Duplex oligonucleotides with enhanced functionality in gene regulation
Disclosed are methods of enhancing functionality of duplex oligonucleotides and compositions made by the methods. The duplex oligonucleotides include siRNAs, miRNA mimics, and piRNA mimics which contain modified nucleotides and mismatches between the two strands of the molecule at specific nucleotide positions.
1. A duplex oligonucleotide complex comprising:
(a) a sense strand that is nineteen nucleotides in length, wherein nucleotides 1 and 2 and all C and all U nucleotides on said sense strand are 2′O-methyl modified;
(b) an antisense strand that is twenty-one nucleotides in length, wherein
(i) all C nucleotides and all U nucleotides on said antisense strand are 2′ F modified; and
(ii) the sense strand and the antisense strand form a duplex having a two nucleotide overhang at the 3′ end of the antisense strand, said two nucleotide overhang comprising phosphorothioate linkages;
(c) a cholesterol molecule attached to the 3′ end of the sense strand via a C5 linker molecule thereby forming a cholesterol-linker-sense strand structure of:
(d) a phosphate group at the 5′ end of the antisense strand; and
(e) three mismatches on the sense strand with the corresponding nucleotides on the antisense strand, wherein the mismatches are between nucleotide 6 on the sense strand and opposite nucleotide 14 on the antisense strand, nucleotide 13 on the sense strand and opposite nucleotide 7 on the antisense strand, and nucleotide 19 on the sense strand and opposite nucleotide 1 on the antisense strand,
wherein each nucleotide number refers to the nucleotide's position in an identified strand as counted from the identified strand's 5′ end, and at all positions other than positions 6, 13 and 19 on the sense strand, there is a nucleotide that is complementary to the nucleotide on the opposite strand.
2. The duplex oligonucleotide complex of claim 1 , wherein at least one of the mismatches is a G across from an A.
3. The duplex oligonucleotide complex of claim 1 , wherein at least one of the mismatches is an A across from a C.
4. The duplex oligonucleotide complex of claim 1 , wherein at least one of the mismatches is an A across from an A.
5. The duplex oligonucleotide of claim 1 , wherein at least one of the mismatches is a G across from a G.
6. The duplex oligonucleotide of claim 1 , wherein at least one of the mismatches is a C across from a C.
7. The duplex oligonucleotide of claim 1 , wherein at least one of the mismatches is a U across from a U.
8. The duplex oligonucleotide complex of claim 1 , wherein the antisense strand is 100% complementary to a target.
9. The duplex oligonucleotide complex of claim 1 , wherein the overhang is UU.
10. A pharmaceutical composition comprising the duplex oligonucleotide complex of claim 1 and at least one pharmaceutically acceptable carrier or diluent.