Oligonucleotide compositions and methods thereof

Abstract

Among other things, the present disclosure relates to designed oligonucleotides, compositions, and methods thereof. In some embodiments, provided oligonucleotide compositions provide altered splicing of a transcript. In some embodiments, provided oligonucleotide compositions have low toxicity. In some embodiments, provided oligonucleotide compositions provide improved protein binding profiles. In some embodiments, provided oligonucleotide compositions have improved delivery. In some embodiments, provided oligonucleotide compositions have improved uptake. In some embodiments, the present disclosure provides methods for treatment of diseases using provided oligonucleotide compositions.

1 . An oligonucleotide composition, comprising a first plurality of oligonucleotides of a particular oligonucleotide type defined by:
 1) base sequence;   2) pattern of backbone linkages;   3) pattern of backbone chiral centers; and   4) pattern of backbone phosphorus modifications,   
       which composition is chirally controlled in that it is enriched, relative to a substantially racemic preparation of oligonucleotides having the same base sequence, for oligonucleotides of the particular oligonucleotide type,
 wherein oligonucleotides of the particular oligonucleotide type each comprise: 
 1) a 5′-end region comprising 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleoside units comprising a 2′-F modified sugar moiety; 
 2) a 3′-end region comprising 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleoside units comprising a 2′-F modified sugar moiety; and 
 3) a middle region between the 5′-end region and the 3′-end region, wherein the middle region comprises one or more Rp internucleotidic linkages. 
 
     
     
         2 - 4 . (canceled) 
     
     
         5 . The composition of  claim 1 , wherein the oligonucleotide composition is characterized in that, when it is contacted with a transcript in a transcript splicing system, splicing of the transcript is altered relative to that observed under reference conditions selected from the group consisting of absence of the composition, presence of a reference composition, and combinations thereof. 
     
     
         6 . The composition of  claim 5  wherein the reference condition is absence of the composition. 
     
     
         7 . The composition of  claim 1 , wherein each internucleotidic linkage in the oligonucleotides of the particularly type is a modified internucleotidic linkage. 
     
     
         8 . The composition of  claim 7 , wherein oligonucleotide of the first plurality each comprises 15 or more bases. 
     
     
         9 . The composition of  claim 8 , wherein each modified internucleotidic linkage is a phosphorothioate linkage. 
     
     
         10 - 13 . (canceled) 
     
     
         14 . The composition of  claim 9 , wherein the oligonucleotides of the particular oligonucleotide type are capable of mediating the skipping of exon 51 of the dystrophin gene. 
     
     
         15 . The composition of  claim 14 , wherein the exon 51 is mutated and can cause a frameshift, premature stop codon and/or deletion of one or more downstream exons. 
     
     
         16 . The composition of  claim 15 , wherein a product of the skipping of exon 51 is a mRNA that encodes a dystrophin protein that has an improved function compared to that encoded by a mRNA without the skipping of exon 51. 
     
     
         17 - 32 . (canceled) 
     
     
         33 . The composition of  claim 9 , wherein each chiral internucleotidic linkage in the first plurality of oligonucleotides is independently chirally controlled, and each oligonucleotide of the first plurality independently comprises at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 0.17. 18, 19, or 20 chirally controlled internucleotidic linkages. 
     
     
         34 . The composition of  claim 9 , wherein at least 10% of the oligonucleotides that have the base sequence of the particular oligonucleotide type are oligonucleotides of the particular oligonucleotide type. 
     
     
         35 . The composition of  claim 9 , wherein at least 10% of the oligonucleotides that have the base sequence, pattern of backbone linkages, and pattern of backbone phosphorus modifications of the particular oligonucleotide type are oligonucleotides of the particular oligonucleotide type. 
     
     
         36 . A method for altering splicing of a target transcript, comprising administering an oligonucleotide composition, wherein the oligonucleotide composition comprises a first plurality of oligonucleotides of a particular oligonucleotide type defined by:
 1) base sequence;   2) pattern of backbone linkages;   3) pattern of backbone chiral centers; and   4) pattern of backbone phosphorus modifications,   
       which composition is chirally controlled in that it is enriched, relative to a substantially racemic preparation of oligonucleotides having the same base sequence, for oligonucleotides of the particular oligonucleotide type,
 wherein oligonucleotides of the particular oligonucleotide type each comprise: 
 1) a 5′-end region comprising 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleoside units comprising a 2′-F modified sugar moiety; 
 2) a 3′-end region comprising 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleoside units comprising a 2′-F modified sugar moiety; and 
 3) a middle region between the 5′-end region and the 3′-end region, wherein the middle region comprises one or more Rp internucleotidic linkages. 
 
     
     
         37 . The method of  claim 36 , wherein the splicing of the target transcript is altered relative to absence of the composition. 
     
     
         38 . The method of  claim 37 , wherein the target transcript is pre-mRNA of dystrophin, and wherein the alteration is that one or more exon is skipped at an increased level relative to absence of the composition. 
     
     
         39 . The method of  claim 38 , wherein exon 51 of dystrophin is skipped at an increased level relative to absence of the composition. 
     
     
         40 . (canceled) 
     
     
         41 . A method for treating Duchenne muscular dystrophy, comprising administering to a subject susceptible thereto or suffering therefrom an oligonucleotide composition, wherein the oligonucleotide composition comprises a first plurality of oligonucleotides of a particular oligonucleotide type defined by:
 1) base sequence;   2) pattern of backbone linkages;   3) pattern of backbone chiral centers; and   4) pattern of backbone phosphorus modifications,   
       which composition is chirally controlled in that it is enriched, relative to a substantially racemic preparation of oligonucleotides having the same base sequence, for oligonucleotides of the particular oligonucleotide type,
 wherein oligonucleotides of the particular oligonucleotide type each comprise: 
 1) a 5′-end region comprising 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleoside units comprising a 2′-F modified sugar moiety; 
 2) a 3′-end region comprising 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more nucleoside units comprising a 2′-F modified sugar moiety; and 
 3) a middle region between the 5′-end region and the 3′-end region, wherein the middle region comprises one or more Rp internucleotidic linkages. 
 
     
     
         42 . The method of  claim 41 , wherein the oligonucleotides of the particular oligonucleotide type are capable of mediating the skipping of exon 51 of the dystrophin gene, wherein a product of the skipping of exon 51 is a mRNA that encodes a dystrophin protein that has an improved function compared to that encoded by a mRNA without the skipping of exon 51.