C-3' protected monomeric nucleotides and synthesis of oligonucleotides on solid support

Abstract

Immobilized nucleotide primers of this invention include a modified nucleotide tethered to a support substrate through a linking group. In particular, the modified nucleotide is constructed such that the C-5′ end of the nucleotide is tetherable to the linking group and the protected C-3′ end is available for further controlled modification, e.g., addition of other nucleotides in specific sequences to the immobilized nucleotide primer. Additionally, the linking group is of sufficient length to allow the immobilized nucleotide primer to be used to synthesize and screen arrays of oligonucleotides, e.g., enzymatic C-3′ primer extension.

What is claimed is:  
     
         1 . A method of producing an immobilized oligonucleotide on a substrate comprising: 
 covalently attaching a first nucleotide or an oligonucleotide via a C-5′ oxygen of the nucleotide to the substrate.    
     
     
         2 . The method of  claim 1 , wherein the first nucleotide has the formula  
       
         
           
           
               
               
           
         
       
       wherein X is selected from the group consisting of a photolabile protecting group and a chemically labile protecting group; R is selected from the group consisting of hydrogen, hydroxyl, and modified hydroxyl; P is selected from the group consisting of hydrogen, a phosphorous activating group, and a phosphate or derivative thereof; and Base is selected from the group consisting of pyrimidine, purine, and derivatives thereof.  
     
     
         3 . The method of  claim 2  further including removing the photolabile protecting group or the Chemically labile protecting group from the C-3′ oxygen of the first nucleotide to form a hydroxyl group.  
     
     
         4 . The method of  claim 3  further including covalently attaching a second nucleotide monomer or oligonucleotide via a C-5′ oxygen of a nucleotide to the first nucleotide.  
     
     
         5 . The method of  claim 4  further including activating the C-3′ hydroxyl group of the first nucleotide with a phosphorous activating group.  
     
     
         6 . The method of  claim 5 , wherein the phosphorous activating group is chloro-N,N-diisopropylamine-β-cyanoethoxyphosphine or bis-N,N-diisopropylamine-β-cyanoethoxyphosphine  
     
     
         7 . The method of  claim 1  further including activating a terminal end of a linking group bound to the substrate.  
     
     
         8 . The method of  claim 7 , wherein the first nucleotide covalently attaches to the activated terminal end of the linking group.  
     
     
         9 . The method of  claim 8 , wherein the linking group has the formula (OCH 2 CH 2 )n-O— and n has value between about 3 and about 30.  
     
     
         10 . The method of  claim 2 , wherein the base is selected from the group consisting of adenyl, guanyl, cytidyl, thymidyl, inosyl, and uridyl.  
     
     
         11 . The method of  claim 10 , wherein the base is inosyl.  
     
     
         12 . The method of  claim 2 , wherein X is a photolabile protecting group selected from the group consisting of NVOC, MBNPEOC, and MeNPOC.  
     
     
         13 . The method of  claim 12 , wherein X is MBNPEOC.  
     
     
         14 . The method of  claim 2 , wherein the first nucleotide has the formula  
       
         
           
           
               
               
           
         
       
       wherein R 1 , R 2 , R 3  each independently is selected from the group consisting of hydrogen, C1-C10 alkyl, C2-C10 alkenyl, aryl, benzyl, and C1-C10 alkoxyl; R 4  is selected from the group consisting of C1-C10 alkyl, C2-C10 alkenyl, aryl, and benzyl; and P is selected from the group consisting of hydrogen and [(i-Pr) 2 N]POCH 2 CH 2 CN.  
     
     
         15 . The method of  claim 1 , wherein the substrate is selected from the group consisting of glass, surface-modified glass, particles, and shaped gel.  
     
     
         16 . A method of synthesizing an oligonucleotide on a substrate, comprising: 
 (a) contacting a modified nucleotide via a C-5′ oxygen to an activated immobilized hydroxyl group to produce a covalently attached nucleotide, wherein the modified nucleotide includes a C-3′ photolabile protecting group and a C-S′ hydroxyl group, and wherein the activated immobilized hydroxyl group is activated with a phosphorous activating group;    (b) irradiating the covalently attached nucleotide to remove the C-3′ photolabile protecting group and form a C-3′ hydroxyl group;    (c) contacting the C-3′ hydroxyl group of the covalently attached nucleotide with a phosphorous activating group to produce an activated immobilized hydroxyl group at the C-3′ position of the covalently attached nucleotide; and    (d) repeating steps (a) to (c).    
     
     
         17 . The method of  claim 16 , wherein the modified nucleotides have the formula  
       
         
           
           
               
               
           
         
       
       wherein X is a photolabile protecting group; R is selected from the group consisting of hydrogen, hydroxyl, and modified hydroxyl; P is hydrogen; and Base is selected from the group consisting of pyrimidine, purine, and derivatives thereof.  
     
     
         18 . The method of  claim 16 , wherein the phosphorous activating group is chloro-N,N-diisopropylamine-β-cyanoethoxyphosphine or bis-N,N-diisopropylamine-β-cyanoethoxyphosphine.  
     
     
         19 . The method of  claim 16 , wherein the surface hydroxyl group is the terminus of a linking group having the formula (OCH 2 CH 2 )n-O—H and n has value between about 3 and about 30.  
     
     
         20 . The method of  claim 16 , wherein the base is selected from the group consisting of adenyl, guanyl, cytidyl, thymidyl, inosyl, and uridyl.  
     
     
         21 . The method of  claim 16 , wherein the photolabile protecting group is selected from the group consisting of NVOC, MBNPEOC, and MeNPOC.  
     
     
         22 . The method of  claim 21 , wherein the photolabile protecting group is MBNPEOC.  
     
     
         23 . The method of  claim 16 , wherein modified nucleotides have the formula  
       
         
           
           
               
               
           
         
       
       wherein R 1 , R 2 , R 3  each independently is selected from the group consisting of hydrogen, C1-C10 alkyl, C2-C10 alkenyl, aryl, benzyl, and C1-C10 alkoxyl; R 4  is selected from the group consisting of C1-C10 alkyl, C2-C10 alkenyl, aryl, and benzyl; and P is selected from the group consisting of hydrogen and [(i-Pr) 2 N]POCH 2 CH 2 CN.  
     
     
         24 . A method of  claim 16  further including contacting the synthesized oligonucleotide with a polymerase, wherein the polymerase is selected from a group consisting of DNA polymerases and RNA polymerases.  
     
     
         25 . A method of  claim 16 , wherein the substrate is selected from the group consisting of glass, surface-modified glass, particles, and shaped gel.  
     
     
         26 . A method of synthesizing an oligonucleotide, comprising: 
 (a) providing a nucleotide or an oligonucleotide having a free terminal C-3′ hydroxyl and a terminal C-5′ that is blocked by a group, wherein the free terminal C-3′ hydroxyl is activated with a phosphorous activating group;    (b) covalently coupling a modified nucleotide via a C-5′ oxygen to the activated hydroxyl group, wherein the modified nucleotide includes a C-3′ photolabile protected group and a C-5′ hydroxyl group;    (c) irradiating the covalently attached nucleotide to remove the C-3′ photolabile protecting group and form a C-3′ hydroxyl group;    (d) contacting the C-3′ hydroxyl group of the covalently attached nucleotide with a phosphorous activating group to produce an activated hydroxyl group at the C-3′ position;    (e) covalently coupling a modified nucleotide via a C-5′ oxygen to the activated hydroxyl group of a previously covalently attached nucleotide; and    (f) repeating steps (c) to (e).    
     
     
         27 . The method of  claim 26 , wherein the modified nucleotides have the formula  
       
         
           
           
               
               
           
         
       
       wherein X is a photolabile protecting group; R is selected from the group consisting of hydrogen, hydroxyl, and modified hydroxyl; P is hydrogen; and Base is selected from the group consisting of pyrimidine, purine, and derivatives thereof.  
     
     
         28 . The method of  claim 27 , wherein the base is selected from the group consisting of adenyl, guanyl, cytidyl, thymidyl, inosyl, and uridyl.  
     
     
         29 . The method of  claim 27 , wherein the photolabile protecting group is selected from the group consisting of NVOC, MBNPEOC, and MeNPOC.  
     
     
         30 . The method of  claim 27 , wherein the photolabile protecting group is MBNPEOC.  
     
     
         31 . The method of  claim 27 , wherein modified nucleotides have the formula  
       
         
           
           
               
               
           
         
       
       wherein R 1 , R 2 , R 3  each independently is selected from the group consisting of hydrogen, C1-C10 alkyl, C2-C10 alkenyl, aryl, benzyl, and C1-C10 alkoxyl; R 4  is selected from the group consisting of C1-C10 alkyl, C2-C10 alkenyl, aryl, and benzyl; and P is selected from the group consisting of hydrogen and [(i-Pr) 2 N]POCH 2 CH 2 CN.  
     
     
         32 . An oligonucleotide array, comprising: 
 A substrate having a plurality of addressable sites; each of the sites of the plurality having an oligonucleotide covalently attached to the substrate via its C-5′ oxygen atom, wherein each site of the plurality is directly adjacent to at least one other site, and wherein the sequence of each oligonucleotide is unique among the plurality.    
     
     
         33 . The oligonucleotide array of  claim 32 , wherein the substrate is selected from the group consisting of glass, surface-modified glass, and shaped gel.  
     
     
         34 . The oligonucleotide array of  claim 32 , wherein the attached oligonucleotides have a density of at least 20 molecules/cm 2 .  
     
     
         35 . The oligonucleotide array of  claim 32 , wherein the attached oligonucleotides have a density of at least 50,000 molecules/cm 2 .  
     
     
         36 . The oligonucleotide array of  claim 32 , wherein the attached oligonucleotides have a density of at least 1,000,000 molecules/cm 2 .  
     
     
         37 . The oligonucleotide array of  claim 32 , wherein the unique sequence has a length of 5 bases to 40 bases.  
     
     
         38 . A compound of the formula  
       
         
           
           
               
               
           
         
       
       wherein X is selected from the group consisting of a photolabile protecting group and a chemically labile protecting group; R is selected from the group consisting of hydrogen, hydroxyl, and alkoxyl; P is selected from the group consisting of hydrogen, a phosphorous activating group, a nucleotide monomer or oligomer, and a phosphate or derivative thereof; and Base is selected from the group consisting of pyrimidine, purine, and derivatives thereof.  
     
     
         39 . The compound of  claim 38  wherein the base is selected from the group consisting of adenyl, guanyl, cytidyl, thymidyl, inosyl, and uridyl.  
     
     
         40 . The compound of  claim 39 , wherein the base is inosyl.  
     
     
         41 . The compound of  claim 38 , wherein X a photolabile protecting group selected from the group consisting of NVOC, MBNPEOC, and MeNPOC.  
     
     
         42 . The compound of  claim 41 , wherein X is MBNPEOC.  
     
     
         43 . The compound of  claim 38 , wherein P is hydrogen.  
     
     
         44 . The compound of  claim 38 , wherein P is a phosphate moiety bound to a linking group attached to a support surface.  
     
     
         45 . The compound of  claim 38 , wherein the linking group has the formula (OCH 2 CH 2 )n-O— and n has value between about 3 and about 30.  
     
     
         46 . A compound of the formula  
       
         
           
           
               
               
           
         
       
       wherein R 1 , R 2 , R 3  each independently is selected from the group consisting of hydrogen, C1-C10 alkyl, C2-C10 alkenyl, aryl, benzyl, and C1-C10 alkoxyl; R 4  is selected from the group consisting of C1-C10 alkyl, C2-C10 alkenyl, aryl, and benzyl; and P is selected from the group consisting of hydrogen and [(i-Pr) 2 N]POCH 2 CH 2 CN.  
     
     
         47 . The compound of  claim 46 , wherein P is a hydrogen atom.  
     
     
         48 . The compound of  claim 46 , wherein P is phosphoramidite.  
     
     
         49 . The compound of  claim 46 , wherein the base is selected from the group consisting of adenyl, guanyl, cytidyl, thymidyl, inosyl, and uridyl.  
     
     
         50 . The compound of  claim 49 , wherein the base is inosyl.  
     
     
         51 . The compound of  claim 46 , wherein P is an oligonucleotide.  
     
     
         52 . A compound of the formula  
       
         
           
           
               
               
           
         
       
       where Y is a C-3′ oxygen of a nucleic acid and R 1  is methyl.