Process for the synthesis of oligomeric compounds

Abstract

Synthetic processes are provided wherein oligomeric compounds are prepared having phosphodiester, phosphorothioate, phosphorodithioate, or other covalent linkages. The oligomers have substantially reduced exocyclic adducts deriving from acrylonitrile or related contaminants.

1 - 112 . (canceled)  
     
     
         113 . A method of preparing a phosphorus-linked oilgonucleotide comprising: 
 providing a sample containing a plurality of oligonucleotides, said oligonucleotides linked to a solid support medium, said oligonucleotides comprising a plurality of nucleosides and a plurality of protected phosphorus linkages;    contacting said oligonucleotides with a deprotecting agent to remove phosphorus protecting groups from said oligonucleotides, wherein said oligonucleotides remain linked to said solid support medium during said contacting;    said deprotecting reagent comprising at least one secondary amine, the conjugate acid of said tertiary amine having a pKa of from about 8 to about 11;    optionally washing said oligonucleotides; and    reacting said oligonucleotides with a cleaving reagent, whereby the oligonucleotides are cleaved from the solid support medium.    
     
     
         114 . The method of  claim 113 , wherein the tertiary amine is an aliphatic amine.  
     
     
         115 . The method of  claim 114 , wherein the aliphatic amine is (R) 3 N, where R is alkyl.  
     
     
         116 . The method of  claim 115 , wherein R is ethyl.  
     
     
         117 . The method of  claim 113 , wherein at least one of the phosphorus protecting groups is a cyanoethyl protecting group.  
     
     
         118 . The method of  claim 113 , wherein at least one of said nucleotides further comprising a 2′-substituent group selected from fluoro, O-alkyl, O-alkylamino, O-alkylalkoxy, protected O-alkylamino, O-alkylaminoalkyl, O-alkyl imidazole, or polyethers of the formula (O-alkyl) m , where m is 1 to about 10.  
     
     
         119 . The method of  claim 118 , wherein the 2′substituent group is O-alkyl or fluoro.  
     
     
         120 . The method of  claim 113 , wherein at least one of the protected phosphorus linkage is a protected phosphorothioate linkage.  
     
     
         121 . An oligonucleotide produced by the method of  claim 120 .  
     
     
         122 . The oligonucleotide of  claim 121 , comprising less than 1% acrylonitrile adduct.  
     
     
         123 . The oligonucleotide of  claim 121 , comprising less than 0.5% acrylonitrile adduct.  
     
     
         124 . The oligonucleotide of  claim 121 , comprising less than 0.1% acrylonitrile adduct.  
     
     
         125 . A method for deprotecting a phosphorus-linked oligonucleotide comprising a plurality of nucleosides and a plurality of protected phosphorus linkages of Formula II:  
       
         
           
           
               
               
           
         
         wherein:  
         each X is O or S;  
         Rt is a phosphorus protecting group of formula:  
           —C(R 10 ) 2 —C(R 10 ) 2 —W or —C(R 10 ) 2 —(CH═CH) p —C(R 10 ) 2 —W  
         each R 10  is independently H or lower alkyl;  
         W is electron withdrawing group;  
         p is 1 to 3;  
         said oligonucleotides being linked to a solid support medium, the method comprising:  
         providing a plurality of said phosphorus-linked oligonucleotides;  
         contacting said oligonucleotides with a deprotecting reagent for a time and under conditions sufficient to remove said R t  groups from said oligonucleotides, wherein said oligonucleotides remain linked to said solid support medium during said contacting;  
         said deprotecting reagent comprising at least one secondary amine, the conjugate acid of said tertiary amine having a pKa of from about 8 to about 11;  
         optionally washing said oligonucleotides; and  
         reacting said oligonucleotides with a cleaving reagent, whereby the oligonucleotides are cleaved from the solid support medium.  
       
     
     
         126 . The method of  claim 125 , wherein R t , is —CH 2 CH 2 —CN.  
     
     
         127 . The method of  claim 125 , wherein the tertiary amine is an aliphatic amine.  
     
     
         128 . The method of  claim 127 , wherein the aliphatic amine is (R) 3 N, where R is alkyl.  
     
     
         129 . The method of  claim 125 , wherein at least one of the phosphorus protecting groups is a cyanoethyl protecting group.  
     
     
         130 . The method of  claim 125 , wherein at least one of the nucleotides further comprising a 2′-substituent group selected from fluoro, O-alkyl, O-alkylamino, O-alkylalkoxy, protected O-alkylamino, O-alkylaminoalkyl, O-alkyl imidazole, or polyethers of the formula (O-alkyl) m , where m is 1 to about 10.  
     
     
         131 . The method of  claim 130 , wherein the 2′-substituent group is O-alkyl or fluoro.  
     
     
         132 . The method of  claim 125 , wherein at least one of the protected phosphorus linkage is a protected phosphorothioate linkage.  
     
     
         133 . An oligonucleotide produced by the method of  claim 132 .  
     
     
         134 . An oligonucleotide of  claim 133 , comprising less than 1% acrylonitrile adduct.  
     
     
         135 . An oligonucleotide of  claim 133 , comprising less than 0.5% acrylonitrile adduct.  
     
     
         136 . An oligonucleotide of  claim 133 , comprising less than 0.1% acrylonitrile adduct.