Modified oligonucleotides targeting SNPs
Novel oligonucleotides that enhance silencing of the expression of a gene containing a single nucleotide polymorphism (SNP) relative to the expression of the corresponding wild-type gene are provided. Methods of using novel oligonucleotides that enhance silencing of the expression of a gene containing a SNP relative to the expression of the corresponding wild-type gene are provided.
1 . A double-stranded RNA (dsRNA) comprising a first strand having 15-35 nucleotides in length, a 5′ end, a 3′ end, and a seed region, wherein the first strand is complementary to a region of a gene comprising an allelic polymorphism, and wherein the first strand comprises:
a single nucleotide polymorphism (SNP) position nucleotide at a position within the seed region, wherein the SNP position nucleotide is complementary to the allelic polymorphism; and a mismatch (MM) position nucleotide located 2-11 nucleotides from the SNP position nucleotide that is a mismatch with a nucleotide in the gene.
2 . An oligonucleotide having 15-35 nucleotides in length, a 5′ end, a 3′ end and a seed region, wherein the oligonucleotide is complementary to a region of a gene comprising an allelic polymorphism, and wherein the oligonucleotide comprises:
a single nucleotide polymorphism (SNP) position nucleotide at a position within the seed region, wherein the SNP position nucleotide is complementary to the allelic polymorphism; and
a mismatch (MM) position nucleotide located 2-11 nucleotides from the SNP position nucleotide that is a mismatch with a nucleotide in the gene.
3 . The oligonucleotide of claim 2 , wherein said oligonucleotide is an ASO.
4 . The dsRNA of claim 1 , wherein the dsRNA further comprises:
a second strand of 15-35 nucleotides that is complementary to a portion of the first strand,
wherein the first strand comprises the SNP position nucleotide at position 2-6 from the 5′ end that is complementary to the allelic polymorphism, and
wherein the first strand comprises the MM position nucleotide located 2-6 nucleotides from the SNP position nucleotide that is a mismatch with a nucleotide in the gene.
5 . The dsRNA of claim 1 , further comprising at least one modified nucleotide.
6 . A double-stranded RNA (dsRNA) comprising:
a first strand of 15-35 nucleotides that is complementary to a region of a gene comprising an allelic polymorphism; and
a second strand of 15-35 nucleotides that is complementary a portion of the first strand,
wherein the first strand comprises a single nucleotide polymorphism (SNP) position nucleotide at position 4 from the 5′ end that is complementary to the allelic polymorphism, and
wherein the first strand comprises a mismatch (MM) position nucleotide located at position 7 from the 5′ end is a mismatch with a nucleotide in the gene.
7 . A double-stranded RNA (dsRNA) comprising:
a first strand of 15-35 nucleotides that is complementary to a region of a gene comprising an allelic polymorphism; and
a second strand of 15-35 nucleotides that is complementary to a portion of the first strand,
wherein the first strand comprises a single nucleotide polymorphism (SNP) position nucleotide at a position 6 from the 5′ end that is complementary to the allelic polymorphism, and
wherein the first strand comprises a mismatch (MM) position nucleotide located at position 11 from the 5′ end is a mismatch with a nucleotide in the gene.
8 . The oligonucleotide of claim 2 , further comprising a 5′ stabilizing moiety selected from the group consisting of phosphate, vinyl phosphonate, C5-methyl (R or S or racemic), C5-methyl on vinyl, and reduced vinyl.
9 . The oligonucleotide of claim 2 , further comprising a conjugate moiety selected from the group consisting of alkyl chain, vitamin, peptide, glycosphingolipid, polyunsaturated fatty acid, secosteroid, steroid hormone, and steroid lipid.
10 . A nucleic acid having 15-35 nucleotides in length, a 5′ end, a 3′ end, and a seed region, that is complementary to a region of a gene comprising an allelic polymorphism, wherein the nucleic acid comprises:
a single nucleotide polymorphism (SNP) position nucleotide at a position within the seed region, wherein the SNP position nucleotide is complementary to the allelic polymorphism;
a mismatch (MM) position that is a mismatch with a nucleotide in the gene; and
at least one modified nucleotide (X) on either side of the SNP position nucleotide, wherein each X is located within four, three or two nucleotides from the SNP position nucleotide.
11 . A nucleic acid having 15-35 nucleotides in length, a 5′ end, a 3′ end and a seed region, that is complementary to a region of a gene comprising an allelic polymorphism, wherein the nucleic acid comprises:
a single nucleotide polymorphism (SNP) position nucleotide at a position within the seed region, wherein the SNP position nucleotide is complementary to the allelic polymorphism;
a mismatch (MM) position that is a mismatch with a nucleotide in the gene; and
at least one modified nucleotide (Y) on either side of the MM position nucleotide, wherein each Y is located within four, three or two nucleotides from the MM position nucleotide.
12 . A nucleic acid having 15-35 nucleotides in length, a 5′ end, a 3′ end, and a seed region, that is complementary to a region of a gene comprising an allelic polymorphism, wherein the nucleic acid comprises:
a single nucleotide polymorphism (SNP) position nucleotide at a position within the seed region, wherein the SNP position nucleotide is complementary to the allelic polymorphism;
a mismatch (MM) position that is a mismatch with a nucleotide in the gene; and
at least one modified nucleotide (X) on either side of the SNP position nucleotide, wherein each X is located within four, three or two nucleotides from the SNP position nucleotide; and
at least one modified nucleotide (Y) on either side of the MM position nucleotide, wherein each Y is located within four, three or two nucleotides from the MM position nucleotide.