Rna-editing oligonucleotides and uses thereof

Abstract

The present disclosure features useful compositions and methods to treat disorders for which deamination of an adenosine in an mRNA produces a therapeutic result, e.g., in a subject in need thereof.

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;   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 at least one of X 1 , X 2 , or X 3  has the structure of any one of Formula I-V:   
       
         
           
           
               
               
           
         
       
       wherein N 1  is hydrogen or a nucleobase;
 R 1  is hydroxy, halogen, or C 1 -C 6  alkoxy; 
 R 2  is hydrogen, hydroxy, halogen, or C 1 -C 6  alkoxy; 
 R 3  is hydrogen, hydroxy, halogen, or C 1 -C 6  alkoxy; 
 R 4  is hydrogen, hydroxy, halogen, or C 1 -C 6  alkoxy; and 
 R 5  is hydrogen, hydroxy, halogen, or C 1 -C 6  alkoxy. 
 
     
     
         2 . The oligonucleotide of  claim 1 , wherein R 4  is hydrogen and R 5  is not hydrogen or hydroxy, R 5  is hydrogen and R 4  is not hydrogen, or R 5  is hydroxy and R 4  is not hydrogen. 
     
     
         3 . The oligonucleotide of  claim 1 , wherein at least 80% of the nucleotides of [A m ] and/or [B n ] include a nucleobase, a sugar, and an internucleoside linkage. 
     
     
         4 . The oligonucleotide of  claim 1 , wherein R 1  is hydroxy, halogen, or OCH 3 . 
     
     
         5 . The oligonucleotide of  claim 1 , wherein R 2  is hydrogen. 
     
     
         6 . The oligonucleotide of  claim 1 , wherein at least one of X 1 , X 2 , or X 3  has the structure of Formula I, Formula II, or Formula V; and none of X 1 , X 2 , or X 3  has the structure of Formula IV or Formula III. 
     
     
         7 . The oligonucleotide of  claim 1 , wherein at least one of X 1 , X 2 , or X 3  has the structure of Formula I or Formula II; and none of X 1 , X 2 , or X 3  has the structure of Formula III, Formula IV, or Formula V. 
     
     
         8 . The oligonucleotide of  claim 1 , wherein the halogen is fluoro. 
     
     
         9 . The oligonucleotide of  claim 1 , wherein at least one of X 1 , X 2 , and X 3  has the structure of Formula I, wherein R 1  is fluoro and N 1  is a nucleobase. 
     
     
         10 - 12 . (canceled) 
     
     
         13 . The oligonucleotide of  claim 1 , wherein at least one of X 1 , X 2 , and X 3  has the structure of Formula I, wherein R 1  is hydroxy and N 1  is a nucleobase. 
     
     
         14 - 16 . (canceled) 
     
     
         17 . The oligonucleotide of  claim 1 , wherein at least one of X 1 , X 2 , and X 3  has the structure of Formula I, wherein R 1  is methoxy and N 1  is a nucleobase. 
     
     
         18 - 20 . (canceled) 
     
     
         21 . The oligonucleotide of  claim 1 , wherein at least one of X 1 , X 2 , and X 3  has the structure of Formula II, wherein R 2  is hydrogen and N 1  is a nucleobase. 
     
     
         22 . (canceled) 
     
     
         23 . The oligonucleotide of  claim 1 , wherein at least one of X 1  and X 2  has the structure of Formula V. 
     
     
         24 . (canceled) 
     
     
         25 - 59 . (canceled) 
     
     
         60 . The oligonucleotide of  claim 1 , wherein at least 20% of the nucleotides of [A m ] and [B n ] combined are 2′-O-methyl-nucleotides. 
     
     
         61 - 63 . (canceled) 
     
     
         64 . The oligonucleotide of  claim 1 , wherein A and B combined consist of 18 to 80 nucleotides. 
     
     
         65 - 66 . (canceled) 
     
     
         67 . The oligonucleotide of  claim 1 , wherein m and n are each, independently, an integer from 5 to 40; at least one of X 1 , X 2 , and X 3  has the structure of Formula I, wherein R 1  is fluoro, hydroxy, or methoxy and N 1  is a nucleobase, or the structure of Formula V, wherein R 4  is hydrogen and R 5  is hydrogen; each of X 1 , X 2 , and X 3  that does not have the structure of Formula I or Formula V is a ribonucleotide; [A m ] and [B n ] each comprise at least five terminal 2′-O-methyl-nucleotides and at least four terminal phosphorothioate linkages; and at least 20% of the nucleotides of [A m ] and [B n ] combined are 2′-O-methyl-nucleotides. 
     
     
         68 . The oligonucleotide of  claim 1 , wherein the oligonucleotide further comprises one or more adenosine deaminase acting on RNA (ADAR)-recruiting domains. 
     
     
         69 . A conjugate comprising an oligonucleotide of  claim 1  conjugated to a targeting moiety. 
     
     
         70 . (canceled) 
     
     
         71 . A complex comprising:
 an oligonucleotide of  claim 1 ; and   an mRNA,   wherein the oligonucleotide or conjugate and mRNA are hybridized to each other and the complex comprises a first mismatch at an adenosine of the mRNA.   
     
     
         72 - 79 . (canceled) 
     
     
         80 . A method of producing a complex, the method comprising contacting a cell with an oligonucleotide of  claim 1 . 
     
     
         81 . A method for deamination of an adenosine in an mRNA, the method comprising contacting a cell with an oligonucleotide of  claim 1 . 
     
     
         82 . 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 . 
     
     
         83 . (canceled)