Modified oligonucleotides

• US 6,653,458 B1
• Filed: 11/08/1999
• Issued: 11/25/2003
• Est. Priority Date: 09/03/1993
• Status: Expired due to Fees

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Manoharan, Muthiah, Cook, Phillip Dan, Guinosso, Charles J.
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US09/435,806
• Time in Patent Office: 1,478 Days
• Field of Search: 536/22.1, 536/23.1, 536/25.3, 536/25.31, 536/25.32, 536/25.33, 536/25.34
• US Class Current: 536/23.1
• CPC Class Codes: A61K 47/51 the non-active ingredient being a modifying agent
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 15/1131 against viruses
• CPC Class Codes: C12N 15/1132 against retroviridae, e.g. HIV
• CPC Class Codes: C12N 15/1133 against herpetoviridae, e.g. HSV
• CPC Class Codes: C12N 15/1135 against oncogenes or tumor suppressor genes
• CPC Class Codes: C12N 15/1138 against receptors or cell surface proteins
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/318 where the PO2 is completely replaced, e.g. MMI or formacetal
• CPC Class Codes: C12N 2310/32 of the sugar
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/3527 Other alkyl chain

Abstract

Modified oligonucleotides containing at least one 2′,5′-internucleotide linkage are provided. The oligonucleotides of the invention may also bear additional substituents at the 2′- and 3′-positions.

Claims

1. An oligonucleotide comprising a plurality of nucleotides covalently linked together by internucleotide linkages, wherein at least one of said internucleotide linkages is selected from the group consisting of phosphodiester linkages and phosphorothioate linkages and at least one of said nucleotides is linked to an adjacent nucleotide by a 2′

,5′

-internucleotide linkage and bears a 3′

-substituent of the formula

2. The oligonucleotide of claim 1 wherein said 3′

-substituent is alkoxyalkoxy, dialkoxyalkoxy, hydroxyalkoxy, dihydroxyalkoxy, aminoalkoxy, alkylaminoalkoxy, dialkylaminoalkoxy, dialkylaminooxyalkoxy, haloalkoxy, dihaloalkoxy or trihaloalkoxy.

3. The oligonucleotide of claim 1 wherein all of said internucleotide linkages are phosphorodiester linkages.

4. The oligonucleotide of claim 1 wherein all of said internucleotide linkages are phosphorothioate linkages.

5. The oligonucleotide of claim 1 wherein at least one of said internucleotide linkages is a phosphodiester linkage and at least one of said internucleotide linkages is a phosphorothioate linkage.

6. The oligonucleotide of claim 1 wherein said 3′

-substituent is methoxyethoxy.

8. The oligonucleotide of claim 1 wherein said 3′

-substituent is hydroxyethoxy.

11. The oligonucleotide of claim 1 wherein Z is O.

12. The oligonucleotide of claim 11 wherein:

R₂₂ is C₁-C₂₀ alkyl; and

R₂₄ is O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, hydroxylamino, hydroxyalkyamino or hydroxydialkylamino.

7. An oligonucleotide comprising a plurality of nucleotides covalently linked together by internucleotide linkages, wherein at least one of said nucleotides is linked to an adjacent nucleotide by a 2′

,5′

-internucleotide linkage and bears a 3′

-substituent of the formula

9. An oligonucleotide comprising a plurality of nucleotides covalently linked together by internucleotide linkages, wherein at least one of said nucleotides is linked to an adjacent nucleotide by a 2′

,5′

-internucleotide linkage and bears a 3′

-substituent of the formula

10. An oligonucleotide comprising a plurality of nucleotides covalently linked together by internucleotide linkages, wherein at least one of said nucleotides is linked to an adjacent nucleotide by a 2′

,5′

-internucleotide linkage and bears a 3′

-substituent of the formula

13. An oligonucleotide comprising a plurality of nucleotides covalently linked together by internucleotide linkages, wherein at least one of said nucleotides is linked to an adjacent nucleotide by a 2′

,5′

-internucleotide linkage and bears a 3′

-substituent having one of the formulas;

where;

y1 is 0 or 1;

y2 is 0 to 10;

y3 is 1 to 10;

E is N(R₄₁)(R₄₂) or N═

C(R₄₁)(R₄₂); and

each R₄₁ and each R₄₂ is independently H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₄₁ and R₄₂ taken together form a nitrogen protecting group;

or R₄₁ and R₄₂ taken together with the N or C atom to which they are attached form a ring structure that can include at least one heteroatom selected from N and O.

14. An oligonucleotide of claim 13 wherein y3 is 1.

15. An oligonucleotide of claim 13 wherein y3 is 1.

16. An oligonucleotide of claim 13 wherein y2 is 2.