Oligonucleotide compositions and methods thereof

Abstract

Among other things, the present disclosure relates to chirally controlled oligonucleotides of select designs, chirally controlled oligonucleotide compositions, and methods of making and using the same. In some embodiments, a provided chirally controlled oligonucleotide composition provides different cleavage patterns of a nucleic acid polymer than a reference oligonucleotide composition. In some embodiments, a provided chirally controlled oligonucleotide composition provides single site cleavage within a complementary sequence of a nucleic acid polymer. In some embodiments, a chirally controlled oligonucleotide composition has any sequence of bases, and/or pattern or base modifications, sugar modifications, backbone modifications and/or stereochemistry, or combination of these elements, described herein.

1 - 41 . (canceled) 
     
     
         42 . A chirally controlled oligonucleotide composition comprising oligonucleotides of a particular oligonucleotide type characterized by:
 1) a common base sequence and length;   2) a common pattern of backbone linkages; and   3) a common pattern of backbone chiral centers;   
       which composition is chirally controlled in that it is enriched, relative to a substantially racemic preparation of oligonucleotides having the same base sequence and length, for oligonucleotides of the particular oligonucleotide type,
 wherein oligonucleotides of the particular oligonucleotide type each comprise a wing-core-wing structure, wherein: 
 each wing region independently has a length of two or more bases, wherein at least one wing comprises one or more natural phosphate linkages, and each independently and optionally comprises one or more chiral internucleotidic linkages; and 
 the core region has a pattern of backbone chiral centers comprising Rp(Sp) 2 . 
 
     
     
         43 . The composition of  claim 42 , wherein the oligonucleotides target a mutant Huntingtin gene, and the length is from about 10 to about 50 nucleotides. 
     
     
         44 . The composition of  claim 43 , wherein each internucleotidic linkage of the Rp(Sp) 2  is independently a phosphorothioate linkage. 
     
     
         45 . The composition of  claim 43 , wherein each wing independently comprises a modified sugar moiety. 
     
     
         46 . The composition of  claim 45 , wherein the modified sugar moiety has a 2′-modification. 
     
     
         47 . The composition of  claim 46 , wherein a 2′-modification is 2′—OR 1 , wherein R 1  is optionally substituted C 1-6  alkyl. 
     
     
         48 . The composition of claim  6 , wherein a 2′-modification is 2′-MOE or 2′-OMe. 
     
     
         49 . The compound of  claim 48 , wherein each sugar moiety of the core region is a natural DNA sugar moiety. 
     
     
         50 . The composition of  claim 49 , wherein each internucleotidic linkage of the core region is a chiral internucleotidic linkage. 
     
     
         51 . The composition of  claim 50 , wherein 50% or more of the chiral internucleotidic linkages in the core region have Sp configuration. 
     
     
         52 . The composition of  claim 51 , wherein each internucleotidic linkage of the core region is a phosphorothioate linkage. 
     
     
         53 . The composition of  claim 42 , wherein the common base sequence comprises a sequence that is 100% complementary to a characteristic sequence element of a target sequence, wherein the characteristic sequence element defines that target sequence relative to a similar sequence. 
     
     
         54 . The composition of  claim 53 , wherein a target sequence is a sequence comprising a characteristic sequence element which is a mutation, and a similar sequence is the wild-type sequence. 
     
     
         55 . The composition of  claim 54 , wherein a characteristic sequence element defines a particular allele of a target gene relative to other alleles of the same target gene. 
     
     
         56 . The composition of  claim 55 , wherein the characteristic sequence element is a single nucleotide polymorph (SNP) associated with a disease. 
     
     
         57 . The composition of  claim 56 , wherein the SNP is associated with Huntington's disease. 
     
     
         58 . A pharmaceutical composition, comprising a composition of  claim 42 , and at least one pharmaceutical acceptable inactive ingredient selected from pharmaceutically acceptable diluents, pharmaceutically acceptable excipients, and pharmaceutically acceptable carriers. 
     
     
         59 . A method for the cleavage of a nucleic acid having a base sequence comprising a target sequence, the method comprising
 contacting a nucleic acid having a base sequence comprising a target sequence with an oligonucleotide composition  claim 42 , wherein the common base sequence is or comprises a sequence that is complementary to the target sequence in the nucleic acid.   
     
     
         60 . A method for preparing an oligonucleotide, comprising providing a compound having the structure of 
       
         
           
           
               
               
           
         
       
       wherein:
 R is a hydroxyl protecting group; 
 B PRO  is a protected nucleobase; 
 R 1  is optionally substituted C 1-6  alkyl; 
 G 1  and G 3  are hydrogen; 
 G 2  is —C(R) 2 Si(R) 3 ; 
 wherein —C(R) 2 — is optionally substituted —CH 2 —, and each R of —Si(R) 3  is independently an optionally substituted group selected from C 1-10  aliphatic, heterocyclyl, heteroaryl and aryl; and 
 G 4  and G 5  are taken together to form 
 
       an optionally substituted saturated, partially unsaturated or unsaturated heteroatom-containing ring of up to about 20 ring atoms which is monocyclic or polycyclic, fused or unfused; and providing a fluoro-containing reagent to remove a chiral auxiliary from an oligonucleotide. 
     
     
         61 . A compound: N-cyanomethylimidazolium triflate.