Process for the synthesis of oligomeric compounds

1. A method of preparing a sample of a phosphate linked oligonucleotide having a substantially reduced content of acrylonitrile adduct

comprising:

providing a sample containing a plurality of oligonucleotides, said oligonucleotides linked to a solid support medium, said oligonucleotides having a plurality of protected phosphorus linkages wherein at least one protected phosphorus linkage is a protected phosphorothioate linkage;

contacting said oligonucleotides with a deprotecting agent to remove phosphorus protecting groups from said oligomers, wherein oligonucleotides remain linked to said solid support medium during said contacting;

said deprotecting reagent comprising at least one amine, the conjugate acid of said amine having a pKa of from about 8 to about 11; said deprotecting reagent optionally further comprising one or more solvents selected from the group consisting of alkyl solvents, haloalkyl solvents, cyanoalkyl solvents, aryl solvents and aralkyl solvents;

optionally washing said oligonucleotides; and

reacting said oligonucleotides with a cleaving reagent.

2. The method of claim 1 , wherein the amine is an aliphatic amine.

3. A method of preparing a sample of a phosphate linked oligonucleotide having a reduced content of acrylonitrile adduct comprising:

providing a sample containing a plurality of solid support-linked oligonucleotides, said oligonucleotides having a plurality of protected phosphorus linkages wherein at least one protected phosphorus linkage is a protected phosphorothioate-linkage;

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;

washing said oligonucleotides with a washing reagent, said washing reagent comprising at least one amine, the conjugate acid of said amine having a pKa of from about 8 to about 11;

said deprotecting reagent comprising at least one amine, the conjugate acid of said amine having a pKa of from about 8 to about 11 and optionally further comprising one or more solvents selected from the group consisting of alkyl solvents, haloalkyl solvents, cyanoalkyl solvents, aryl solvents and aralkyl solvents; and

reacting said oligonucleotides with a cleaving reagent.

4. The method of claim 3 , wherein the amine is an aliphatic amine.

5. A method for deprotecting a phosphate-linked oligonucleotides, said oligonucleotides having a plurality of protected phosphorus linkages of Formula II:

wherein:

each X is O or S;

R t 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 an electron withdrawing group;

p is 1 to 3;

said oligonucleotides being linked to a solid support medium and wherein at least one protected phosphorus linkage is a phosphorothioate linkage, the method comprising:

providing a sample containing a plurality of said phosphate-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;

washing said deprotected oligonucleotides with a washing reagent comprising at least one amine, the conjugate acid of said amine having a pKa of from about 8 to about 11;

said deprotecting reagent comprising at least one amine, the conjugate acid of said amine having a pKa of from about 8 to about 11 and optionally further comprising one or more solvents selected from the group consisting of alkyl solvents, haloalkyl solvents, cyanoalkyl solvents, aryl solvents and aralkyl solvents; and

reacting said oligonucleotides with a cleaving reagent, whereby the oligonucleotides are cleaved from the solid support medium with the proviso that at least one R t is —CH 2 —CH 2 —CN.

6. The method of claim 5 , wherein R t is —CH 2 CH 2 —CN.

7. A method for deprotecting a phosphate-linked oligonucleotides, said oligonucleotides having a plurality of protected phosphorus linkages of Formula II:

wherein:

Each X is O or S;

R t 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 an electron withdrawing group;

p is 1 to 3;

said oligonucleotides being linked to a solid support medium, the method comprising:

providing a sample containing a plurality of said phosphate-linked oligonucleotides, said phosphate-linked oligonucleotides linked to a solid support medium, said phosphate-linked oligonucleotides having a plurality of protected phosphorus linkages wherein at least one of the pretected phosphorus linkages is a protected phosphorothioate linkage;

contacting said phosphate-linked oligonucleotides with a deprotecting agent to remove phosphorus protecting groups from said phosphate-linked oligonucleotides, wherein said oligonucleotides remain linked to said solid support medium during said contacting;

said deprotecting reagent comprising at least one amine, the conjugate acid of said amine having a pKa of from about 8 to about 11;

said deprotecting reagent optionally further comprising one or more solvents selected from the group consisting of alkyl solvents, haloalkyl solvents, cyanoalkyl solvents, aryl solvents and aralkyl solvents;

optionally washing said phosphate-linked oligonucleotides; and

reacting said phosphate-linked oligonucleotides with a cleaving reagent with the proviso that at least one R t is —CH 2 —CH 2 —CN.

8. The method of claim 7 , wherein the amine is an aliphatic amine.

9. The method of claim 8 , wherein the aliphatic amine is selected from (R) 3 N, (R) 2 NH, or RNH 2, where R is alkyl.

10. The method of claim 8 , wherein the aliphatic amine is triethylamine.

11. The method of claim 7 , wherein R t is —CH 2 —CH 2 —CN.

12. The method of claim 2 , wherein the aliphatic amine is selected from (R) 3 N, (R) 2 NH, or RNH 2, where R is alkyl.

13. The method of claim 4 , wherein the aliphatic amine is selected from (R) 3 N, (R) 2 NH, or RNH 2, R is alkyl.

14. The method of claim 13 , wherein the aliphatic amine is triethylamine.

15. The method of claim 5 , wherein the amine is an aliphatic amine.

16. The method of claim 15 , wherein the aliphatic amine is selected from (R) 3 N, (R) 2 NH, or RNH 2, where R is alkyl.

17. The method of claim 16 , wherein the aliphatic amine is triethylamine.