Fluorescent dyes, energy transfer couples and methods

Abstract

Fluorescent dyes, fluorescence energy transfer dye couples, multi-color dye sets, can be employed in art-recognized assays and certain novel methods, such as in proximity assays.

1 . A fluorescence energy transfer dye comprising Formula I:  
       --L1—D1—FETL—D2--L2—  (Formula I)  
     where: 
 L1 is a link for attachment to a probe or target, for attachment to a solid support, or is absent;  
 L2 is a link for attachment to a probe or target, for attachment to a solid support, or is absent;  
 FETL is a fluorescence energy transfer linker;  
 D1 is a donor dye represented by the formula:  
                     
 where:  
 X is O or C(R*R**), where R* and R** are independently lower alkyl or —CH 2 -Z;  
 R 1  is H, CF 3 , perfluoropropyl, lower alkyl acid, substituted aryl, substituted heteroaryl or Z;  
 R 2  is H, halo, SO 3   − , or is taken together with R 3  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 3  is halo, Z, or is taken together with R 2  and/or R 4  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 4  is ═O or OH, —N(R 4′ R 4″ ) or ═N + (R 4′ R 4″ ), or is taken together with R 3  and/or R 5  to form an optionally substituted fused ring having 5 to 7 atoms, 
 where R 4′  is H, lower alkyl or L1, and  
 R 4″  is H, lower alkyl or CH 2 -Z;  
 
 R 5  is H, halo, Z, or is taken together with R 4  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 6  is H, halo, Z, or is taken together with R 7  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 7  is ═O or OH, —N(R 7′ R 7″ ) or ═N + (R 7′ R 7″ ), or is taken together with R 6  and/or R 8  to form an optionally substituted fused ring having 5 to 7 atoms, 
 where R 7′  is H, lower alkyl or L1, and  
 R 7″  is H, lower alkyl or CH 2 -Z;  
 
 R 8  is halo, Z, or is taken together with R 7  and/or R 9  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 9  is H, halo, SO 3   − , or is taken together with R 8  to form an optionally substituted fused ring having 5 to 7 atoms; and  
 Z is a group of the formula: -Z*-Z 1 -(L1, L2 or FETL), where: 
 Z* is methylene, methoxy, ethoxy, aminomethyl, aminoethyl, aminopropynyl, aminobutynyl, carboxyethenyl, carboxyethynyl, optionally substituted aryl or optionally substituted heteroaryl;  
 Z 1  is —C(O)—, —N(Z 2 )-, —CH 2 —O—, —CH 2 —C(O)—, —CH 2 —N(Z 2 )-, —CH 2 —S—, —CH 2 —S(O)—, —CH 2 —S(O 2 )— or is absent; and  
 Z 2  is H, C 1  to C 8  optionally substituted lower alkyl, or optionally substituted aryl; and  
 D2 is an acceptor/reporter dye represented by formula D1 or by a formula of the group:  
                     
 where:  
 
 at least one of R 21  to R 36  is joined to FETL,  
 n is zero, 1, 2 or 3;  
 R 21  and R 30  are independently —CH 2 -Z, activated lower alkyl, or optionally substituted aralkyl;  
 R 22  to R 29  are independently H, S 3   − , or optionally substituted alkyl, or R 22  and R 23 , R 23  and R 24  R 24  and R 25 , R 26  and R 27 , R 27  and R 28 , and/or R 28  and R 29  taken together form an optionally substituted fused ring having 6 atoms;  
 R 31  and R 32  are independently H, optionally substituted alkyl, aryl, or taken together form an optionally substituted fused ring having 6 atoms;  
 R 33  to R 36  are independently H, SO 3   − , optionally substituted alkyl, aryl, or R 33  and R 34 , R 34  and R 35  and/or R 35  and R 36  taken together form an optionally substituted fused ring having 6 atoms; and  
 Y is —O— or —N(Y 1 )— where Y 1  is —CH 2 -Z, activated lower alkyl, or optionally substituted aralkyl;  
 provided that at least one of R 3  to R 8  is Z where Z* is optionally substituted aryl or optionally substituted heteroaryl, or a probe-, target- and/or support-conjugate thereof.  
 
   
   
       2 . The fluorescence energy transfer dye of  claim 1  having one or more of the following: 
 R 1  is H, CF 3 , perfluoropropyl, lower alkyl acid, 5-6 membered mono or 10-12 membered fused substituted aryl or heteroafyl, or Z;    R 2  is H, halo, SO 3   − , or is taken together with R 3  to form an optionally substituted fused 6-membered aryl ring;    R 3  is halo, Z, or is taken together with R 2  and/or R 4  to form an optionally substituted fused 6-membered ring;    R 4  is ═O or OH, —N(R 4′ R 4″ ) or ═N + (R 4′ R 4″ ), or is taken together with R 3  and/or R 5  to form an optionally substituted fused 6-membered ring;    R 5  is H, halo, Z, or is taken together with R 4  to form an optionally substituted fused 6-membered ring;    R 6  is H, halo, Z, or is taken together with R 7  to form an optionally substituted fused 6-membered ring;    R 7  is ═O or OH, —N(R 7′ R 7″ ) or ═N + (R 7′ R 7″ ), or is taken together with R 6  and/or R 8  to form an optionally substituted fused 6-membered ring;    R 8  is halo, Z, or is taken together with R 7  and/or R 9  to form an optionally substituted fused 6-membered ring;    R 9  is H, halo, SO 3   − , or is taken together with R 8  to form an optionally substituted fused 6-membered aryl ring;    R 4  is —N(R 4′ R 4″ ) or ═N + (R 4′ R 4″ ) and R 7  is -N(R 7′ R 7″ ) or ═N + (R 7′ R 7″ ) when X is C(R*R**);    Z is a group of the formula: -Z*-Z 1 -(L1, L2 or FETL), where: 
 Z* is methylene, methoxy, ethoxy, aminomethyl, aminoethyl, aminopropynyl, aminobutynyl, carboxyethenyl, carboxyethynyl, optionally substituted aryl or optionally substituted heteroaryl,  
 Z 1  is —C(O)—, —N(Z 2 )- —CH 2 —O—, —CH 2 —C(O)—, —CH 2 —N(Z 2 )- —CH 2 —S—, —CH 2 —S(O)—, —CH 2 —S(O 2 )— or is absent, and  
 Z 2  is H, or is C 1  to C 8  lower alkyl or aryl optionally substituted with SO 3   − , COOH, NH 2 , CH 2 NH 2 , SH, or SCH 3 ;  
   FETL comprises a symmetric, rigid or sterically hindered, divalent moiety joined to D1 and D2 via an amine, carbonyl, activated carboxylic acid ester, disulfide, thiol or thiol ester;    R 21  or R 30  is carboxy-naphthyl-methyl, mono- or di-ortho-substituted benzyl having an ortho-, meta- or para- carbonyl or activating group, or an activated C 1  to C 6  lower alkyl;    R 22  to R 29  are independently H, SO 3   −  or optionally substituted alkyl, or R 22  and R 23 , R 23  and R 24 , R 24  and R 25 , R 26  and R 27 , R 27  and R 28 , and/or R 28  and R 29  taken together form a fused, sulfonated 6-membered aryl ring;    R 31  and R 32  are independently H, optionally substituted alkyl, aryl, or taken together form a fused, sulfonated 6-membered carbocyclic or heterocyclic ring;    R 33  to R 36  are independently H, SO 3   − , optionally substituted alkyl, aryl, or R 33  and R 34 , R 34  and R 35 , and/or R 35  and R 36  taken together form a fused, sulfonated 6-membered carbocyclic or heterocyclic ring; and/or    at least one of R 22  to R 29  or R 33  to R 36  is SO 3   − .    
   
   
       3 . The fluorescence energy transfer dye of  claim 2  having one or more of the following: 
 R 1  is H, CF 3 , perfluoropropyl, lower alkyl acid, an optionally substituted ortho-benzoic acid, or Z;    R 2  is H, halo or SO 3   − ;    R 3  is halo or Z;    R 4  is ═O or OH, —N(R 4′ R 4″ ) or ═N + (R 4′ R 4″ );    R 5  is H, halo or Z;    R 6  is H, halo or Z;    R 7  is ═O or OH, —N(R 7′ R 7″ ) or ═N + (R 7′ R 7″ );    R 8  is Z;    R 9  is H, halo or SO 3   − ;    Z is a group of the formula: -Z*-Z 1 -(L1, L2 or FETL), where: 
 Z* is an optionally substituted aryl or heteroaryl of the group: phenyl, adamantyl, norboranyl, biphenyl, naphthyl, furanyl, bifuranyl, thiophenyl, bithienyl, pyrrolyl, indolyl, isoindolyl, benzofuranyl, isobenzofuranyl, benzothiophenyl, benzothienyl, chromenyl and isochromenyl, and  
 Z 1  is —C(O)—, —N(H)—, —CH 2 —O—, —CH 2 —C(O)—, —CH 2 —N(H)—, or is absent;  
   R 22  to R 29  are independently H, SO 3   −  or optionally substituted alkyl, or R 24  and R 25  and/or R 26  and R 27  taken together form a fused, sulfonated 6-membered aryl ring;    R 31  and R 32  are independently H, optionally substituted alkyl or aryl; and/or    R 33  to R 36  are independently H, SO 3   − , optionally substituted alkyl or aryl.    
   
   
       4 . The fluorescence energy transfer dye of  claim 3  where R 1  is a group represented by Formula R1.1:  
     
       
         
         
             
             
         
       
     
     where: 
 R 1a  is H, halo or —C(O)O − ;  
 R 1b  is H, halo or —C(O)-(L1, L2 or FETL);  
 R 1c  is halo; and  
 r is 0, 1, 2 or 3.  
 
   
   
       5 . The fluorescence energy transfer dye of  claim 1  where at least one of R 3  to R 8  is Z where Z* is optionally substituted aryl selected from phenyl, adamantyl, norboranyl, biphenyl and naphthyl.  
   
   
       6 . The fluorescence energy transfer dye of  claim 5  where Z* is phenyl and Z 1  is —C(O)—.  
   
   
       7 . The fluorescence energy transfer dye of  claim 1  where: 
 R 1  is H, CF 3 , perfluoropropyl, lower alkyl acid, an optionally substituted ortho-benzoic acid, or Z;    R 2  is H, halo or SO 3   − ;    R 3  is halo or Z;    R 4  is ═O or OH, —N(R 4′ R 4″ ) or ═N + (R 4′ R 4″ );    R 5  is H, halo or Z;    R 6  is H, halo or Z;    R 7  is ═O or OH, —N(R 7′ R 7″ ) or ═N + (R 7′ R 7″ );    R 8  is Z;    R 9  is H, halo or SO 3   − ;    Z is a group of the formula: -Z*-Z 1 -(L1, L2 or FETL), where: 
 Z* is an optionally substituted aryl or heteroaryl of the group: phenyl, adamantyl, norboranyl, biphenyl, naphthyl, furanyl, bifuranyl, thiophenyl, bithienyl, pyrrolyl, indolyl, isoindolyl, benzofuranyl, isobenzofuranyl, benzothiophenyl, benzothienyl, chromenyl and isochromenyl, and  
 Z 1  is —C(O)—, —N(H)—, —CH 2 —O—, —CH 2 —C(O)—, —CH 2 —N(H)—, or is absent;  
   R 21  or R 30  is carboxy-naphthyl-methyl, mono- or di-ortho-substituted benzyl having an ortho-, meta- or para- carbonyl or activating group, or an activated C 1  to C 6  lower alkyl;    R 22  to R 29  are independently H, SO 3   −  or optionally substituted alkyl, or R 24  and R 25  and/or R 26  and R 27  taken together form a fused, sulfonated 6-membered aryl ring;    R 31  and R 32  are independently H, optionally substituted alkyl or aryl; and    R 33  to R 36  are independently H, SO 3   − , optionally substituted alkyl or aryl.    
   
   
       8 . The fluorescence energy transfer dye of  claim 1  where FETL is represented by a formula of the group:  
     
       
         
         
             
             
         
       
     
     where: 
 R 10  is D1-C(O)—, D1-N(H)—CH 2 —, D1-S—C(O)—, D1-O—C(S)— or D1-S—CH 2 —; and  
 R 11  is —C(O)-D2, —CH 2 —N(H)-D2; —C(O)—S-D2, —C(S)—O-D2 or CH 2 —S-D2;  
                     
 where:  
 p is independently 0, 1, 2 or 3; and  
                     
 where:  
 q is zero or 1;  
 R 12  is H, halo, or optionally substituted-alkyl, -alkenyl, -alkynyl or -aryl;  
 R 13  is H, SO 3   −  or optionally substituted-alkyl, -alkenyl, -alkynyl or -aryl; and  
 R 14  is a secondary or tertiary amine or heterocyclyl, particularly N(H) or piperazine.  
 
   
   
       9 . The fluorescence energy transfer dye of  claim 8  where FETL is FETL1 and: 
 R 10  is D1-C(O)— or D1-N(H)—CH 2 —; and    R 11  is —C(O)-D2 or —CH 2 —N(H)-D2.    
   
   
       10 . An compound represented by the formula:  
     
       
         
         
             
             
         
       
     
     where: 
 X is O or C(R*R**), where R* and R** are independently lower alkyl or —CH 2 -Z;  
 R 1  is H, CF 3 , perfluoropropyl, lower alkyl acid, substituted aryl, substituted heteroaryl or Z;  
 R 2  is H, halo, SO 3   − , or is taken together with R 3  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 3  is halo, Z, or is taken together with R 2  and/or R 4  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 4  is ═O or OH, —N(R 4′ R 4″ ) or ═N + (R 4′ R 4″ ), or is taken together with R 3  and/or R 5  to form an optionally substituted fused ring having 5 to 7 atoms, 
 where R 4′  is H, lower alkyl or L1, and  
 R 4″  is H, lower alkyl or CH 2 -Z;  
 
 R 5  is H, halo, Z, or is taken together with R 4  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 6  is H, halo, Z, or is taken together with R 7  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 7  is ═O or OH, —N(R 7′ R 7″ ) or ═N + (R 7′ R 7″ ), or is taken together with R 6  and/or R 8  to form an optionally substituted fused ring having 5 to 7 atoms, 
 where R 7′  is H, lower alkyl or L1, and  
 R 7″  is H, lower alkyl or CH 2 -Z;  
 
 R 8  is halo, Z, or is taken together with R 7  and/or R 9  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 9  is H, halo, SO 3   − , or is taken together with R 8  to form an optionally substituted fused ring having 5 to 7 atoms; and  
 Z is a group of the formula: -Z*-Z 1 -(L1, L2 or FETL), where: 
 Z* is methylene, methoxy, ethoxy, aminomethyl, aminoethyl, aminopropynyl, aminobutynyl, carboxyethenyl, carboxyethynyl, optionally substituted aryl or optionally substituted heteroaryl;  
 Z 1  is —C(O)—, —N(Z 2 )- —CH 2 —O—, —CH 2 —C(O)—, —CH 2 —N(Z 2 )-, —CH 2 —S—, —CH 2 —S(O)—, —CH 2 —S(O 2 )— or is absent; and  
 Z 2  is H, C 1  to C 8  optionally substituted lower alkyl, or optionally substituted aryl;  
 L1 being a link for attachment to a probe or target, for attachment to a solid support, or is absent;  
 L2 being a link for attachment to a probe or target, for attachment to a solid support, or is absent; and  
 FETL being a fluorescence energy transfer linker.  
 provided that at least one of R 3  to R 8  is Z, where Z* is optionally substituted aryl or optionally substituted heteroaryl, or a FETL-, probe-, target- and/or support-conjugate thereof.  
 
 
   
   
       11 . The compound of  claim 10  having one or more of the following: 
 R 1  is H, CF 3 , perfluoropropyl, lower alkyl acid, 5-6 membered mono or 10-12 membered fused substituted aryl or heteroafyl, or Z;    R 2  is H, halo, SO 3   − , or is taken together with R 3  to form an optionally substituted fused 6-membered aryl ring;    R 3  is halo, Z, or is taken together with R 2  and/or R 4  to form an optionally substituted fused 6-membered ring;    R 4  is ═O or OH, —N(R 4′ R 4″ ) or ═N + (R 4′ R 4″ ), or is taken together with R 3  and/or R 5  to form an optionally substituted fused 6-membered ring;    R 5  is H, halo, Z, or is taken together with R 4  to form an optionally substituted fused 6-membered ring;    R 6  is H, halo, Z, or is taken together with R 7  to form an optionally substituted fused 6-membered ring;    R 7  is ═O or OH, —N(R 7′ R 7″ ) or ═N + (R 7′ R 7″ ), or is taken together with R 6  and/or R 8  to form an optionally substituted fused 6-membered ring;    R 8  is halo, Z, or is taken together with R 7  and/or R 9  to form an optionally substituted fused 6-membered ring;    R 9  is H, halo, SO 3   − , or is taken together with R 8  to form an optionally substituted fused 6-membered aryl ring;    R 4  is —N(R 4′ R 4″ ) or ═N + (R 4′ R 4″ ) and R 7  is -N(R 7′ R 7″ ) or ═N + (R 7′ R 7″ ) when X is C(R*R**); and/or    Z is a group of the formula: -Z*-Z 1 -(L1, L2 or FETL), where: 
 Z* is methylene, methoxy, ethoxy, aminomethyl, aminoethyl, aminopropynyl, aminobutynyl, carboxyethenyl, carboxyethynyl, optionally substituted aryl or optionally substituted heteroaryl,  
 Z 1 is —C(O)—, —N(Z 2 )-, —CH 2 —O—-, —CH 2 —C(O)—, —CH 2 —N(Z 2 )-, —CH 2 —S—, —CH 2 —S(O)—, —CH 2 —S(O 2 )— or is absent, and  
 Z 2 is H, or is C 1  to C 8  lower alkyl or aryl optionally substituted with SO 3   − , COOH, NH 2 , CH 2 NH 2 , SH, or SCH 3 .  
   
   
   
       12 . A fluorescence energy transfer dye represented by Formula II:  
       Probe--L1—(D1 or D2)—FETL-(low affinity false target)   (Formula II)  
     where: 
 Probe is a polynucleotide, antibody, triglyceride, low density lipoprotein or lectin;  
 L1 is a link for attachment to a the Probe;  
 FETL is a fluorescence energy transfer linker comprising a symmetric, rigid or sterically hindered, divalent moiety joined to D1 and D2 via an amine, carbonyl, activated carboxylic acid ester, disulfide, thiol or thiol ester;  
 low affinity false target is an analyte for the Probe disposed on FETL to deactivate, block or otherwise prevent coupling of FETL to a corresponding D2 or D1 until said low affinity false target is displaced by a higher affinity true target;  
 D1 is a donor dye represented by the formula:  
                     
 where:  
 X is O or C(R*R**), where R* and R** are independently lower alkyl or —CH 2 -Z;  
 R 1  is H, CF 3 , perfluoropropyl, lower alkyl acid, substituted aryl, substituted heteroaryl or Z;  
 R 2  is H, halo, SO 3   − , or is taken together with R 3  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 3  is halo, Z, or is taken together with R 2  and/or R 4  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 4  is ═O or OH, —N(R 4′ R 4″ ) or ═N + (R 4′ R 4″ ), or is taken together with R 3  and/or R 5  to form an optionally substituted fused ring having 5 to 7 atoms, 
 where R 4′  is H, lower alkyl or L1, and  
 R 4″  is H, lower alkyl or CH 2 -Z;  
 
 R 5 is H, halo, Z, or is taken together with R 4  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 6  is H, halo, Z, or is taken together with R 7  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 7  is ═O or OH, —N(R 7′ R 7″ ) or ═N + (R 7′ R 7″ ), or is taken together with R 6  and/or R 8  to form an optionally substituted fused ring having 5 to 7 atoms, 
 where R 7′  is H, lower alkyl or L1, and  
 R 7″  is H, lower alkyl or CH 2 -Z;  
 
 R 8  is halo, Z, or is taken together with R 7  and/or R 9  to form an optionally substituted fused ring having 5 to 7 atoms;  
 R 9  is H, halo, SO 3   − , or is taken together with R 8  to form an optionally substituted fused ring having 5 to 7 atoms; and  
 Z is a group of the formula: -Z*-Z 1 -(L1, L2 or FETL), where: 
 Z* is methylene, methoxy, ethoxy, aminomethyl, aminoethyl, aminopropynyl, aminobutynyl, carboxyethenyl, carboxyethynyl, optionally substituted aryl or optionally substituted heteroaryl;  
 Z 1  is —C(O)—, —N(Z 2 )-, —CH 2 —O—, —CH 2 —C(O)—, —CH 2 —N(Z 2 )-, —CH 2 —S—, —CH 2 —S(O)—, —CH 2 —S(O 2 )— or is absent; and  
 Z 2  is H, C 1  to C 8  optionally substituted lower alkyl, or optionally substituted aryl; and  
 
 D2 is an acceptor/reporter dye represented by formula D1 or by a formula of the group:  
                     
 where:  
 at least one of R 21  to R 36  is joined to FETL,  
 n is zero, 1, 2 or 3;  
 R 21  and R 30  are independently —CH 2 -Z, activated lower alkyl, or optionally substituted arlkyl;  
 R 22  to R 29  are independently H, SO 3   − , or optionally substituted alkyl, or R 22  and R 23 , R 23  and R 24  R 24  and R 25 , R 26  and R 27 , R 27  and R 28 , and/or R 28  and R 29  taken together form an optionally substituted fused ring having 6 atoms; and  
 R 31  and R 32  are independently H, optionally substituted alkyl, aryl, or taken together form an optionally substituted fused ring having 6 atoms;  
 R 33  to R 36  are independently H, SO 3   − , optionally substituted alkyl, aryl, or R 33  and R 34 , R 34  and R 35  and/or R 35  and R 36  taken together form an optionally substituted fused ring having 6 atoms; and  
 Y is —O— or —N(Y 1 )— where Y 1  is —CH 2 -Z, activated lower alkyl, or optionally substituted aralkyl.  
 
   
   
       13 . An assay requiring no pre-analysis purification for removal of unbound dye, comprising the steps of: 
 (a) contacting a substance to be tested and a target site specific Probe-L1-(D1 or D2)-FETL-(low affinity false target) conjugate of  claim 12  in a suitable assay vessel under conditions suitable for preferential binding of the Probe to the target site, as opposed to the low affinity false target;    (b) introducing a D2 or D1 fluorescence energy transfer dye having an activated site for coupling to the FETL into the vessel, under conditions suitable for coupling to FETL where the low affinity false target is not bound to the Probe;    (c) causing D1 to absorb energy; and    (d) measuring the level of D2 emission.    
   
   
       14 . A proximity assay comprising the steps of: 
 (a) contacting a substance to be tested and a target-site-specific donor dye in a suitable assay vessle;    (b) introducing a target-site-specific fluorescence energy transfer reporter dye of  claim 1  into the vessel, where said reporter dye's target is either spatially proximate to said donor dye target or specific for a given target to be tested for spatial proximity to said donor dye target, and said reporter dye's energy absorption spectra overlaps the emission spectra of said donor dye;    (c) causing the donor dye to absorb energy; and    (d) measuring the level of reporter dye emission.    
   
   
       15 . The proximity assay of  claim 14  wherein: 
 step (b) further comprises introducing two or more of said target-site-specific fluorescence energy transfer reporter dyes into the vessel, said reporter dyes having energy absorption spectra overlapping the emission spectra of said donor dye, distinct emission spectra, and having different targets to be tested for spatial proximity to said donor dye target; and    step (d) further comprises measuring the level of reporter dye emission at the wavelengths characteristic of said reporter dyes.