Water soluble fluorscent or colored dyes comprising conjugating groups

Abstract

Compounds useful as fluorescent or colored dyes are disclosed. The compounds have the following structure (I): or a stereoisomer, tautomer or salt thereof, wherein R 1 , R 2 , R 3 , R 4 , R 5 , L 1 , L 3 , L 4 , L 6 , L 7 , L 8 , M 1 , M 2 , q, w and n are as defined herein. Methods associated with preparation and use of such compounds are also provided.

What is claimed is: 
     
         1 . A compound having the following structure (II): 
       
         
           
           
               
               
           
         
       
       or a salt or stereoisomer thereof, wherein:
 M 1  is, at each occurrence, independently a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M 1  is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof; 
 L 1 , L 3 , and L 7  are, at each occurrence, independently optional alkylene or heteroalkylene linkers; 
 R 1  is, at each occurrence, independently H, alkyl or alkoxy; 
 R 2  is an electron pair, H, phospho, thiophospho, alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether; or R 2  is -L 9 -(L 10 ) z -L 11 -Q or -L 9 -(L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 -I, where I represents, independently, a further compound of structure (I); 
 R 3  is H, OH, SH, —NH 2 , alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, phosphate, thiophosphate, alkylphospho, alkylthiophospho, —Oalkylphospho, —Oalkylthiophospho, alkyletherphospho, alkyletherthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho phosphoalkyl, phosphoalkylether, thiophosphoalkyl, thiophosphoalkylether, —Ophosphoalkyl, —Ophosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether; or R 3  is -L 9 -L 10 ) z -L 11 -Q or -L 9 -(L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 -I, where I represents, independently, a further compound of structure (I) 
 R 4  is, at each occurrence, independently O − , S − , OZ, SZ or N(R 6 ) 2 , where Z is a cation and each R 6  is independently H or alkyl; 
 R 5  is, at each occurrence, independently oxo, thioxo or absent; 
 L 9  and L 11  are, at each occurrence, independently an optional linker; 
 L 10  is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene, aminoalkylene, hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene; 
 Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support; 
 n is an integer from 1 to 20; and 
 z is an integer from 1 to 10, 
 provided at least one of R 2  or R 3  is -L 9 -L 10 ) z -L 11 -Q or -L 9 -(L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 -I, where I represents, independently, a further compound of structure (I). 
 
     
     
         2 . The compound of  claim 1 , wherein R 3  is -L 9 -(L 10 ) z -L 11 -Q, and R 2  is alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, wherein R 2  is optionally substituted with a substituent selected from —OH, —NH 2  and —SH. 
     
     
         3 . The compound of  claim 2 , wherein R 2  has one of the following structures: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         wherein: 
         R 2a  is —OH, —SH, —NH 2 , phosphate or thiophosphate; 
         R 4a  and R 4b  are independently O − , S −  OZ or SZ, where Z is a cation; 
         R 5a  and R 5b  are independently oxo, or thioxo; and 
         a, b and c are each independently integers from 1 to 10. 
       
     
     
         4 . The compound of  claim 1 , wherein R 2  is -L 9 -L 10 ) z -L 11 -Q, and R 3  is OH or phosphate. 
     
     
         5 . The compound of  claim 1 , wherein R 2  is -L 9 -(L 10 ) z -L 11 -Q, and R 3  is, phosphate, thiophosphate, phospho, thiophospho, —Oalkylphospho, —Oalkylthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho, —Ophosphoalkyl, —Ophosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether optionally substituted with a substituent selected from —OH, —NH 2  and —SH. 
     
     
         6 . The compound of  claim 5 , wherein R 3  has one of the following structures: 
       
         
           
           
               
               
           
         
         wherein: 
         R 3a  is —OH, —SH, —NH 2 , phosphate or thiophosphate; 
         R 4a  and R 4b  are independently O − , S −  OZ or SZ, where Z is a cation; 
         R 5a  and R 5b  are independently oxo, or thioxo; and 
         b and c are each independently integers from 1 to 10. 
       
     
     
         7 . The compound of  claim 6 , wherein R 4  is O −  and R 5  is oxo at each occurrence. 
     
     
         8 . The compound of  claim 7 , wherein L 1 , L 3  and L 7  are each alkylene linkers. 
     
     
         9 . The compound of  claim 7 , wherein L 1  and L 3  are each alkylene linkers and L 7  is absent. 
     
     
         10 . The compound of  claim 8 , wherein alkylene is methylene. 
     
     
         11 . A method for visually detecting a biomolecule, the method comprising:
 (a) admixing the compound of  claim 1  with one or more biomolecules; and   (b) detecting the compound by its visible properties.   
     
     
         12 . A compound having the following structure (III): 
       
         
           
           
               
               
           
         
       
       or a salt or stereoisomer thereof, wherein:
 M 1  is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof; 
 R 1  is H, alkyl or alkoxy; 
 R 2  is H, an electron pair or a cation; or R 2  is -L 9 -L 10 ) z -L 11 -Q or -L 9 -(L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 -I, where I represents, independently, a further compound of structure (I); 
 R 3  is H, phosphate or OH; or R 3  is -L 9 -(L 10 ) z -L 11 -Q or -L 9 -(L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 -I, where I represents, independently, a further compound of structure (I); 
 R 4  is O, S, OZ, SZ where Z is a cation; 
 R 5  is oxo or thioxo; 
 R 7 , R 8 , R 9 , R 10 , R 11  and R 12  are, at each occurrence, independently H or alkyl; 
 L 9  and L 11  are, at each occurrence, independently an optional linker; 
 L 10  is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene, aminoalkylene, hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene; 
 Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support; and 
 x, y and z are, at each occurrence, independently an integer from 0 to 5; and 
 z is an integer from 1 to 10, 
 provided at least one of R 2  or R 3  is -L 9 -L 10 ) z -L 11 -Q or -L 9 -(L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 -I, where I represents, independently, a further compound of structure (I). 
 
     
     
         13 . The compound of  claim 12 , wherein x, y and z are each 1. 
     
     
         14 . The compound of  claim 12 , wherein x is 0 and y and z are each 1. 
     
     
         15 . The compound of  claim 12 , wherein L 9  is present and is C 1 -C 6  alkylene. 
     
     
         16 . The compound of  claim 12 , wherein (L 10 ) z  has one of the following structures: 
       
         
           
           
               
               
           
         
         wherein b is an integer from 2 to 10. 
       
     
     
         17 . The compound of  claim 12 , wherein M 1  has one of the following structures: 
       
         
           
           
               
               
           
         
       
     
     
         18 . The compound of  claim 12 , wherein M 1 , at each occurrence, independently comprises at least one substituent, wherein the substituent is a fluoro, chloro, bromo, iodo, amino, alkylamino, arylamino, hydroxy, sulfhydryl, alkoxy, aryloxy, phenyl, aryl, methyl, ethyl, propyl, butyl, isopropyl, t-butyl, carboxy, sulfonate, amide, or formyl group. 
     
     
         19 . The compound of  claim 12 , wherein Q is sulfhydryl, disulfide, activated ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, α-haloamide, biotin, amino or a maleimide. 
     
     
         20 . A method for visually detecting a biomolecule, the method comprising:
 (a) admixing the compound of  claim 12  with one or more biomolecules; and   (b) detecting the compound by its visible properties.