Xanthene dyes

Abstract

The invention provides a novel class of xanthene dyes, some of which are functionalized to allow their coupling to conjugation partners of interest, e.g. biomolecules, drugs, toxins and the like. Also provided are conjugates of the dyes, methods of preparing and using the dyes and their conjugates and kits including the dyes and their conjugates.

1 . A xanthene dye having the formula: 
       
         
           
           
               
               
           
         
       
       in which
 R 1 , R 2 , R 4 , R 5 , R 6 , R 7 , R 8 , R 9 , R 10  and R 11  are independently selected from substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, halogen, H, NO 2 , CN and C(Z 1 )R 14 , NR 15 R 16  and Z 2 R 16 ; 
 R 3  is selected from Z 2 R 16  and NR15R 16    
 wherein
 Z 1  is a member selected from O, S and NH; 
 Z 2  is a member selected from O and S; 
 R 15  is a member selected from H, substituted or unsubstituted alkyl, and substituted or unsubstituted heteroalkyl; 
 R 16  is selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, C(Z 3 )R 17 , and a nitrogen-containing reactive group comprising R 15  and R 16 , together with the nitrogen to which they are attached, wherein said reactive group is a member selected from —NHNH 2 , —N═C═S and —N═C═O 
 wherein
 Z 3  is a member selected from O, S and NH; 
 R 17  is a member selected from substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, OR 18 , and NR 19 R 20    
 wherein
 R 18  is a member selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and C(O)R 1    
 wherein 
  R 21  is substituted or unsubstituted alkyl or substituted or unsubstituted heteroalkyl; 
 R 19  and R 20  are members independently selected from H, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl 
 
 
 
 Y is a member selected from C(O) and S(O) 2 ; 
 X is a member selected from (NR 22 R 23 ) and (O) 
 wherein
 R 22  and R 23  are members independently selected from H, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl; and 
 
 R 12  and R 13  are members independently selected from substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted-aryl and substituted or unsubstituted heteroaryl, with the proviso that at least one of R 12  or R 13  comprises a member selected from a bond to a carrier molecule, a bond to a linker bound to a carrier molecule, a bond to a solid support, a bond to a linker attached to a solid support, a bond to a fluorescence quencher, a bond to a linker to a fluorescence quencher and an oxygen-containing reactive group, and further with the proviso that when R 12  and R 13 , together with the nitrogen to which they are attached form a piperazine ring said oxygen-containing reactive group is a phosphoramidite and said bond to a carrier molecule is other than a bond to a peptide.