  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, when A is —NR 3 ′R 3 ″, R 4  may be taken together with R 3″  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 4  may be taken together with R 4′  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 4′  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 4′  may be taken together with R 4  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 5  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, when B is —NR 6′ R 6″+ , R 5  may be taken together with R 6″  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 6″ , when present, is selected from (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively R 6″  may be taken together with R 5  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 6′ , when present, is selected from hydrogen, (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 6′  may be taken together with R 7  to form a 5- or 6-membered ring optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 7  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 7  may be taken together with R 8  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, when B is —NR 6′ R 6″+ , R 7  may be taken together with R 6′  to form a 5- or 6-membered ring optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 8  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 8  together with R 7  may form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 11  and R 15  are each, independently of one another, selected from halo, (C1-C20) alkyl, haloalkyl, —OR y , —SR y , —SOR y , —SO 2 R y , and nitrile;   R 12 , R 13  and R 14  are each, independently of one another, selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R x  is selected from —NR c R c , —OR d , —SR d , halo, haloalkyl, —CN, —NC, —OCN, —SCN, —NO, —NO 2 , —N 3 , —S(O)R d , —S(O) 2 R d , —S(O) 2 OR d , —S(O)NR c R c , —S(O) 2 NR c R c , —OS(O)R d , —OS(O) 2 R d , —OS(O) 2 NR c R c , —C(O)R d , —C(O)OR d , —C(O)NR c R c , —C(NH)NR c R c , —OC(O)R d , —OC(O)OR d , —OC(O)NR c R c  and —OC(NH)NR c R c ;   R y  is selected from (C1-C20) alkyls or heteroalkyls optionally substituted with lipophilic substituents, (C5-C20) aryls or heteroaryls optionally substituted with lipophilic substituents and (C2-C26) arylalkyl or heteroarylalkyls optionally substituted with lipophilic substituents;   R a  is selected from hydrogen, (C1-C8) alkyl or heteroalkyl, (C5-C20) aryl or heteroaryl and (C6-C28) arylalkyl or heteroarylalkyl;   R b  is selected from —NR c R c , ═O, —OR d , ═S, —SR d , ═NR d , ═NOR d , halo, haloalkyl, —CN, —NC, —OCN, —SCN, —NO, —NO 2 , ═N2, —N 3 , —S(O)R d , —S(O) 2 R d , —S(O) 2 OR d , —S(O)NR c R c , —S(O) 2 NR c R c , —OS(O)R d , —OS(O) 2 R d , —OS(O) 2 NR c R c , —OS(O) 2 OR d , —OS(O) 2 NR c R c , —C(O)R d , —C(O)OR d , —C(O)NR c R c , —C(NH)NR c R c , —OC(O)R d , —OC(O)OR d , —OC(O)NR c R c  and —OC(NH)NR c R c ;   each R c  is independently hydrogen or R d , or alternatively, each R c  is taken together with the nitrogen atom to which it is bonded to form a 5- to 8-membered saturated or unsaturated ring which may optionally include one or more of the same or different additional heteroatoms and which may optionally be substituted with one or more of the same or different R a  or R d  groups;   each R d  is independently R a  or R a  substituted with one or more of the same or different R a  or R e  groups; and   each R e  is selected from —NR a R a , ═O, —OR a , ═S, —SR a , ═NR a , ═NOR a , halo, haloalkyl, —CN, —NC, —OCN, —SCN, —NO, —NO 2 , ═N 2 , —N 3 , —S(O)R a , —S(O) 2 R a , —S(O) 2 OR a , —S(O)NR a R a , —S(O) 2 NR a R a , —OS(O)R a , —OS(O) 2 R a , —OS(O) 2 NR a R a , —OS(O) 2 OR d , —OS(O) 2 NR a R a , —C(O)R a , —C(O)OR a , —C(O)NR a R a , —C(NH)NR c R a , —OC(O)R a , —OC(O)OR a , —OC(O)NR a R a  and —OC(NH)NR a R a      or, alternatively, one or more of R 2 , R 3′ , R 3″ , R 4 , R 5 , R 6′ , R 6″ , R 7 , R 12 , R 13  and R 14  are each, independently of one another, selected from the group consisting of —S-LG and —S 1 -LK-S 2 —CS, wherein   each S, which may be the same or different, is a direct bond or linker;   each LG, which may be the same or different, is a linking group;   each S 1  and S 2 , independently, is a direct bond or linker;   each LK is a linkage formed from a reacted linking group; and   each CS, which may be the same or different, is a conjugated substance.   
     
     
         88 . The phenyl xanthene dye of  claim 85 , wherein the dye comprises core structure (III) and the substituents therein are further defined as follows:
 R 1  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 1  may be taken together with R 2  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 2  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 2  may be taken together with R 1  or R 2′  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 2′  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 2′  may be taken together with R 2  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, when A is —NR 3′ R 3″ , R 2 ′ may be taken together with R 3′  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 3′ , when present, is selected from hydrogen, (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 3′  may be taken together with R 2′  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 3″ , when present, is selected from (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 3″  may be taken together with R 4  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 4  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, when A is —NR 3′ R 3″ , R 4  may be taken together with R 3″  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 4  may be taken together with R 4′  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 4′  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 4′  may be taken together with R 4  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 5′  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 5′  may be taken together with R 5  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 5  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, when B is —NR 6′ R 6″+ , R 5  may be taken together with R 6″  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, R 5  may be taken together with R 5′  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 6″ , when present, is selected from (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively R 6″  may be taken together with R 5  to form a 5- or 6-membered ring which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 6′ , when present, is selected from hydrogen, (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 6′  may be taken together with R 7′  to form a 5- or 6-membered ring optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 7′  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, when B is —NR 3′ R 3″+ , R7′ may be taken together with R 6′  to form a 5- or 6-membered ring optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 7′  may be taken together with R 7  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 7  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 7  may be taken together with R 7′  or R 8  to form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups, or alternatively, when B is —NR 6′ R 6″+ , R 7  may be taken together with R 6′  to form a 5- or 6-membered ring optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 8  is selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups, or, alternatively, R 8  together with R 7  may form part of a benzo, naptho or polycyclic aryleno group which is optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R 11  and R 15  are each, independently of one another, selected from halo, (C1-C20) alkyl, haloalkyl, —OR y , —SR y , —SOR y , —SO 2 R y , and nitrile;   R 12 , R 13  and R 14  are each, independently of one another, selected from hydrogen, R x , (C1-C20) alkyl or heteroalkyl optionally substituted with one or more of the same or different R b  groups, (C5-C20) aryl or heteroaryl optionally substituted with one or more of the same or different R a  or suitable R b  groups and (C6-C40) arylalkyl or heteroaryl alkyl optionally substituted with one or more of the same or different R a  or suitable R b  groups;   R x  is selected from —NR c R c , —OR d , —SR d , halo, haloalkyl, —CN, —NC, —OCN, —SCN, —NO, —NO 2 , —N 3 , —S(O)R d , —S(O) 2 R d , —S(O) 2 OR d , —S(O)NR c R c , —S(O) 2 NR c R c , —OS(O)R d , —OS(O) 2 R d , —OS(O) 2 NR c R c , —C(O)R d , —C(O)OR d , —C(O)NR c R c , —C(NH)NR c R c , —OC(O)R d , —OC(O)OR d , —OC(O)NR c R c  and —OC(NH)NR c R c ;   R y  is selected from (C1-C20) alkyls or heteroalkyls optionally substituted with lipophilic substituents, (C5-C20) aryls or heteroaryls optionally substituted with lipophilic substituents and (C2-C26) arylalkyl or heteroarylalkyls optionally substituted with lipophilic substituents;   R a  is selected from hydrogen, (C1-C8) alkyl or heteroalkyl, (C5-C20) aryl or heteroaryl and (C6-C28) arylalkyl or heteroarylalkyl;   R b  is selected from —NR c R c , ═O, —OR d , ═S, —SR d , ═NR d , ═NOR d , halo, haloalkyl, —CN, —NC, —OCN, —SCN, —NO, —NO 2 , ═N2, —N 3 , —S(O)R d , —S(O) 2 R d , —S(O) 2 OR d , —S(O)NR c R c , —S(O) 2 NR c R c , —OS(O)R d , —OS(O) 2 R d , —OS(O) 2 NR c R c , —OS(O) 2 OR d , —OS(O) 2 NR c R c , —C(O)R d , —C(O)OR d , —C(O)NR c R c , —C(NH)NR c R c , —OC(O)R d , —OC(O)OR d , —OC(O)NR c R c  and —OC(NH)NR c R c ;   each R c  is independently hydrogen or R d , or alternatively, each R c  is taken together with the nitrogen atom to which it is bonded to form a 5- to 8-membered saturated or unsaturated ring which may optionally include one or more of the same or different additional heteroatoms and which may optionally be substituted with one or more of the same or different R a  or R d  groups;   each R d  is independently R a  or R a  substituted with one or more of the same or different R a  or R e  groups; and   each R e  is selected from —NR a R a , ═O, —OR d , ═S, —SR a , ═NR a , ═NOR a , halo, haloalkyl, —CN, —NC, —OCN, —SCN, —NO, —NO 2 , ═N 2 , —N 3 , —S(O)R a , —S(O) 2 R a , —S(O) 2 OR a , —S(O)NR a R a , —S(O) 2 NR a R a , —OS(O)R a , —OS(O) 2 R a , —OS(O) 2 NR a R a , —OS(O) 2 OR d , —OS(O) 2 NR a R a , —C(O)R a , —C(O)OR a , —C(O)NR a R a , —C(NH)NR c R a , —OC(O)R a , —OC(O)OR a , —OC(O)NR a R a  and —OC(NH)NR a R a  or, alternatively, one or more of R 2 , R 3′ , R 3″ , R 4 , R 5 , R 6′ , R 6″ , R 7 , R 12 , R 13  and R 14  are each, independently of one another, selected from the group consisting of —S-LG and —S 1 -LK-S 2 —CS, wherein   each S, which may be the same or different, is a direct bond or linker;   each LG, which may be the same or different, is a linking group;   each S 1  and S 2 , independently, is a direct bond or linker;   each LK is a linkage formed from a reacted linking group; and   each CS, which may be the same or different, is a conjugated substance.   
     
     
         89 . The phenyl xanthene dye of  claim 85  wherein —S is a direct bond or a spacing moiety. 
     
     
         90 . The phenyl xanthene dye of  claim 85  wherein -LG is an electrophilic group selected from activated esters, acrylamides, acyl azides, acyl halides, acyl nitriles, aldehydes, ketones, alkyl halides, alkyl sulfonates, anhydrides, aryl halides, aziridines, boronates, carboxylic acids, carbodiimides, diazoalkenes, epoxides, haloacetamides, halotriazines, imido esters, isocyanates, isothiocyanates, maleimides, phosphoramidites, silyl halides, sulfonate esters, and sulfonyl halides. 
     
     
         91 . The phenyl xanthene dye of  claim 85  wherein -LG is a nucleophilic group selected from amines, anilines, alcohols, phenols, thiols, hydrazines, and hydroxylamines. 
     
     
         92 . The phenyl xanthene dye of  claim 85  wherein —CS is a polymer, glass substrate, metal substrate, biomolecule or second dye. 
     
     
         93 . The phenyl xanthene dye of  claim 92  wherein the biomolecule is selected from peptides, polypeptides, proteins, amino acids, enzymes, receptors, antibodies, hormones, polysaccharides, carbohydrates, oligonucleotides, polynucleotides, nucleosides, and nucleic acids. 
     
     
         94 . The phenyl xanthene dye of  claim 92  wherein the second dye is selected from phenyl xanthene dyes, cyanine dyes, phthalocyanine dyes, squarine dyes, acridine dyes, alizarene dyes, azo dyes, anthraquinine dyes, BODIPY® dyes, coumarin dyes, lanthanide complexes, oxazine dyes, phenazathionium dyes, phenazoxonium dyes, porphyrin dyes, pyrene dyes, pyrilium dyes, perylene dyes, phenoxazine dyes and phenezine dyes.