Synthesis of modified oligonucleotides with increased stability
AssigneeUniversity of Massachusetts
InventorsAnastasia Khvorova, Loïc Maurice René Jean Roux, Ken Yamada
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Abstract
This disclosure relates to the synthesis of novel modified oligonucleotides. The synthesis of novel phosphoramidites are also provided.
Claims23
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(CH2)n, wherein n is 1 to 10;
- X is selected from the group consisting of H, OH, OR, F, SH, SR, NR22 and C1-6-alkoxy;
- Y is selected from the group consisting of O−, OH, OR, OR2, NH−, NH2, NR22, BH3, S−, R1, and SH;
- Z is O or O(CH2)n wherein n is 1 to 10;
- R1 is alkyl, allyl or aryl;
- and
- R2 is alkyl, allyl or aryl.
2-6. (canceled)
(canceled)
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, NR22, MOE, alkyl, allyl, aryl, and C1-6-alkoxy;
- Z is O or OCH2:
- R is OMe or OCE (cyanoethyl):
- le is alkyl, allyl or aryl;
- and
- R2 is alkyl, allyl or aryl.
The phosphoramidite derivative of Formula (VII) wherein the base pairing moiety B is selected from the group consisting of adenine, guanine, cytosine, and uracil.
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, NR22, MOE, alkyl, allyl, aryl, and C1-6-alkoxy;
- R1 is alkyl, allyl or aryl;
- and
- R2 is alkyl, allyl or aryl.
The phosphoramidite derivative of Formula (VIII) wherein the base pairing moiety B is selected from the group consisting of adenine, guanine, cytosine, and uracil.
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, NR22, MOE, alkyl, allyl, aryl, and C1-6-alkoxy;
- le is alkyl, allyl or aryl;
- and
- R2 is alkyl, allyl or aryl.
The phosphoramidite derivative of Formula (IX) wherein the base pairing moiety B is selected from the group consisting of adenine, guanine, cytosine, and uracil.
A method for synthesizing a modified oligonucleotide comprising a 5′ end, a 3′ end and at least one modified intersubunit linkage 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.
A method for coupling a phosphoramidite derivative of Formula (VII)
- to a 5′-terminus of a nucleoside or an oligonucleotide comprising adding the phosphoramidite derivative of Formula (VII) to the nucleoside or the oligonucleotide in an organic solvent comprising an aromatic heterocyclic acid.
A method for synthesizing a exNA phosphoramidite:
- (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;
- (g) phosphitylating 3′-hydroxyl group to produce a 3′-phosphoramidite.
Dependencies are inferred from the claim text.