Modified polynucleotides for reducing off-target effects in RNA interference

• US 7,595,387 B2
• Filed: 12/22/2004
• Issued: 09/29/2009
• Est. Priority Date: 04/01/2004
• Status: Expired due to Term

• Current Assignee: Merck & Co., Inc., Dharmacon Incorporated (Revvity, Inc.)
• Original Assignee: Merck & Co., Inc., Dharmacon Incorporated (Revvity, Inc.)
• Inventors: Marshall, William, Khvorova, Anastasia, Linsley, Peter S., Reynolds, Angela, Leake, Devin
• Primary Examiner(s): Chong; Kimberly
• Application Number:
  US11/019,831
• Publication Number:
  US 20050223427A1
• Time in Patent Office: 1,742 Days
• Field of Search: 536/24.5, 536/24.3, 536/24.31, 536/24.33
• US Class Current: 536/24.5
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• CPC Class Codes: C12N 15/1137 against enzymes viral enzymes C12N15/1131; receptors C12N15/1138
• CPC Class Codes: C12N 15/1138 against receptors or cell surface proteins
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2320/11 for the determination of target sites, i.e. of active nucleic acids
• CPC Class Codes: C12N 2330/30 chemically synthesised
• CPC Class Codes: C12Y 207/11024 Mitogen-activated protein kinase (2.7.11.24), i.e. MAPK or MAPK2 or c-Jun N-terminal kinase
• CPC Class Codes: C12Y 301/03001 Alkaline phosphatase (3.1.3.1)

Abstract

Methods and compositions for performing RNA interference with decreased off-target effects are provided The methods and compositions permit effective and efficient applications of RNA interference to applications such as diagnostics and therapeutics through the use of modifications to the siRNA. Uniquely modified siRNAs have been developed that reduce off-target effects incurred in gene-silencing. The modifications comprise 2′-O-alkyl or mismatch modification(s) at specific positions on the sense and/or antisense strands.

Claims

1. A double stranded polyribonucleotide comprising:

a. a sense strand comprising a sense region, wherein said sense region comprises;

i. a first 5′

sense nucleotide, wherein said first 5′

sense nucleotide comprises a first 2′

-O-alkyl modification, and

ii. a second 5′

sense nucleotide, wherein said second 5′

sense nucleotide comprises a second 2′

-O-alkyl modification; and

b. an antisense strand comprising an antisense region, wherein said antisense region comprises;

i. a first 5′

antisense nucleotide, wherein said first 5′

antisense nucleotide is phosphorylated, and

ii. a second 5′

antisense nucleotide, wherein said second 5′

antisense nucleotide comprises a third 2′

-O-alkyl modification,

wherein said sense region and said antisense region are capable of forming a duplex of 18-24 base pairs of nucleotides that has at least 80% complementarity over the range of the duplex, and within said duplex said first 5′

sense nucleotide is the 5′

most nucleotide of the sense strand, said second 5′

sense nucleotide is immediately adjacent to and downstream of the first 5′

sense nucleotide, said first 5′

antisense nucleotide is the 5′

most nucleotide of the antisense strand and said second 5′

antisense nucleotide is immediately adjacent to and downstream of the first 5′

antisense nucleotide, wherein all nucleotides of each strand of said double stranded polyribonucleotide other than said first 5′

sense nucleotide, said second 5′

sense nucleotide, and said second 5′

antisense nucleotide comprises a 2′

-OH, and wherein said antisense strand is capable of silencing a target gene with reduced off-target gene silencing.

2. The double stranded polyribonucleotide of claim 1, wherein said first 2′

-O-alkyl modification comprises 2′

-O-methyl, said second 2′

-O-alkyl modification comprises 2′

-O-methyl, and said third 2′

-O-alkyl modification comprises 2′

-O-methyl.

3. The double stranded polyribonucleotide of claim 1, wherein the double stranded polyribonucleotide comprises a 3′

overhang, and said 3′

overhang is 1 to 6 bases on at least one of said sense strand or said antisense strand.

4. The double stranded polyribonucleotide of claim 1, wherein said first 2′

-O-alkyl modification, second 2′

-O-alkyl modification, and third 2′

-O-alkyl modification are independently selected from the group consisting of 2′

-O- ethyl, 2′

-O-propyl, 2′

-O-isopropyl, 2′

-O-butyl, 2′

-O-isobutyl, 2′

-O-ethyl-O-methyl, and 2′

-O-ethyl-OH.

5. The double stranded polyribonucleotide of claim 1, wherein only said first 5′

antisense nucleotide is phosphorylated.

6. The double stranded polyribonucleotide of claim 3, wherein said 3′

overhang is 2 bases on at least one of said sense strand or said antisense strand.

7. The double stranded polyribonucleotide of claim 1, wherein said double stranded polyribonucleotide has reduced off-target gene silencing activity compared to a double stranded polyribonucleotide having the same nucleotide sequence as said double stranded polyribonucleotide, but does not contain 2′

-O-alkyl modifications in said sense and antisense strands.

8. The double stranded polyribonucleotide of claim 1, wherein said double stranded polyribonucleotide has reduced off-target gene silencing activity compared to a double stranded polyribonucleotide having the same nucleotide sequence as said double stranded polyribonucleotide, but does not contain 2′

-O-alkyl modifications in said antisense strand.

9. A double stranded polyribonucleotide comprising:

a. a sense strand comprising a sense region, wherein said sense region comprises;

i. a first 5′

sense nucleotide, wherein said first 5′

sense nucleotide comprises a first 2′

-O-methyl modification, and

ii. a second 5′

sense nucleotide, wherein said second 5′

sense nucleotide comprises a second 2′

-O-methyl modification; and

b. an antisense strand comprising an antisense region, wherein said antisense region comprises;

i. a first 5′

antisense nucleotide, wherein said first 5′

antisense nucleotide is phosphorylated, and

ii. a second 5′

antisense nucleotide, wherein said second 5′

antisense nucleotide comprises a third 2′

-O-methyl modification,

wherein said sense region and said antisense region are capable of forming a duplex of 19 base pairs of nucleotides that has at least 80% complementarity over the range of the duplex, and within said duplex said first 5′

sense nucleotide is the 5′

most nucleotide of the sense strand, said second 5′

sense nucleotide is immediately adjacent to and downstream of the first 5′

sense nucleotide, said first 5′

antisense nucleotide is the 5′

most nucleotide of the antisense strand and said second 5′

antisense nucleotide is immediately adjacent to and downstream of the first 5′

antisense nucleotide, wherein all nucleotides of each strand of said double stranded polyribonucleotide other than said first 5′

sense nucleotide, said second 5′

sense nucleotide, and said second 5′

antisense nucleotide comprises a 2′

-OH, wherein the double stranded polyribonucleotide comprises an overhang of two nucleotides at the 3′

termini of both said sense strand and said antisense strand and wherein said antisense strand is capable of silencing a target gene with reduced off-target gene silencing.

10. The double stranded polyribonucleotide of claim 9, wherein said duplex of 19 base pairs of nucleotides has 100% complementarity over the range of the duplex and the two nucleotides of said overhangs at the 3′

termini of the sense strand and the antisense strand are UU.