Method of preventing modification of synthetic oligonucleotides

Abstract

The present invention relates to a method of preventing modification of a synthetic oligonucleotide or oligonucleotide analog during removal of at least one cyanoethyl protecting group from the oligonucleotide or oligonucleotide analog. The method involves contacting the oligonucleotide or oligonucleotide analog with a basic solution having at least one acrylonitrile scavenger, such as t-butylamine, at a sufficient temperature and for a sufficient period of time to remove at least one β-cyanoethyl protecting group. The present invention also relates to a method of producing a synthetic oligonucleotide or oligonucleotide analog.

1 . A method of substantially preventing modification of a synthetic oligonucleotide or an oligonucleotide analog during cleavage of at least one β-cyanoethyl protecting group from the oligonucleotide or oligonucleotide analog, comprising the step of contacting a β-cyanoethyl protected oligonucleotide or oligonucleotide analog with an organic solution comprising a nitrile solvent and at least one acrylonitrile scavenger under conditions sufficient to remove at least one β-cyanoethyl protecting group, provided that when the acrylonitrile scavenger comprises a primary aliphatic amine or a primary aliphatic thiol, the primary aliphatic amine or the primary aliphatic thiol is sterically hindered.  
   
   
       2 . The method of  claim 1 , further comprising the step of contacting the oligonucleotide or oligonucleotide analog, treated with the organic solution, with an aqueous basic solution having at least one acrylonitrile scavenger, provided that when the acrylonitrile scavenger comprises a primary aliphatic amine or a primary aliphatic thiol, the primary aliphatic amine or the primary aliphatic thiol is sterically hindered.  
   
   
       3 . The method of  claim 1 , wherein the acrylonitrile scavenger is a substituted or unsubstituted, sterically-hindered primary aliphatic amine.  
   
   
       4 . The method of  claim 3 , wherein the substituted or unsubstituted, sterically-hindered primary aliphatic amine is t-butylamine.  
   
   
       5 . The method of  claim 1 , wherein the synthetic oligonucleotide or oligonucleotide analog is attached to a solid support by a covalent bond.  
   
   
       6 . The method of  claim 1 , wherein the nitrile solvent is acetonitrile.  
   
   
       7 . The method of  claim 3 , wherein the nitrile solvent is acetonitrile.  
   
   
       8 . The method of  claim 4 , wherein the nitrile solvent is acetonitrile.  
   
   
       9 . The method of  claim 5 , wherein the nitrile solvent is acetonitrile.  
   
   
       10 . A method of producing an oligonucleotide or oligonucleotide analog, wherein modification of the oligonucleotide or oligonucleotide analog during removal of the β-cyanoethyl protecting group is substantially prevented, comprising the steps of: 
 a) synthesizing an oligonucleotide or oligonucleotide analog having at least one β-cyanoethyl protecting group; and    b) contacting the β-cyanoethyl protected oligonucleotide or oligonucleotide analog with an organic solution comprising a nitrile solvent and at least one acrylonitrile scavenger under conditions sufficient to remove at least one β-cyanoethyl protecting group, provided that when the acrylonitrile scavenger comprises a primary aliphatic amine or a primary aliphatic thiol, the primary aliphatic amine or the primary aliphatic thiol is sterically hindered.    
   
   
       11 . The method of  claim 10 , further comprising the step of contacting the oligonucleotide or oligonucleotide analog, treated with the organic solution, with an aqueous basic solution having at least one acrylonitrile scavenger, provided that when the acrylonitrile scavenger comprises a primary aliphatic amine or a primary aliphatic thiol, the primary aliphatic amine or the primary aliphatic thiol is sterically hindered.  
   
   
       12 . The method of  claim 10 , wherein the synthetic oligonucleotide or oligonucleotide analog is attached to a solid support by a covalent bond.  
   
   
       13 . The method of  claim 12 , wherein the oligonucleotide or oligonucleotide analog is cleaved from the solid support after contact with the organic solution comprising a nitrile solvent and at least one acrylonitrile scavenger.  
   
   
       14 . The method of  claim 10 , wherein the acrylonitrile scavenger is a substituted or unsubstituted sterically hindered primary aliphatic amine.  
   
   
       15 . The method of  claim 14 , wherein the acrylonitrile scavenger is t-butylamine.  
   
   
       16 . A method of producing an oligonucleotide or oligonucleotide analog comprising the steps of: 
 a) synthesizing an oligonucleotide or oligonucleotide analog having at least one β-cyanoethyl protecting group; and    b) contacting the β-cyanoethyl protected oligonucleotide or oligonucleotide analog with a solution comprising acetonitrile and t-butylamine under conditions sufficient to remove at least one β-cyanoethyl protecting group.    
   
   
       17 . The method of  claim 16 , further comprising the step of contacting the oligonucleotide or oligonucleotide analog, treated with the solution comprising acetonitrile and t-butylamine, with an aqueous basic solution having at least one acrylonitrile scavenger, provided that when the acrylonitrile scavenger comprises a primary aliphatic amine or a primary aliphatic thiol, the primary aliphatic amine or the primary aliphatic thiol is sterically hindered.  
   
   
       18 . The method of  claim 17 , wherein the acrylonitrile scavenger is t-butylamine.  
   
   
       19 . The method of  claim 16 , wherein the synthetic oligonucleotide or oligonucleotide analog is attached to a solid support by a covalent bond.  
   
   
       20 . The method of  claim 19 , wherein the oligonucleotide or oligonucleotide analog is cleaved from the solid support after contact with the solution comprising acetonitrile and t-butylamine.