Synthesis of modified oligonucleotides with increased stability

1. A modified oligonucleotide comprising a 5′ end, a 3′ end and at least one modified intersubunit linkage of Formula I:

wherein:

B is a base pairing moiety;

W is O or O(CH 2 ) n , wherein n is 1 to 10;

X is selected from the group consisting of H, OH, OR, F, SH, SR, NR 2 2 and C 1-6 -alkoxy;

Y is selected from the group consisting of O − , OH, OR, OR 2 , NH − , NH 2 , NR 2 2 , BH 3 , S − , R 1 , and SH;

Z is O(CH 2 ) n , wherein n is 1 to 10 and the oxygen from the O(CH 2 ) n is bonded to the phosphorus from the Formula I;

R is a substituted or unsubstituted C 1-6 alkyl, alkenyl, alkynyl, or aryl;

R 1 is alkyl, allyl or aryl; and

R 2 is alkyl, allyl or aryl.

2. The modified oligonucleotide of claim 1 , wherein the base pairing moiety B is selected from the group consisting of adenine, guanine, cytosine, and uracil.

3. The modified oligonucleotide of claim 2 , wherein Y is O.

4. The modified oligonucleotide of claim 1 wherein the at least one modified intersubunit linkage of Formula I comprises Formula III:

wherein:

B is a base pairing moiety;

R is alkyl, allyl or aryl.

5. The modified oligonucleotide of claim 4 , wherein the base pairing moiety B is selected from the group consisting of adenine, guanine, cytosine, and uracil.

6. The modified oligonucleotide of claim 1 wherein the at least one modified intersubunit linkage of Formula I comprises Formula IV:

wherein:

B is a base pairing moiety;

R is alkyl, allyl or aryl.

7. The modified oligonucleotide of claim 6 , wherein the base pairing moiety B is selected from the group consisting of adenine, guanine, cytosine, and uracil.

8. The modified oligonucleotide of claim 1 wherein the at least one modified intersubunit linkage of Formula I comprises Formula V:

wherein:

B is a base pairing moiety;

R is alkyl, allyl or aryl.

9. The modified oligonucleotide of claim 8 , wherein the base pairing moiety B is selected from the group consisting of adenine, guanine, cytosine, and uracil.

10. The modified oligonucleotide of claim 1 wherein the at least one modified intersubunit linkage of Formula I comprises Formula VI:

wherein:

B is a base pairing moiety;

R is alkyl, allyl or aryl.

11. The modified oligonucleotide of claim 10 , wherein the base pairing moiety B is selected from the group consisting of adenine, guanine, cytosine, and uracil.

12. The modified oligonucleotide of claim 1 , wherein Z is O(CH 2 ) n , n is 1, W is O, and Y is O − .

13. The modified oligonucleotide of claim 1 , wherein Z is O(CH 2 ) n ,

n is 1, W is O(CH 2 ) n , and Y is O − .

14. The modified oligonucleotide of claim 1 , wherein Z is O(CH 2 ) n , n is not 1, W is O(CH 2 ) n , and Y is O − .

15. A method for synthesizing the modified oligonucleotide of claim 1 , the method comprising:

(a) providing a nucleoside having a 5′-protecting group linked to a solid support;

(b) removal of the protecting group;

(c) combining the deprotected nucleoside with a phosphoramidite derivative of Formula (VII) to form a phosphite triester;

(d) capping the phosphite triester;

(e) oxidizing the phosphite triester;

(f) repeating steps (b) through (e) using an additional phosphoramidite; and

(g) cleaving from the solid support;

wherein B, Z, X and R are defined as in Formula (I).

16. A method for synthesizing the modified oligonucleotide of claim 1 , the method comprising coupling a phosphoramidite derivative of Formula (VII)

to a 5′-terminus of a nucleoside or an oligonucleotide by adding the phosphoramidite derivative of Formula (VII) to the nucleoside or the oligonucleotide in an organic solvent comprising an aromatic heterocyclic acid; wherein B, Z, X and R are defined as in Formula (I).

17. A method for synthesizing the modified oligonucleotide of claim 1 , the method comprising:

(a) providing a nucleoside having 3′-protecting group;

(b) oxidizing 5′-hydroxyl group of the nucleoside to a 5′-aldehyde group;

(c) converting 5′-aldehyde group of the nucleoside to a 5′-vinyl group by Wittig olefination;

(d) conducting hydroboration/oxidation on the 5′-vinyl group to produce a 6′-hydroxyl group;

(e) protecting the 6′-hydroxyl group with a DMTr group;

(f) removing the 3′-protecting group of the nucleoside; and

(g) phosphitylating3′-hydroxyl group to produce a 3′-phosphoramidite,

thereby synthesizing the modified oligonucleotide.