Oligonucleotide synthesis with alternative solvents

1. A method of manufacturing an oligonucleotide comprising a pentavalent phosphate triester, said method comprising:

(a) providing a 5′ blocked-nucleoside;

(b) deblocking the 5′ blocked-nucleoside to form a 5′ OH-nucleoside;

(c) coupling the 5′ OH-nucleoside with a phosphoramidite of formula (IV)

wherein Y is 0, S, CH 2 , CHF, CF 2 or —CH═CH—;

bg is a 5′-blocking group;

R′ 2 is H, OZ, a 2′-substituent, or together with R′ 4 forms a bridge; R′ 4 is H, OZ, a 2′-substituent, or together with R′ 2 forma a bridge; Z is H or a removable protecting group;

Bx is a nucleobase;

pg is a phosphorus protecting group; each G is 0 or S;

L is an amine leaving group;

G 1 is 0 or S; and

q′ is 0 or 1;

to form an oligonucleotide comprising a trivalent phosphite triester; and

(d) oxidizing the oligonucleotide comprising a trivalent phosphite triester to form the oligonucleotide comprising a pentavalent phosphate triester;

wherein at least a wash between any of the steps above is with a solvent wash comprising a toluene, pyridine, lutidine, hexane, cyclohexane, cyclohexene, a halogenated benzene, alkylated benzenes, a haloalkylbenzene, acetone, ethylacetate, methanol, ethanol, phenol, cyclic ethers, acyclic ethers, halogenated alkanes or mixtures thereof.

2. The method of claim 1 , wherein a wash between any of the steps above is with at least one solvent wash comprising a toluene.

3. The method of claim 1 , wherein the 5′ blocked-nucleoside is linked to another nucleoside.

4. The method of claim 1 , wherein the 5′ blocked-nucleoside is linked to a solid support.

5. The method of claim 1 wherein the 5′ blocked-nucleoside comprises a sugar moiety and a base.

6. The method of claim 1 , wherein the solvent wash comprises a toluene and an acetonitrile.

7. The method of claim 1 , wherein the solvent wash is substantially free of an acetonitrile.

8. A method of manufacturing a compound of Formula I:

wherein Y is O, S, CH 2 , CHF, CF 2 or —CH═CH—;

bg is a 5′-blocking group;

n is a positive integer;

each R′ 2 is, independently, H, OZ, a 2′-substituent, or together with R′ 4 forms a bridge; each R′ 4 is, independently, H, OZ, a 2′-substituent, or together with R′ 4 forms a bridge; each R′ 4 is, protecting group;

each Bx is independently a nucleobase;

each pg is independently a phosphorus protecting group; each G is 0 or S;

each G, is 0 or S;

each q′ is independently 0 or 1; and

SS is a solid support; said process comprising:

(a) contacting a compound of Formula II:

with a deblocking agent to produce a compound of Formula III:

(b) contacting the compound of Formula III with a first solvent wash;

(c) contacting the compound of Formula III with a compound of Formula IV:

wherein L is a leaving group, to form a compound of Formula V:

(d) contacting the compound of Formula V with a second solvent wash; and

(e) contacting the compound of Formula V with an oxidation reagent to form the compound of Formula I;

wherein at least one of the first and second solvent wash comprises a toluene, pyridine, lutidine, hexane, cyclohexane, cyclohexene, a halogenated benzene, alkylated benzenes, a haloalkylbenzene, acetone, ethylacetate, methanol, ethanol, phenol, cyclic ethers, acyclic ethers, halogenated alkanes or mixtures thereof.

9. The method of claim 8 , wherein the first solvent wash comprises the toluene.

10. The method of claim 8 , wherein the first solvent wash comprises the toluene and an acetonitrile.

11. The method of claim 8 , wherein the first solvent wash is substantially free of an acetonitrile.

12. The process according to claim 8 , wherein the second solvent wash comprises a toluene.

13. The method of claim 8 , wherein the second solvent wash comprises the toluene and an acetonitrile.

14. The method of claim 8 , wherein the second solvent wash is substantially free of an acetonitrile.

15. The method of claim 8 , after (e), further comprising:

(f) contacting the compound of Formula I with a third solvent wash.

16. The method of claim 15 , after (f), further comprising:

(g) capping any compound of Formula III that has not reacted with the compound of Formula IV.

17. The method of claim 15 , wherein the third solvent wash comprises at least one of a toluene, an acetonitrile, or mixture thereof.

18. The method of claim 15 , wherein the third solvent wash is substantially free of an acetonitrile.

19. The method of claim 8 , after (e), further comprising capping any compound of Formula IV that has not reacted with the compound of Formula IV.

20. The process according to claim 8 , wherein each Y is 0.

21. The process of claim 8 , wherein n is about 7 to about 79.

22. The process of claim 8 , wherein each R′ 2 is H or a 2′-substituent.

23. The process of claim 8 , wherein each R′ 2 is H or a 2′-substituent, said 2′-substituent being a member of the group consisting of 2′-O—CH 3 , 2′-O—CH 2 CH 2 OCH 3 , or 2′-O—(CH 2 ) 3 NH 2 .

24. The process of claim 8 , wherein said 2′-substituent is 2′-OCH 2 CH 2 OCH 3 .

25. The process of claim 8 , wherein each q′ is 1.

26. The process of claim 8 , wherein each G is S.

27. A process of claim 8 , further comprising cleaving the compound of Formula I from the solid support to form a compound of Formula X:

wherein the variables have the same definitions as in claim 8 .