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:
 the oligonucleotide composition being 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, and a desired splicing product is increased by 2 fold or more relative to that observed under reference conditions. 
 
     
     
         2 . The composition of  claim 1 , wherein the reference condition is absence of the composition, and the pattern of backbone chiral centers comprises at least two chirally controlled centers independently selected from Rp and Sp. 
     
     
         3 . The composition of  claim 2 , wherein the pattern of backbone linkages comprises one or more backbone linkages selected from phosphodiester, phosphorothioate and phosphodithioate linkages. 
     
     
         4 . The composition of  claim 3 , wherein oligonucleotides of the particular oligonucleotide type each further comprise one or more sugar modifications. 
     
     
         5 . The composition of  claim 4 , wherein the sugar modifications comprise one or more modifications selected from: 2′-O-methyl, 2′-MOE, 2′-F, morpholino and bicyclic sugar moieties. 
     
     
         6 . The composition of  claim 5 , wherein the sugar modifications comprise one or more 2′-F sugar moieties. 
     
     
         7 . The composition of  claim 5 , wherein the sugar modifications comprise one or more 2′-O-methyl sugar moieties. 
     
     
         8 - 11 . (canceled) 
     
     
         12 . The composition of  claim 2 , wherein the base sequence comprises a sequence having no more than 5 mismatches from a 20 base long portion of the dystrophin gene or its complement, the length is no more than 50 bases, the pattern of backbone chiral centers comprises at least three chirally controlled centers independently of Rp or Sp, and the oligonucleotides of the particular oligonucleotide type are capable of mediating the skipping of an exon of the dystrophin gene. 
     
     
         13 . The composition of  claim 12 , wherein the oligonucleotides of the particular oligonucleotide type are capable of mediating the skipping of exon 51 of the dystrophin gene. 
     
     
         14 . The composition of  claim 13 , wherein the exon 51 is mutated and can cause a frameshift, premature stop codon and/or deletion of one or more downstream exons. 
     
     
         15 . The composition of  claim 14 , wherein the desired product is a mRNA that does not include exon 51 of the dystrophin gene and that encodes a dystrophin protein that has an improved function compared to that encoded by a mRNA product without exon 51 skipping. 
     
     
         16 . The composition of  claim 4 , wherein oligonucleotide of the first plurality each comprises 15 or more bases. 
     
     
         17 . (canceled) 
     
     
         18 . The composition of  claim 16 , wherein each chiral internucleotidic linkage in oligonucleotides of the particular type is independently a phosphorothioate diester linkage. 
     
     
         19 - 33 . (canceled) 
     
     
         34 . The composition of  claim 18 , 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 18 , 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 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:   the oligonucleotide composition being characterized in that, when it is contacted with the target 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, and a desired splicing product is increased by 2 fold or more relative to that observed under reference conditions.   
     
     
         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 - 41 . (canceled) 
     
     
         42 . A method for treating Duchenne muscular dystrophy, comprising administering to a subject susceptible thereto or suffering therefrom a composition of  claim 18 .