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

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,

wherein:

Z is O(CH 2 ) n and W is O; or

Z is O and W is O(CH 2 ) n ; or

Z is O(CH 2 ) n and W is O(CH 2 ) n .

2 - 6 . (canceled)

7 . The modified oligonucleotide of claim 1 , 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 II:

wherein:

B is a base pairing moiety;

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;

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.

9 . (canceled)

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

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

wherein:

the base is a base pairing moiety;

R is alkyl, allyl, or aryl.

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

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

wherein:

the base is a base pairing moiety;

R is alkyl, allyl, or aryl.

14 . The modified oligonucleotide of claim 13 , wherein the base pairing moiety is selected from the group consisting of adenine, guanine, cytosine, and uracil.

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

wherein:

the base is a base pairing moiety;

R is alkyl, allyl, or aryl.

16 . The modified oligonucleotide of claim 15 , wherein the base pairing moiety is selected from the group consisting of adenine, guanine, cytosine, and uracil.

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

wherein:

the base is a base pairing moiety;

R is alkyl, allyl, or aryl.

18 . The modified oligonucleotide of claim 17 , wherein the base pairing moiety is selected from the group consisting of adenine, guanine, cytosine, and uracil.

19 . A phosphoramidite derivative of Formula (VII):

wherein:

B is a base pairing moiety;

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

Z is O or OCH 2 ;

R is OMe or OCE (cyanoethyl);

and

R 2 is alkyl, allyl, or aryl.

20 . The phosphoramidite derivative of claim 19 , wherein the base pairing moiety B is selected from the group consisting of adenine, guanine, cytosine, and uracil.

21 . A phosphoramidite derivative of Formula (VIII):

wherein:

B is a base pairing moiety;

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

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

and

R 2 is alkyl, allyl, or aryl.

22 . The phosphoramidite derivative of claim 21 , wherein the base pairing moiety B is selected from the group consisting of adenine, guanine, cytosine, and uracil.

23 . A phosphoramidite derivative of Formula (IX):

wherein:

B is a base pairing moiety;

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

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

R 2 is alkyl, allyl, or aryl.

24 . The phosphoramidite derivative of claim 23 , wherein the base pairing moiety B is selected from the group consisting of adenine, guanine, cytosine, and uracil.

25 . A method for synthesizing a modified oligonucleotide comprising a 5′ end, a 3′ end, and at least one modified intersubunit linkage, the method comprising:

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

(b) removing the 5′-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 is a base pairing moiety;

Z is O or O(CH 2 ) 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;

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

R 2 is alkyl, allyl, or aryl.

26 . A method for coupling a phosphoramidite derivative of Formula (VII)

to a 5′-terminus of a nucleoside or an oligonucleotide, the method comprising adding the phosphoramidite derivative of Formula (VII) to the nucleoside or the oligonucleotide in an organic solvent comprising an aromatic heterocyclic acid, wherein:

B is a base pairing moiety;

Z 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;

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

R 2 is alkyl, allyl, or aryl.

27 . A method for synthesizing an extended nucleic acid (exNA) phosphoramidite, the method comprising:

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

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

(c) converting a 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) phosphitylating a 3′-hydroxyl group to produce a 3′-phosphoramidite.