Deprotection of phosphorus in oligonucleotide synthesis

1. A method of using a phosphorus-deprotecting compounds,

wherein the compound is 2-methyl-5-t-butylthiophenol;

the method comprising contacting said phosphorus-deprotecting compound and a protected phosphorus-containing compound of formula II:

wherein Ak is C 1 -C 10 alkyl, G is O or S, and L 1 and L 2 include one or more of: nucleotides linked by phosphate or thiophosphate groups, or oligonucleotide chains,

for a period sufficient to remove Ak from the phosphorus-containing compound, thereby forming a deprotected compound of the formula:

wherein G, has the same meaning as in formula II,

L′ 1 is L 1 optionally having at least one deprotected phosphorus group, and

L′ 2 is L 2 optionally having at least one deprotected phosphorus group.

2. The method of claim 1 , wherein L 1 is of the formula:

wherein each W is a monomeric nucleoside,

each A is H or a phosphorus protecting group,

n is 0 or a positive integer,

each G is 0 or S,

and Y 1 is H, a protecting group, or a linking group to a solid support.

3. The process of claim 2 , wherein each W is of the formula:

wherein Q is O,

B x is a nucleobase,

R 2 is H, OH, protected OH, SH, alkyl, alkenyi, alkynyl, aryl, alkoxy, alkenyloxy, alkynyloxy, aminoalkoxy, alkoxyalkoxy, alkylaminoalkoxy, imidazolylalkoxy, alkenylthio, alkynylthio, alkenylamino, alkynylamino, aryloxy, arylthio, aralkyloxy, aralkylthio, aralkylamino, N-phthalimido, halogen, carboxyl, nitro, nitroso, cyano, trifluoromethyl, trifluoromethoxy, imidazolyl, azido, hydrazino, aminooxy, isocyanato, isothiocyanato, sulfoxide, sulfone, disulfide, silyl, a heterocycle, a carbocycle, a polyamine, a polyamide, a polyalkylene glycol, or a polyether of the formula (O-alkyl) m , where m is 1 to about 10,

and R 4 is H,

or R 2 and R 4 together form 2′-O—(CH 2 ) q -4′ or 2′-(CH 2 ) q -4′, wherein q is 1 or 2, or R 2 and R 4 together form 2′-CH 2 —O—CH 2 -4′; and

r is 0 or 1.

4. The method of claim 3 , wherein Q is O and r is 1.

5. The method of claim 1 , wherein L 2 is of the formula:

wherein each V is a monomeric nucleoside,

m is 0 or a positive integer,

each A is H or a phosphorus protecting group,

each G is O or S, and

Y 2 is H, a protecting group, or a linking group to a solid support.

6. The process of claim 5 , wherein each V has the formula:

wherein Q is O,

B x is a nucleobase,

R 2 is H, OH, SH, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkenyloxy, alkynyloxy, aminoalkoxy, alkoxyalkoxy, alkylaminoalkoxy, imidazolylalkoxy, alkenylthio, alkynylthio, alkenylamino, alkynylamino, aryloxy, arylthio, aralkyloxy, aralkylthio, aralkylamino, N-phthalimido, halogen, carboxyl, nitro, nitroso, cyano, trifluoromethyl, trifluoromethoxy, imidazolyl, azido, hydrazino, aminooxy, isocyanato, isothiocyanato, sulfoxide, sulfone, disulfide, silyl, a heterocycle, a carbocycle, a polyamine, a polyamide, a polyalkylene glycol, or a polyether of the formula (O-alkyl) m , where in is 1 to about 10,

and R 4 is H, or R 2 and R 4 together form 2′-O—(CH 2 ) q -4′ or 2′-(CH 2 ) q -4′,

wherein q is 1 or 2, or R 2 and R 4 together form 2′-CH 2 —O—CH 2 -4′; and t is 0 or 1.

7. The method of claim 1 , wherein L 1 is of the formula:

and L 2 is of the formula:

wherein each W is a monomeric nucleoside moiety

each V is a monomeric nucleoside moiety

n is 0 or a positive integer,

m is 0 or a positive integer,

each G is O or S,

each A is H or a phosphorus protecting group,

Y 1 is H, a protecting group or a linking group, wherein said linking group is conjugated to a solid support, and

Y 2 is H, a protecting group or a linking group, wherein said linking group is conjugated to a solid support, with the proviso that Y 1 and Y 2 may not simultaneously be a linking group to a solid support.

8. The process of claim 7 , wherein:

each W is a monomeric nucleoside of the formula:

each V is a monomeric nucleoside of the formula:

wherein each r and each t is independently 0 or 1,

each Q is O,

B x is a nucleobase,

R 2 is H, OH, protected OH, SH, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkenyloxy, alkynyloxy, aminoalkoxy, alkoxyalkoxy, alkylaminoalkoxy, imidazolylalkoxy, alkenylthio, alkynylthio, alkenylamino, alkynylamino, aryloxy, arylthio, aralkyloxy, aralkylthio, aralkylamino, N-phthalimido, halogen, carboxyl, nitro, nitroso, cyano, trifluoromethyl, trifluoromethoxy, imidazolyl, azido, hydrazino, aminooxy, isocyanato, isothiocyanato, sulfoxide, sulfone, disulfide, silyl, a heterocycle, a carbocycle, a polyamine, a polyamide, a polyalkylene glycol, or a polyether of the formula (O-alkyl) m , where m is 1 to about 10,

and R 4 is H,

or R 2 and R 4 together form 2′-O—(CH 2 ) q -4′ or 2′-(CH 2 ) q -4′, wherein q is 1 or 2, or R 2 and R 4 together form 2′-CH 2 —O—CH 2 -4′;

each r is 0 or 1; and

each t is 0 or 1.

9. The process of claim 8 , wherein each Q is O, each r is 1, each t is 1, and each R 2 is H, OH, protected OH, OCH 3 , or OCH 2 CH 2 OCH 3 .

10. The process of claim 9 , wherein the sum of m and n is 0 to 60.

11. The process of claim 10 , wherein the sum of m and n is 4 to 30.

12. The process of claim 11 , wherein the sum of m and n is 4 to 20.

13. The process of claim 1 , wherein L′ 1 has the formula:

wherein each W is a monomeric nucleoside,

each A′ is H or a phosphorus protecting group,

n is 0 or a positive integer,

each G is O or S, and

Y 1 is H, a protecting group, or a linking group to a solid support; and

L′ 2 has the formula:

wherein each V is a monomeric nucleoside,

in is 0 or a positive integer,

each A′ is H or a phosphorus protecting group,

each G is 0 or S,

Y 2 is H, a protecting group, or a linking group to a solid support, except that Y 1 and

Y 2 cannot both be linking groups to a solid support.

14. The process of claim 13 , wherein the sum of n and m is 0 to 60.

15. The process of claim 14 , wherein, when the sum of n and m is 2 or greater, at least about 50% of the moieties A′ are H.

16. The process of claim 13 , wherein n is 0 or 1 and m is 0 or 1 and the sum of n and m is 0 or 1.

17. The process of claim 16 , wherein each A′ is H.

18. The process of claim 13 , wherein the sum of n and m is 4 to 30.

19. The process of claim 18 , wherein at least about 75% of the moieties A′ are H.

20. The process of claim 13 , wherein the sum of n and m is 10 to 30.

21. The process of claim 20 , wherein at least about 90% of the moieties A′ are H.

22. The process according to claim 13 , wherein Y 1 is a 4,4′-dimethoxytriphenylmethyl (DMT) group.

23. The process according to claim 13 , wherein Y 2 is H or is conjugated to a solid support.

24. The process according to claim 13 , wherein each W is:

wherein Q is O,

B x is a nucleobase,

R 2 is H, OH, protected OH, SH, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkenyloxy, alkynyloxy, aminoalkoxy, alkoxyalkoxy, alkylaminoalkoxy, imidazolylalkoxy, alkenylthio, alkynylthio, alkenylamino, alkynylamino, aryloxy, arylthio, aralkyloxy, aralkylthio, aralkylamino, N-phthalimido, halogen, carboxyl, nitro, nitroso, cyano, trifluoromethyl, trifluoromethoxy, imidazolyl, azido, hydrazino, aminooxy, isocyanato, isothiocyanato, sulfoxide, sulfone, disulfide, silyl, a heterocycle, a carbocycle, a polyamine, a polyamide, a polyalkylene glycol, or a polyether of the formula (O-alkyl) m , where m is 1 to about 10,

and R 4 is H,

or R 2 and R 4 together form 2′-O—(CH 2 ) q -4′ or 2′-(CH 2 ) q -4′, wherein q is 1 or 2, or R 2 and R 4 together form 2′-CH 2 —O—CH 2 -4′; and

r is 0 or 1, and each V is:

wherein Q is O,

B x is a nucleobase,

R 2 is H, OH, protected OH, SH, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkenyloxy, alkynyloxy, aminoalkoxy, alkoxyalkoxy, alkylaminoalkoxy, imidazolylalkoxy, alkenylthio, alkynylthio, alkenylamino, alkynylamino, aryloxy, arylthio, aralkyloxy, aralkylthio, aralkylamino, N-phthalimido, halogen, nitro, nitroso, cyano, trifluoromethyl, trifluoromethoxy, imidazolyl, azido, hydrazino, aminooxy, isocyanato, isothiocyanato, sulfoxide, sulfone, disulfide, silyl, a heterocycle, a carbocycle, a polyamine, a polyamide, a polyalkylene glycol, or a polyether of the formula (O-alkyl) m , where m is 1 to about 10,

and R 4 is H,

or R 2 and R 4 together form 2′-O—(CH 2 ) q -4′ or 2′-(CH 2 ) q -4′, wherein q is 1 or 2, or R 2 and R 4 together form 2′-CH 2 —O—CH 2 -4′; and

t is 0 or 1.

25. The process of claim 24 , wherein each Q is O, each r is 1, each r is 1, and each R 2 is independently H, OH, OCH 3 or OCH 2 CH 2 OCH 3 .

26. A process of making a compound of the formula:

wherein each X is independently a nucleoside monomer,

G is O or S,

Y 1 is H, a protecting group or a linking group conjugated to a solid support;

Y 2 is H, a protecting group or a linking group conjugated to a solid support, except that Y 1 and Y 2 cannot be simultaneously a linking group conjugated to a solid support;

p is a positive integer;

the process comprising contacting a phosphorus-protected compound of the formula:

wherein A is a phosphorus protecting group,

with a phosphorus-deprotection non-malodorous thiol compound selected from 2-methyl-5-t-butylthiophenol for a time sufficient to remove said phosphorus protecting group.

27. The process according to claim 26 , wherein each X independently has the formula:

wherein each B x is a nucleobase;

each r is independently 0 or 1;

each Q is independently O;

R 2 is H, OH, SH, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkenyloxy, alkynyloxy, aminoalkoxy, alkoxyalkoxy, alkylaminoalkoxy, imidazolylalkoxy, alkenylthio, alkynylthio, alkenylamino, alkynylamino, aryloxy, arylthio, aralkyloxy, aralkylthio, aralkylamino, N-phthalimido, halogen, carboxyl, nitro, nitroso, cyano, trifluoromethyl, trifluoromethoxy, imidazolyl, azido, hydrazino, aminooxy, isocyanato, isothiocyanato, sulfoxide, sulfone, disulfide, silyl, a heterocycle, a carbocycle, a polyamine, a polyamide, a polyalkylene glycol, or a polyether of the formula (O-alkyl) m , where m is 1 to about 10,

and R 4 is H, or R 2 and R 4 together from —(CH 2 ) q —, wherein q is 1 or 2.

28. The process of claim 27 , wherein each Q is O and each r is 1.

29. The process of claim 27 , wherein each R 2 is independently H, OH, protected OH, protected OH, OCH 3 or OCH 2 CH 2 OCH 3 .

30. The process of claim 27 , wherein each A is independently C 1 -C 10 alkyl.

31. The process of claim 20 , wherein each A is methyl.

32. The process of claim 26 , wherein p is an integer in the range of 1 to 60.

33. The process of claim 30 , wherein p is 2.

34. The process of claim 26 , wherein p is an integer in the range of about 10 to about 25.

35. The process of claim 34 , wherein each Q is O, each r is 1, each R 2 is independently H, OH, protected OH, OCH 3 or OCH 2 CH 2 OCH 3 .

36. A process of deprotecting a phosphorus-protected oligonucleotide, the process comprising contacting said phosphorus-protected oligonucleotide with a non-malodorous deprotecting agent for a time sufficient to remove the phosphorus protecting group, said phosphorus protecting group being alkyl, wherein said non-malodorous deprotecting agent is 2-methyl-5-t-butylthiophenol.

37. The process of claim 36 , wherein the phosphorus protecting group is unsubstituted C 1 -C 10 alkyl.

38. The process of claim 37 , wherein the phosphorus protecting group is methyl.

39. The method of claim 2 , wherein said monomeric nucleoside includes at least one of a ribonucleoside, a 2′-deoxynucleoside, a 2′-modified nucleoside, a locked nucleoside, a sugar-modified nucleoside, a base-modified nucleoside, an erythro-nucleoside, or an arabino-nucleoside.

40. The method of claim 3 , wherein R 5 further comprises at least one of a halo, nitro, nitroso, OH, SH, CN, phenyl, phenoxy, benzyloxy, heteroaryl, partially saturated heterocyclyl, fully saturated heterocyclyl, or silyl group.

41. The method of claim 5 , wherein said monomeric nucleoside includes at least one of a ribonucleoside, a 2′-deoxynucleoside, a 2′-modified nucleoside, a locked nucleoside, a sugar-modified nucleoside, a base-modified nucleoside, an erythro-nucleoside, or an arabino-nucleoside.

42. The method of claim 7 , wherein said W and V monomeric nucleosides each optionally include at least one of a ribonucleoside, a 2′-deoxynucleoside, a 2′-modified nucleoside, a locked nucleoside, a sugar-modified nucleoside, a base-modified nucleoside, an erythro-nucleoside, or an arabino-nucleoside.

43. The method of claim 13 , wherein said W and V monomeric nucleosides each optionally include at least one of a ribonucleoside, a 2′-deoxynucleoside, a 2′-modified nucleoside, a locked nucleoside, a sugar-modified nucleoside, a base-modified nucleoside, an erythro-nucleoside, or an arabino-nucleoside.

44. The method of claim 36 , wherein the alkyl phosphorus protecting group further comprises at least one of a halo, nitro, nitroso, OH, SH, CN, phenyl, phenoxy, benzyloxy, heteroaryl, partially saturated heterocyclyl, fully saturated heterocyclyl, or silyl group.