Labelled oligonucleotides synthesized on solid-supports

Abstract

Methods and compositions to label oligonucleotides and analogs directly on a solid-support having the structure where S is a solid-support, A is a cleavable linker, X is a moiety with three or more attachment sites, L is a label, Y is a nucleophile, i.e. O, NH, NR or S, and P 1 is an acid cleavable protecting group are provided. The labelled solid-support is reacted in a cyclical fashion to synthesize a labelled oligonucleotide on a solid-support in the 5′ to 3′ direction, having the structure: Labelled oligonucleotides are also synthesized by reacting: (i) a label reagent bearing functionality consisting of carboxylic acid, sulfonic acid, phosphonic acid, or phosphoric acid, (ii) an oligonucleotide on solid support with nucleophilic functionality, and (iii) a coupling reagent, whereby an ester, amide, thioester, sulfonamide, sulfonate, phosphonate, phosphoramidate, phosphorothioate, or phosphate bond is formed. The labelling reaction may be conducted at label sites including the 5′ terminus, the 3′ terminus, a nucleobase, an internucleotide linkage, a sugar, amino, sulfide, hydroxyl, and carboxyl.

1 . A method for synthesis of labelled oligonucleotides comprising the steps of: 
 a. providing a labelled solid-support having the structure                          where,    S is a solid-support;    A is a cleavable linker;    X is a moiety with three or more attachment sites;    L is a label;    Y is selected from the group consisting of oxygen, NH, NR where R is methyl, lower alkyl, substituted alkyl, phenyl, aryl, and substituted aryl, and sulfur; and    P 1  is an acid-cleavable protecting group; 
 b. reacting the labelled solid-support with acid to remove the acid-cleavable protecting group, P 1 ; and  
 c. adding a 5′-phosphoramidite, 3′ protected nucleoside and an activator, thereby forming a bond between Y and the nucleoside.  
   
     
     
         2 . The method of  claim 1  further comprising the steps of 
 d. capping any unreacted sites on the solid-support; and    e. adding an oxidizing reagent.    
     
     
         3 . The method of  claim 1  further comprising the steps of 
 d. capping any unreacted sites on the solid-support;    e. adding an oxidizing reagent; and    f. repeating steps b. to e. until the labelled oligonucleotide is completely synthesized.    
     
     
         4 . The method of  claim 3  further comprising the step of deprotecting the labelled oligonucleotide.  
     
     
         5 . The method of  claim 3  further comprising the steps of cleaving the labelled compound from the solid-support and deprotecting the labelled oligonucleotide.  
     
     
         6 . The method of  claim 1  wherein the solid-support S is selected from the group consisting of polystyrene, controlled-pore-glass, silica gel, silica, polyacrylamide, magnetic beads, polyacrylate, hydroxyethylmethacrylate, polyamide, polyethylene, polyethyleneoxy, and copolymers and grafts of such.  
     
     
         7 . The method of  claim 1  wherein the form of the solid support S is selected from the group consisting of small particles, beads, membranes, frits, slides, plates, micromachined chips, alkanethiol-gold layers, non-porous surfaces, addressable arrays, and polynucleotide-immobilizing media.  
     
     
         8 . The method of  claim 1  wherein the cleavable linker A is selected from the group consisting of:  
       
         
           
           
               
               
           
         
       
     
     
         9 . The method of  claim 1  wherein the linker X is selected from the group consisting of:  
       
         
           
           
               
               
           
         
       
       where n is 1 to 12.  
     
     
         10 . The method of  claim 1  wherein the label L is selected from the group consisting of hybridization-stabilizing moieties, fluorescent dyes, fluorescence quenchers, energy-transfer dye sets, chemiluminescent dyes, amino acids, proteins, peptides, enzymes, and affinity ligands.  
     
     
         11 . The method of  claim 10  where the fluorescent dyes and fluorescence quenchers are selected from the group consisting of FAM, TET, HEX, JOE, TAMRA, d-TAMRA, JODA, ROX, VIC, NED, dJON, dR139, DABCYL, DABSYL, malachite green, 4,7-dichloro-fluoresceins, 4,7-dichloro-rhodamines, NTB, and cyanines.  
     
     
         12 . The method of  claim 10  where the hybridization-stabilizing moieties are selected from the group consisting of Hoechst 33258, CDPI 1-3 , MGB1, netropsin, and distamycin.  
     
     
         13 . The method of  claim 1  wherein the acid-cleavable protecting group P 1  is selected from the group consisting of DMT, MMT, trityl, substituted trityl, pixyl, and trialkylsilyl.  
     
     
         14 . The method of  claim 1  wherein the 5′-phosphoramidite, 3′ protected nucleoside monomer has the structure:  
       
         
           
           
               
               
           
         
       
       where, 
 R is selected from the group consisting of cyanoethyl, methyl, lower alkyl, substituted alkyl, phenyl, aryl, and substituted aryl;  
 R 1  and R 2  are individually selected from the group consisting of isopropyl, morpholino, methyl, ethyl, lower alkyl, cycloalkyl, and aryl;  
 P 2  is an exocyclic nitrogen protecting group selected from the group consisting of benzoyl, isobutyryl, acetyl, phenoxyacetyl, aryloxyacetyl, dimethylformamidine, dialkylformamidine, and dialkylacetamidine; and  
 P 3  is an acid-labile protecting group selected from the group consisting of DMT, MMT, pixyl, trityl, and trialkylsilyl.  
 
     
     
         15 . The method of  claim 3  wherein the oligonucleotide comprises one or more DNA, RNA, and nucleic acid analog monomer units.  
     
     
         16 . The method of  claim 15  wherein the nucleic acid analog is selected from the group consisting of nucleobase analogs, sugar analogs, and internucleotide analogs.  
     
     
         17 . The method of  claim 16  wherein nucleobase analogs are selected from the group consisting of C-5-alkyl pyrimidine, 2,6-diaminopurine, 2-thiopyrimidine, C-5-propyne pyrimidine, phenoxazine, 7-deazapurine, isocytidine, pseudo-isocytidine, isoguanosine, hypoxanthine, 8-oxopurine, and universal base.  
     
     
         18 . The method of  claim 16  wherein sugar analogs are selected from the group consisting of 2′-O-alkyl-ribonucleotides, 2′-O-methyl-ribonucleotides, 2′-O-allyl-ribonucleotides, 2′-allyl ribonucleotides, 2′-halo-ribonucleotides, 2′-O-methoxyethyl-ribonucleotides, 2′-branching group-ribonucleotides, 2′-O-branching group-ribonucleotides, 4′-α-anomeric nucleotides, and 1′-α-anomeric nucleotides.  
     
     
         19 . The method of  claim 16  wherein internucleotide analogs are selected from the group consisting of 2-aminoethylglycine (PNA), 2′-5′-linkage, inverted 3′-3′ linkage, inverted 5′-5′ linkage, phosphorothioate, methyl phosphonate, non-bridging N-substituted phosphoramidate, alkylated phosphotriester branched structure, and 3′-N-phosphoramidate.  
     
     
         20 . The method of  claim 1  wherein the labelled solid-support comprises a compound of the formula  
       
         
           
           
               
               
           
         
       
       where S is polystyrene or controlled-pore-glass; and 
 L is a label.  
 
     
     
         21 . A solid-support comprising a compound of the formula  
       
         
           
           
               
               
           
         
       
       where, 
 S is a solid-support;  
 A is a cleavable linker;  
 X is a moiety with three or more attachment sites;  
 L is a label;  
 Y is selected from the group consisting of O, NH, NR, and S;  
 R is selected from the group consisting of cyanoethyl, methyl, lower alkyl, substituted alkyl, phenyl, aryl, and substituted aryl;  
 P 2  is an exocyclic nitrogen protecting group selected from the group consisting of benzoyl, isobutyryl, acetyl, phenoxyacetyl, aryloxyacetyl, dimethylformamidine, dialkylformamidine, and dialkylacetamidine; and  
 P 3  is acid-labile protecting group selected from the group consisting of DMT, MMT, trityl, substituted trityl, pixyl, and trialkylsilyl.  
 
     
     
         22 . A solid-support comprising a compound of the formula  
       
         
           
           
               
               
           
         
       
       where, 
 S is a solid-support;  
 A is a cleavable linker;  
 X is a moiety with three or more attachment sites;  
 L is a label;  
 Y is selected from the group consisting of O, NH, NR, and S;  
 R is cyanoethyl, methyl, lower alkyl, substituted alkyl, phenyl, aryl, and substituted aryl;  
 P 2  is an exocyclic nitrogen protecting group selected from the group consisting of benzoyl, isobutyryl, acetyl, phenoxyacetyl, aryloxyacetyl, dimethylformamidine, dialkylformamidine, and dialkylacetamidine.  
 
     
     
         23 . A method to synthesize a labelled oligonucleotide comprising: 
 coupling a label reagent with functionality consisting of carboxylic acid, sulfonic acid, phosphonic acid, or phosphoric acid; an oligonucleotide on solid support with nucleophilic functionality consisting of alcohol, amine, or thiol; and a coupling reagent;    wherein an ester, amide, thioester, sulfonamide, sulfonate, phosphonate, phosphoramidate, phosphorothioate, or phosphate bond is formed.    
     
     
         24 . The method of  claim 23  wherein the label reagents are selected from the group consisting of hybridization-stabilizing moieties, fluorescent dyes, fluorescence quenchers, energy-transfer dye sets, chemiluminescent dyes, amino acids, proteins, peptides, enzymes, and affinity ligands.  
     
     
         25 . The method of  claim 24  where the fluorescent dyes and fluorescence quenchers are selected from the group consisting of FAM, TET, HEX, JOE, TAMRA, d-TAMRA, JODA, ROX, VIC, NED, dJON, dR139, DABCYL, DABSYL, malachite green, 4,7-dichloro-fluoresceins, 4,7-dichloro-rhodamines, NTB, and cyanines.  
     
     
         26 . The method of  claim 24  where the hybridization-stabilizing moieties are selected from the group consisting of Hoechst 33258, CDPI 1-3 , MGB1, netropsin, and distamycin.  
     
     
         27 . The method of  claim 23  wherein the labels are attached to the oligonucleotide at label sites consisting of the 5′ terminus, the 3′ terminus, a nucleobase, an internucleotide linkage, a sugar, amino, sulfide, hydroxyl, and carboxyl.  
     
     
         28 . The method of  claim 23  wherein the solid-support comprises a compound of the formula  
       
         
           
           
               
               
           
         
       
       where, 
 S is a solid-support;  
 A is a cleavable linker;  
 X is a moiety with three or more attachment sites;  
 L is a label;  
 Y is selected from the group consisting of oxygen, NH, NR, where R is methyl, lower alkyl, substituted alkyl, phenyl, aryl, and substituted aryl, and sulfur; and  
 P 1  is an acid-cleavable protecting group.  
 
     
     
         29 . The method of  claim 23  wherein the solid-support is selected from the group consisting of polystyrene, controlled-pore-glass, silica gel, silica, polyacrylamide, magnetic beads, polyacrylate, hydroxethylmethacrylate, polyamide, polyethylene, polyethyleneoxy, and copolymers or grafts of such.  
     
     
         30 . The method of  claim 29  wherein the form of the solid support is selected from the group consisting of small particles, beads, membranes, frits, non-porous surfaces, slides, plates, micromachined chips, alkanethiol-gold layers, addressable arrays, or polynucleotide-immobilizing media.  
     
     
         31 . The method of  claim 23  wherein the oligonucleotide comprises one or more DNA, RNA, PNA and nucleic acid analog monomer units.  
     
     
         32 . The method of  claim 31  wherein the nucleic acid analog is selected from the group consisting of nucleobase analogs, sugar analogs, and internucleotide analogs.  
     
     
         33 . The method of  claim 32  wherein nucleobase analogs are selected from the group consisting of C-5-alkyl pyrimidine, 2,6-diaminopurine, 2-thiopyrimidine, C-5-propyne pyrimidine, phenoxazine, 7-deazapurine, isocytidine, pseudo-isocytidine, isoguanosine, hypoxanthine, 8-oxopurine, and universal base.  
     
     
         34 . The method of  claim 32  wherein sugar analogs are selected from the group consisting of 2′-O-alkyl-ribonucleotides, 2′-O-methyl-ribonucleotides, 2′-O-allyl-ribonucleotides, 2′-allyl ribonucleotides, 2′-halo-ribonucleotides, 2′-O-methoxyethyl-ribonucleotides, 2′-branching group-ribonucleotides, 2′-O-branching group-ribonucleotides, 4′-α-anomeric nucleotides, and 1′-α-anomeric nucleotides.  
     
     
         35 . The method of  claim 32  wherein internucleotide analogs are selected from the group consisting of 2-aminoethylglycine (PNA), 2′-5′-linkage, inverted 3′-3′ linkage, inverted 5′-5′ linkage, phosphorothioate, methyl phosphonate, non-bridging N-substituted phosphoramidate, alkylated phosphotriester branched structure, and 3′-N-phosphoramidate.  
     
     
         36 . The method of  claim 23  wherein the direction of oligonucleotide synthesis is 5′ to 3′.  
     
     
         35 . The method of  claim 23  wherein the direction of oligonucleotide synthesis is 3′ to 5′.