Chemically modified double stranded nucleic acid molecules that mediate RNA interference

A double stranded nucleic acid molecule having structure SII:

• B---------------NX3--------------(N)X2 B -3′
• B (N)X1---------------NX4------------[N]X5 -5′
• SI
• wherein the upper strand is the sense strand and the lower strand is the antisense strand of the double stranded nucleic acid molecule, each N is independently a nucleotide;
• each B is a terminal cap moiety that can be present or absent;
• (N) represents non-base paired or overhanging nucleotides which can be unmodified or chemically modified;
• [N] represents nucleotide positions wherein any purine nucleotides when present are ribonucleotides;
• X1 and X2 are independently integers from about 0 to about 4;
• X3 is an integer from about 9 to about 30;
• X4 is an integer from about 11 to about 30, provided that the sum of X4 and X5 is between 17-36;
• X5 is an integer from about 1 to about 6;
• NX3 is complementary to NX4 and NX5;
• and
• (a) any pyridmidine nucleotides present in the antisense strand are 2′-deoxy-2′-fluoro nucleotides;
• any purine nucleotides present in the antisense strand are 2′-O-methyl nucleotides;
• (b) any pyrimidine nucleotides present in the sense strand are ribonucleotides;
• any purine nucleotides present in the sense strand are ribonucleotides;
• and
• (c) any (N) nucleotides are 2′-O-methyl nucleotides.

A double stranded nucleic acid molecule having structure SIII:

• B---------------NX3---------------(N)X2 B -3′
• B (N)X1--------------NX4-------------[N]X5 -5′
• SII
• wherein the upper strand is the sense strand and the lower strand is the antisense strand of the double stranded nucleic acid molecule, each N is independently a nucleotide;
• each B is a terminal cap moiety that can be present or absent;
• (N) represents non-base paired or overhanging nucleotides which can be unmodified or chemically modified;
• [N] represents nucleotide positions wherein any purine nucleotides when present are ribonucleotides;
• X1 and X2 are independently integers from about 0 to about 4;
• X3 is an integer from about 9 to about 30;
• X4 is an integer from about 11 to about 30, provided that the sum of X4 and X5 is between 17-36;
• X5 is an integer from about 1 to about 6;
• NX3 is complementary to NX4 and NX5;
• and
• (a) any pyridmidine nucleotides present in the antisense strand are 2′-deoxy-2′-fluoro nucleotides;
• any purine nucleotides present in the antisense strand are 2′-O-methyl nucleotides;
• (b) any pyrimidine nucleotides present in the sense strand are 2′-deoxy-2′-fluoro nucleotides;
• any purine nucleotides present in the sense strand are ribonucleotides;
• and
• (c) any (N) nucleotides are 2′-O-methyl nucleotides.

A double stranded nucleic acid molecule having structure SIV:

• B---------------NX3---------------(N)X2 B -3′
• B (N)X1--------------NX4-------------[N]X5 -5′
• SIV
• wherein the upper strand is the sense strand and the lower strand is the antisense strand of the double stranded nucleic acid molecule, each N is independently a nucleotide;
• each B is a terminal cap moiety that can be present or absent;
• (N) represents non-base paired or overhanging nucleotides which can be unmodified or chemically modified;
• [N] represents nucleotide positions wherein any purine nucleotides when present are ribonucleotides;
• X1 and X2 are independently integers from about 0 to about 4;
• X3 is an integer from about 9 to about 30;
• X4 is an integer from about 11 to about 30, provided that the sum of X4 and X5 is between 17-36;
• X5 is an integer from about 1 to about 6;
• NX3 is complementary to NX4 and NX5;
• and
• (a) any pyridmidine nucleotides present in the antisense strand are 2′-deoxy-2′-fluoro nucleotides;
• any purine nucleotides present in the antisense strand are 2′-O-methyl nucleotides;
• (b) any pyrimidine nucleotides present in the sense strand are 2′-deoxy-2′-fluoro nucleotides;
• any purine nucleotides present in the sense strand are deoxyribonucleotides;
• and
• (c) any (N) nucleotides are 2′-O-methyl nucleotides.

A double stranded nucleic acid molecule having structure SV:

• B---------------NX3---------------(N)X2 B -3′
• B (N)X1--------------NX4-------------[N]X5 -5′
• SV
• wherein the upper strand is the sense strand and the lower strand is the antisense strand of the double stranded nucleic acid molecule, each N is independently a nucleotide;
• each B is a terminal cap moiety that can be present or absent;
• (N) represents non-base paired or overhanging nucleotides which can be unmodified or chemically modified;
• [N] represents nucleotide positions wherein any purine nucleotides when present are ribonucleotides;
• X1 and X2 are independently integers from about 0 to about 4;
• X3 is an integer from about 9 to about 30;
• X4 is an integer from about 11 to about 30, provided that the sum of X4 and X5 is between 17-36;
• X5 is an integer from about 1 to about 6;
• NX3 is complementary to NX4 and NX5;
• and
• (a) any pyridmidine nucleotides present in the antisense strand are nucleotides having a ribo-like, Northern or A-form helix configuration;
• any purine nucleotides present in the antisense strand are 2′-O-methyl nucleotides;
• (b) any pyrimidine nucleotides present in the sense strand are nucleotides having a ribo-like, Northern or A-form helix configuration;
• any purine nucleotides present in the sense strand are 2′-O-methyl nucleotides;
• and
• (c) any (N) nucleotides are 2′-O-methyl nucleotides.

A double stranded nucleic acid molecule having structure SVII:

• B---------------NX3---------------(N)X2 B -3′
• B (N)X1--------------NX4--------------- -5′
• SVII
• wherein the upper strand is the sense strand and the lower strand is the antisense strand of the double stranded nucleic acid molecule, each N is independently a nucleotide;
• each B is a terminal cap moiety that can be present or absent;
• (N) represents overhang nucleotides;
• X1 and X2 are independently integers from about 1 to about 4;
• X3 is an integer from about 9 to about 30;
• X4 is an integer from about 11 to about 30;
• NX3 is complementary to NX4;
• and any (N) purine nucleotide is a 2′-O-methyl nucleotide and any (N) pyrimidine nucleotide is a 2′-deoxy-2′-fluoro nucleotide.

A double stranded nucleic acid molecule having structure SVIII:

• B---------NX7----[N]X6--NX3--------(N)X2 B -3′
• /
• B(N)X1----------------NX4------------[N]X5 -5′
• SVIII
• wherein each N is independently a nucleotide;
• each B is a terminal cap moiety that can be present or absent;
• (N) represents non-base paired or overhanging nucleotides which can be unmodified or chemically modified;
• [N] represents nucleotide positions comprising sequence that renders the 5′-end of the antisense strand (lower strand) less thermally stable than the 5′-end of the sense strand (upper strand);
• [N] represents nucleotide positions that are ribonucleotides;
• X1 and X2 are independently integers from about 0 to about 4;
• X3 is an integer from about 9 to about 15;
• X4 is an integer from about 11 to about 30, provided that the sum of X4 and X5 is between 17-36;
• X5 is an integer from about 1 to about 6;
• X6 is an integer from about 1 to about 4;
• X7 is an integer from about 9 to about 15;
• NX7, NX6, and NX3 are complementary to NX4 and NX5, and
• (a) any pyridmidine nucleotides present in the antisense strand (lower strand) are 2′-deoxy-2′-fluoro nucleotides;
• any purine nucleotides present in the antisense strand (lower strand) other than the purines nucleotides in the [N] nucleotide positions, are independently 2′-O-methyl nucleotides, 2′-deoxyribonucleotides or a combination of 2′-deoxyribonucleotides and 2′-O-methyl nucleotides;
• (b) any pyrimidine nucleotides present in the sense strand (upper strand) are 2′-deoxy-2′-fluoro nucleotides other than [N] nucleotides;
• any purine nucleotides present in the sense strand (upper strand) are independently 2′-deoxyribonucleotides, 2′-O-methyl nucleotides or a combination of 2′-deoxyribonucleotides and 2′-O-methyl nucleotides other than [N] nucleotides;
• and
• (c) any (N) nucleotides are 2′-O-methyl nucleotides.