Phosphorodiamidate backbone linkage for oligonucleotides

1. A compound of formula (I):

wherein

R 1 is hydrogen, an amino protecting group, or an oligonucleotide;

R 2 is hydrogen, a hydroxyl protecting group, solid support, or an oligonucleotide;

each R 3 is independently selected from hydrogen, hydroxyl, and —O—R 3a ;

wherein each R 3a is C 1-6 alkyl or C 1-6 alkyl substituted with —NR 3b R 3c , imidazolyl, —(CH 2 ) a O(CH 2 ) b NR 3b R 3c , or —(CH 2 ) a ONR 3d (CH 2 ) b NR 3b R 3c ;

wherein each R 3b is hydrogen or C 1-2 alkyl;

each R 3c is hydrogen or C 1-2 alkyl;

each R 3d is hydrogen or C 1-2 alkyl;

each a is an integer selected from one to 4;

each b is an integer selected from one to 4;

each R 4 is independently C 1-6 alkyl or C 1-6 alkyl substituted with —NR 4a R 4b ;

wherein R 4a is hydrogen or C 1-2 alkyl and R 4b is hydrogen or C 1-2 alkyl;

each R 5 is independently C 1-6 alkyl or C 1-6 alkyl substituted with —NR 5a R 5b ;

wherein R 5a is hydrogen or C 1-2 alkyl and R 5b is hydrogen or C 1-2 alkyl; or

R 4 and R 5 taken together with the nitrogen to which they are attached form a monocyclic heterocyclyl or a monocyclic heterocyclyl substituted with C 1-6 alkyl, sperminyl, or spermidinyl;

each W is independently selected from O, S, and Se;

each B 1 is independently selected from a heterocyclic base moiety or a protected heterocyclic base moiety; and

n is an integer selected from one to 50;

or a salt thereof.

2. The compound of claim 1 , or a salt thereof, wherein each W is O.

3. The compound of claim 1 , or a salt thereof, wherein each B 1 is independently selected from purinyl and pyrimidinyl.

4. The compound of claim 1 , or a salt thereof, wherein each B 1 is independently selected from 4-benzoyl-1-cytosinyl, 6-benzoyl-9-adeninyl, 6-dimethylformamidino-9-adeninyl, 2-isobutyryl-9-guaninyl, 2-dimethylformamidino-9-guaninyl, 9-adeninyl, 9-guaninyl, 1-cytosinyl, 1-thyminyl and 1-uracilyl.

5. The compound of claim 1 , or a salt thereof, wherein n is an integer from 2 to 30.

6. A compound of claim 1 , wherein the compound comprises a sequence which includes a region that is complementary to any portion of a sequence of a telomerase RNA (SEQ ID NO:1).

7. The compound of claim 1 , or a salt thereof, wherein n is an integer from 6 to 30.

8. A pharmaceutical composition comprising a compound of claim 1 , or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.

9. A kit comprising a compound of claim 1 , or a salt thereof.

10. A compound of formula (III)

wherein

R 1 is hydrogen or an amino protecting group;

R 2 is hydrogen, a hydroxyl protecting group, or solid support;

each R 3 is independently selected from hydrogen, hydroxyl, and —O—R 3a ;

wherein each R 3a is C 1-6 alkyl or C 1-6 alkyl substituted with —NR 3b R 3c , imidazolyl, —(CH 2 ) a O(CH 2 ) b NR 3b R 3c , or —(CH 2 ) a ONR 3d (CH 2 ) b NR 3b R 3c ;

wherein each R 3b is hydrogen or C 1-2 alkyl;

each R 3c is hydrogen or C 1-2 alkyl;

each R 3d is hydrogen or C 1-2 alkyl;

each a is an integer selected from one to 4;

each b is an integer selected from one to 4;

each R 4 is C 1-6 alkyl or C 1-6 alkyl substituted with —NR 4a R 4b ;

wherein R 4a is hydrogen or C 1-2 alkyl and R 4b is hydrogen or C 1-2 alkyl;

each R 5 is C 1-6 alkyl or C 1-6 alkyl substituted with —NR 5a R 5b ;

wherein R 5a is hydrogen or C 1-2 alkyl and R 5b is hydrogen or C 1-2 alkyl; or

R 4 and R 5 taken together with the nitrogen to which they are attached form a monocyclic heterocyclyl or a monocyclic heterocyclyl substituted with C 1-6 alkyl, sperminyl or spermidinyl;

each W is independently selected from O, S, and Se; and

each B 1 is independently selected from a heterocyclic base moiety and a protected heterocyclic base moiety;

or a salt thereof.

11. The compound of claim 10 , or a salt thereof, wherein W is O.

12. The compound of claim 10 , or a salt thereof, wherein each B 1 is independently selected from purinyl and pyrimidinyl.

13. The compound of claim 10 , or a salt thereof, wherein each B 1 is independently selected from 4-benzoyl-1-cytosinyl, 6-benzoyl-9-adeninyl, 6-dimethylformamidino-9-adeninyl, 2-isobutyryl-9-guaninyl, 2-dimethylformamidino-9-guaninyl, 9-adeninyl, 9-guaninyl, 1-cytosinyl, 1-thyminyl and 1-uracilyl.

14. The compound of claim 10 , or a salt thereof, wherein R 2 is a hydroxyl protecting group or a solid support.

15. The compound of claim 10 , or a salt thereof, wherein the compound is selected from:

16. An oligonucleotide, wherein the nucleoside subunits of the oligonucleotide are joined by intersubunit linkages,

wherein at least one of the intersubunit linkages is a phosphorothioate or phosphate diester linkage, and

wherein the oligonucleotide has formula (I)

wherein

R 1 is selected from hydrogen and an oligonucleotide;

R 2 is selected from hydrogen and an oligonucleotide;

each R 3 is independently selected from hydrogen, hydroxyl, and —O—R 3a ;

wherein each R 3a is C 1-6 alkyl or C 1-6 alkyl substituted with —NR 3b R 3c , imidazolyl, —(CH 2 ) a O(CH 2 ) b NR 3b R 3c , or —(CH 2 ) a ONR 3d (CH 2 ) b NR 3b R 3c ;

wherein each R 3b is hydrogen or C 1-2 alkyl;

each R 3c is hydrogen or C 1-2 alkyl;

each R 3d is hydrogen or C 1-2 alkyl;

each a is an integer selected from one to 4;

each b is an integer selected from one to 4;

each R 4 is independently C 1-6 alkyl or C 1-6 alkyl substituted with —NR 4a R 4b ;

wherein R 4a is hydrogen or C 1-2 alkyl and R 4b is hydrogen or C 1-2 alkyl;

each R 5 is independently C 1-6 alkyl or C 1-6 alkyl substituted with —NR 5a R 5b ;

wherein R 5a is hydrogen or C 1-2 alkyl and R 5b is hydrogen or C 1-2 alkyl; or

R 4 and R 5 taken together with the nitrogen to which they are attached form a monocyclic heterocyclyl or a monocyclic heterocyclyl substituted with C 1-6 alkyl, sperminyl or spermidinyl;

each W is independently selected from O, S, and Se;

each B 1 is independently selected from a heterocyclic base moiety or a protected heterocyclic base moiety; and

n is an integer selected from one to 25;

or a salt thereof.

17. The oligonucleotide of claim 16 , or a salt thereof, wherein:

R 1 is H; and

R 2 is an oligonucleotide which comprises a central region comprising intersubunit linkages independently selected from phosphorothioate and phosphate diester linkages joined to a terminal 5′-flanking region having the formula:

wherein each n is independently an integer selected from one to 25.

18. The oligonucleotide of claim 16 , or a salt thereof, wherein:

R 1 is an oligonucleotide comprising intersubunit linkages independently selected from phosphorothioate and phosphate esters; and

R 2 is an oligonucleotide comprising intersubunit linkages independently selected from phosphorothioate and phosphate esters.

19. The oligonucleotide of claim 16 , or a salt thereof, wherein the oligonucleotide prevents translation of the mRNA by steric hindrance.

20. The oligonucleotide of claim 16 , or a salt thereof, wherein the oligonucleotide is a substrate for RNase-H-mediated degradation of the mRNA from a gene.

21. An oligonucleotide of claim 16 , wherein the oligonucleotide comprises a sequence which includes a region that is complementary to any portion of a sequence of a telomerase RNA (SEQ ID NO:1).

22. A pharmaceutical composition comprising an oligonucleotide of claim 16 , or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable carrier.

23. A kit comprising an oligonucleotide of claim 16 , or a salt thereof.

24. A method of preparing a compound of formula (I):

wherein

R 1 is hydrogen or an amino protecting group;

R 2 is hydrogen or a hydroxyl protecting group;

each R 3 is independently selected from hydrogen, hydroxyl, and —O—R 3a ;

wherein each R 3a is C 1-6 alkyl or a C 1-6 alkyl substituted with —NR 3b R 3c , imidazolyl, —(CH 2 ) a O(CH 2 ) b NR 3b R 3c , or —(CH 2 ) a ONR 3d (CH 2 ) b NR 3b R 3c ;

wherein each R 3b is hydrogen or C 1-2 alkyl;

each R 3c is hydrogen or C 1-2 alkyl;

each R 3d is hydrogen or C 1-2 alkyl;

each a is an integer selected from one to 4;

each b is an integer selected from one to 4;

each W is independently selected from O, S, and Se;

each B 1 is independently selected from a heterocyclic base moiety and a protected heterocyclic base moiety;

each R 4 is independently C 1-6 alkyl or a C 1-6 alkyl substituted with —NR 4a R 4b ;

wherein R 4a is hydrogen or C 1-2 alkyl and R 4b is hydrogen or C 1-2 alkyl;

each R 5 is independently C 1-6 alkyl or a C 1-6 alkyl substituted with —NR 5a R 5b ;

wherein R 5a is hydrogen or C 1-2 alkyl and R 5b is hydrogen or C 1-2 alkyl; or

R 4 and R 5 taken together with the nitrogen to which they are attached form a monocyclic heterocyclyl or a monocyclic heterocyclyl substituted with C 1-6 alkyl, sperminyl, or spermidinyl; and

n is an integer selected from one to 50;

or a salt thereof;

wherein the method comprises:

a) contacting a compound of formula (II)

with a compound of formula (B):