RNA-editing oligonucleotides and uses thereof
The present disclosure features useful compositions and methods to treat disorders for which deamination of an adenosine in an mRNA produces a therapeutic result.
1. An oligonucleotide comprising the structure:
[A m ]-X 1 —X 2 —X 3 —[B n ]
wherein each of A and B is a nucleotide, wherein at least 20% of the nucleotides of [A m ] and [B n ] combined are 2′-O-methyl-nucleotides;
m and n are each, independently, an integer from 1 to 50;
X 1 , X 2 , and X 3 are each, independently, a nucleotide, wherein X 2 has the structure of Formula II:
wherein N 1 is a nucleobase;
R 8 is hydrogen; and
R 9 is hydrogen.
2. The oligonucleotide of claim 1 , wherein at least 80% of the nucleotides of [A m ] and [B n ] include a nucleobase, a sugar, and an internucleoside linkage.
3. The oligonucleotide of claim 1 , wherein at least 90% of the nucleotides of [A m ] and [B n ] include a nucleobase, a sugar, and an internucleoside linkage.
4. The oligonucleotide of claim 1 , wherein at least 95% of the nucleotides of [A m ] and [B n ] include a nucleobase, a sugar, and an internucleoside linkage.
5. The oligonucleotide of claim 1 , wherein each of X 1 and X 3 is, independently, a ribonucleotide, a 2′-O—C 1 -C 6 alkyl-nucleotide, a 2′-amino-nucleotide, an arabinonucleic acid-nucleotide, a bicyclic-nucleotide, a 2′-F-nucleotide, 2′-O-methoxyethyl-nucleotide, a constrained ethyl-nucleotide, an LNA-nucleotide, or a DNA-nucleotide.
6. The oligonucleotide of claim 1 , wherein when each of X 1 and X 3 is, independently, a 2′-O—C 1 -C 6 alkyl-nucleotide, a 2′-F-nucleotide, an arabinonucleic acid-nucleotide, or a DNA-nucleotide.
7. The oligonucleotide of claim 1 , wherein X 1 includes a uracil or thymine nucleobase and X 3 includes a hypoxanthine nucleobase.
8. The oligonucleotide of claim 1 , wherein X 2 includes a cytosine nucleobase.
9. The oligonucleotide of claim 6 , wherein X 1 and X 3 are not 2′-O-methyl-nucleotides.
10. The oligonucleotide of claim 1 , wherein [A m ] comprises at least one 2′-O-methyl-nucleotide, at least one 2′-F-nucleotide, at least one 2′-O-methoxyethyl-nucleotide, at least one cEt-nucleotide, at least one LNA-nucleotide, and/or at least one DNA-nucleotide.
11. The oligonucleotide of claim 1 , wherein [A m ] comprises at least one phosphorothioate linkage.
12. The oligonucleotide of claim 1 , wherein [A m ] comprises at least four terminal phosphorothioate linkages.
13. The oligonucleotide of claim 1 , wherein [B n ] comprises at least one 2′-O-methyl-nucleotide, at least one 2′-F-nucleotide, at least one 2′-O-methoxyethyl-nucleotide, at least one cEt-nucleotide, at least one LNA-nucleotide, and/or at least one DNA-nucleotide.
14. The oligonucleotide of claim 1 , wherein [B n ] comprises at least one phosphorothioate linkage.
15. The oligonucleotide of claim 1 , wherein [B n ] comprises at least four terminal phosphorothioate linkages.
16. The oligonucleotide of claim 1 , wherein at least 30% of the nucleotides of [A m ] and [B n ] combined are 2′-O-methyl-nucleotides.
17. The oligonucleotide of claim 1 , wherein A and B combined consist of 27 to 71 nucleotides.
18. The oligonucleotide of claim 1 , wherein m is 12 to 32.
19. The oligonucleotide of claim 18 , wherein n is 7 to 17.
20. The oligonucleotide of claim 1 , wherein X 1 includes a uracil or thymine nucleobase and X 3 includes a hypoxanthine nucleobase; X 2 includes a cytosine nucleobase; and each of X 1 and X 3 is, independently, a 2′-O—C 1 -C 6 alkyl-nucleotide, a 2′-F-nucleotide, an arabinonucleic acid-nucleotide, or a DNA-nucleotide.
21. The oligonucleotide of claim 20 , wherein at least 95% of the nucleotides of [A m ] and [B n ] include a nucleobase, a sugar, and an internucleoside linkage; each of [A m ] and [B n ] comprises at least one phosphorothioate linkage; each of [A m ] and [B n ] comprises at least one 2′-O-methyl-nucleotide, at least one 2′-F-nucleotide, at least one 2′-O-methoxyethyl-nucleotide, at least one cEt-nucleotide, at least one LNA-nucleotide, and/or at least one DNA-nucleotide; and A and B combined consist of 27 to 71 nucleotides.
22. A complex comprising:
an oligonucleotide of claim 1 ; and an mRNA,
wherein the oligonucleotide and mRNA are hybridized to each other and the complex comprises a first mismatch at an adenosine of the mRNA.
23. A method for deamination of an adenosine in an mRNA, the method comprising contacting a cell with an oligonucleotide of claim 1 .
24. A method of treating a disorder in a subject in need thereof, the method comprising administering to the subject an effective amount of an oligonucleotide of claim 1 .
25. The method of claim 24 , wherein the disorder is alpha-1-antitrypsin deficiency.
26. A method of treating a disorder in a subject in need thereof, the method comprising administering to the subject an effective amount of an oligonucleotide of claim 21 .
27. The method of claim 26 , wherein the disorder is alpha-1-antitrypsin deficiency.