Phosphoramidite building blocks for sugar-conjugated oligonucleotides

1. A compound of Formula I:

wherein:

R 1 is an optionally protected nucleic base selected from 9-adeninyl, 1-cytosinyl, 9-guaninyl, 1-thyminyl, 1-uracilyl, 2-amino-9-adeninyl, N 6 -methyl-9-adeninyl, 7-deaza-9-adeninyl, 7-deaza-8-aza-9-adeninyl, 8-amino-9-adeninyl, 5-methyl-1-cytosinyl, N 4 -ethyl-1-cytosinyl, 7-deaza-9-guaninyl, 7-deaza-8-aza-9-guaninyl, 8-amino-9-guaninyl, 7 deaza-9-xanthinyl, 9-hypoxanthinyl, N 6 -benzoyl-9-adeninyl, N 6 -phenoxyacetyl-9-adeninyl, N 6 -(4-isopropylphenoxy)acetyl-9-adeninyl, N 4 -benzoyl-1-cytosinyl, N 4 -acetyl-1-cytosinyl, N 4 -phenoxyacetyl-1-cytosinyl, N 4 -(4-isopropylphenoxy)acetyl-1-cytosinyl, N 4 -benzoyl-5-methyl-1-cytosinyl, N 4 -acetyl-5-methyl-1-cytosinyl, N 4 -phenoxyacetyl-5-methyl-1-cytosinyl, N 4 -(4-isopropylphenoxy)acetyl-5-methyl-1-cytosinyl, N 2 -isobutyryl-9-guaninyl, N 2 -phenoxyacetyl-9-guaninyl, N 2 -(4-isopropylphenoxy)acetyl-9-guaninyl, and N 2 —(N,N-dimethylformamidino)-9-guaninyl;

one of R 2 and R 2a is a protecting group of the trityl type selected from (4-methoxyphenyl)diphenylmethyl, bis-(4-methoxyphenyl)phenylmethyl, tris-(methoxyphenyl)methyl, 9-phenylxanthen-9-yl, and 9-(p-methoxyphenyl)xanthen-9-yl, and the other is a phosphoramidite moiety:

wherein:

each R 4 and R 5 is, independently, C 1 to C 6 alkyl, or R 4 and R 5 together with the nitrogen atom they are attached to form a cycle, wherein R 4 +R 5 =(CH 2 ) n X(CH 2 ) m ,

wherein:

X is an atom of oxygen or CH 2 group;

each n and m is, independently, an integer from 2 to about 5;

L is a linking moiety —[(CH 2 ) p Y(CH 2 ) q ] r — wherein:

each p, q, and r is, independently, an integer from 1 to 18;

Y is a chemical bond, oxygen atom, sulfur atom, Q 1 , —N(Q 1 )C(═O)N(Q 2 )-, —C(═O)N(Q 1 )-, or —N(Q 1 )C(═O)—, wherein:

each Q 1 and Q 2 is hydrogen atom, a methyl group, an ethyl group, a propyl group, an isopropyl group, an acetyl group, a trifluoroacetyl group, a phenoxyacetyl group, a benzoyl group, or a 9-fluorenylmethyloxycarbonyl group;

R 6 is a substituted monosaccharide residue of Formula II

wherein:

each R 10 is, independently, an acyl protecting group, a trityl-type protecting group, a silyl protecting group, an alkyl group containing from 1 to 18 atoms of carbon, a benzyl group, a 4-methoxybenzyl group, a propargyl group, or one of R 10 is a protected monosaccharide residue of Formula II, and the other R 10 is an acetyl group;

A is a chemical bond or CHOR 10 ,

A is a hydrogen, OR 10 , or N(Q 2a )Q 3 wherein:

each Q 2a and Q 3 is, independently, a hydrogen atom, a methyl group, an ethyl group, a propyl group, an isopropyl group, an acetyl group, a trifluoroacetyl group, a phenoxyacetyl group, a benzoyl group, or a 9-fluorenylmethyloxycarbonyl group;

R 3 is a hydrogen atom, a fluorine atom, a substituted hydroxy group OR 7 , or a substituted amino group NR 8 R 9 wherein:

each R 7 is, independently, a C 1 to C 6 alkyl, 2-alkoxyethyl group, or an N-methylcarboxamidomethyl group; and

each R 8 and R 9 is, independently, a hydrogen atom, a methyl group, an ethyl group, a propyl group, an isopropyl group, an acetyl group, a trifluoroacetyl group, a phenoxyacetyl group, a benzoyl group, or a 9-fluorenylmethyloxycarbonyl group.

2. The compound of claim 1 wherein R 1 is a nucleic base selected from the group consisting of N 6 -benzoyl-9-adeninyl, N 6 -phenoxyacetyl-9-adeninyl, N 6 -(4-isopropylphenoxy)acetyl-9-adeninyl, 9-adeninyl, N 4 -benzoyl-1-cytosinyl, N 4 -acetyl-1-cytosinyl, N 4 -phenoxyacetyl-1-cytosinyl, N 4 -(4-isopropylphenoxy)acetyl-1-cytosinyl, N 4 -benzoyl-5-methyl-1-cytosinyl, N 4 -acetyl-5-methyl-1-cytosinyl, 1-cytosinyl, N 4 -phenoxyacetyl-5-methyl-1-cytosinyl, N 4 -(4-isopropylphenoxy)acetyl-5-methyl-1-cytosinyl, 5-methyl-1-cytosinyl, N 2 -isobutyryl-9-guaninyl, N 2 -phenoxyacetyl-9-guaninyl, N 2 -(4-isopropylphenoxy)acetyl-9-guaninyl, N 2 —(N,N-dimethylformamidino)-9-guaninyl, 9-guaninyl, 1-thyminyl, and 1-uracilyl.

3. The compound of claim 1 wherein R 2 is a 4,4′-dimethoxytrityl group and R 2a is

4. The compound of claim 1 wherein R 2a is a 4,4′-dimethoxytrityl group and R 2 is

5. The compound of claim 1 wherein R 3 is a hydrogen atom.

6. The compound of claim 1 wherein R 3 is OCH 3 .

7. The compound of claim 1 wherein R 3 is a fluorine atom.

8. The compound of claim 1 wherein each R 4 and R 5 is an isopropyl group.

9. The compound of claim 1 wherein L is —(CH 2 ) 3 —.

10. The compound of claim 1 wherein L is —(CH 2 ) 4 —.

11. The compound of claim 1 wherein L is —[(CH 2 ) 2 —O] 2 —.

12. The compound of claim 1 wherein L is —[(CH 2 ) 2 —O] 3 —.

13. The compound of claim 1 wherein L is —[(CH 2 ) 2 —O] 4 —.

14. The compound of claim 1 wherein L is —[(CH 2 ) 2 —O] 5 —.

15. The compound of claim 1 wherein R 6 is a protected β-D-glucopyranosidyl group.

16. The compound of claim 1 wherein R 6 is a protected β-D-galactopyranosidyl group.

17. The compound of claim 1 wherein R 6 is a protected 2-amino-2-deoxy-β-D-glucopyranosidyl group.

18. The compound of claim 17 wherein one of Q 2a and Q 3 is a hydrogen atom, and the other is an acetyl group.

19. The compound of claim 1 wherein R 6 is a protected 2 amino-2-deoxy-3-D-galactopyranosidyl group.

20. The compound of claim 19 wherein one of Q 2a and Q 3 is a hydrogen atom, and the other is an acetyl group.

21. The compound of claim 1 wherein each of R 10 is an acetyl group.

22. The compound of claim 1 wherein each of R 10 is a benzoyl group.

23. The compound of claim 1 wherein each of R 10 is a butyryl group.

24. The compound of claim 1 wherein each of R 10 is an isobutyryl group.

25. The compound of claim 1 wherein each of R 10 is a propionyl group.

26. The compound of claim 1 wherein each of R 10 is a 4-methylbenzoyl group.

27. The compound of claim 1 wherein one of R 10 is a protected monosaccharide residue of Formula II, and the other R 10 is an acetyl group.

28. An oligomeric compound of Formula III:

wherein:

each R 1 is, independently, an optionally protected nucleic base selected from the group consisting of 9-adeninyl, 1-cytosinyl, 9-guaninyl, 1-thyminyl, 1-uracilyl, 2-amino-9-adeninyl, N 6 -methyl-9-adeninyl, 7-deaza-9-adeninyl, 7-deaza-8-aza-9-adeninyl, 8-amino-9-adeninyl, 5-methyl-1-cytosinyl, N 4 -ethyl-1-cytosinyl, 7-deaza-9-guaninyl, 7-deaza-8-aza-9-guaninyl, 8-amino-9-guaninyl, 7-deaza-9-xanthinyl, and 9-hypoxanthinyl;

each R 3 is, independently, a hydrogen atom, a fluorine atom, a substituted hydroxy group OR 7 , or a substituted amino group NR 8 R 9 wherein:

R 7 is a C 1 to C 6 alkyl, a 2-methoxyethyl group, or an N-methylcarboxamidomethyl group;

each R 8 and R 9 is, independently, a hydrogen atom, a methyl group, an ethyl group, a propyl group, an isopropyl group, an acetyl group, a trifluoroacetyl group, a benzoyl group, or a 9-fluorenylmethyloxycarbonyl group;

L is a linking moiety —[(CH 2 ) p Y(CH 2 ) q ] r — wherein:

each p, q, and r is, independently, an integer from 1 to 18;

Y is a chemical bond, an oxygen atom, a sulfur atom, or NR 8 ;

R 6 is a substituted monosaccharide residue of Formula II

wherein:

each R 10 is, independently, an acyl protecting group selected from the group consisting of acetyl, propionyl, butyryl, isobutyryl, pivaloyl, benzoyl, and 4-methylbenzoyl, a trityl-type protecting group selected from the group consisting of (4-methoxyphenyl)diphenylmethyl, bis-(4-methoxyphenyl)phenylmethyl, tris-(methoxyphenyl)methyl, 9-phenylxanthen-9-yl, and 9-(p-methoxyphenyl)xanthen-9-yl, a silyl protecting group selected from the group consisting of triisopropylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, and diphenylmethylsilyl, an alkyl group containing from 1 to 18 atoms of carbon, a benzyl group, a 4-methoxybenzyl group, or a propargyl group or one of R 10 is a protected monosaccharide residue of Formula II, and the other R 10 is an acetyl group;

A is a chemical bond or CHOR 10

Z is a hydrogen atom, OR 10 , or N(R 8 )R 9 ;

each R 11 is, independently, a negative charge compensated by a cation, a phosphate protecting group, or R 6 O-L-;

each R 12 and R 13 is, independently, a hydrogen atom, or a protecting group selected from the group consisting of (4-methoxyphenyl)diphenylmethyl, bis-(4-methoxyphenyl)phenylmethyl, tris-(methoxyphenyl)methyl, 9-phenylxanthen-9-yl, and 9-(p-methoxyphenyl)xanthen-9-yl; or a point of attachment to solid phase material with the proviso that R 12 and R 13 are not both simultaneously a linker connected to a solid support;

each of W 1 , W 2 , and W 3 is, independently, an oxygen atom or a sulfur atom; and

each s and t is, independently, an integer from 0 to 100.