OLIGONUCLEOTIDE COMPOSITIONS AND METHODS THEREOF
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 up-take. 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 oligonucleotides of the first plurality comprise one or more natural phosphate linkages.
2 . A composition of claim 1 , wherein the oligonucleotides comprise one or more wing regions and a core region, wherein:
oligonucleotides of the first plurality have the same base sequence;
each wing independently has a length of two or more bases, and independently comprises one or more modified internucleotidic linkages and optionally one or more natural phosphate linkages; and
the core region independently has a length of two or more bases and independently comprises one or more modified internucleotidic linkages.
3 . A composition of claim 2 , wherein a wing has one or more natural phosphate linkages.
4 . A composition of claim 1 , wherein the first plurality of oligonucleotides comprises at least about 50% of the oligonucleotides in the composition.
5 . A composition of claim 1 , wherein oligonucleotides of the particular oligonucleotide type have a common pattern of base modification and pattern of sugar modification.
6 . A composition of claim 1 , wherein the level of the first plurality of oligonucleotides is pre-determined.
7 . A composition of claim 2 , wherein each internucleotidic linkage within a wing is a natural phosphate linkage.
8 . A composition of claim 2 , wherein each wing independently has a length of three or more bases.
9 . A composition of claim 8 , wherein the core region has a length of five or more bases.
10 . A composition of claim 9 , wherein the core region has a pattern of backbone chiral centers comprising (Np)t(Rp)n(Sp)m, wherein t is 1-10, n is 1-10, m is 1-50, and each Np is independent Rp or Sp.
11 . A composition of claim 10 , wherein 50% or more of the chiral internucleotidic linkages in the core region have Sp configuration.
12 . A composition of claim 11 , wherein each internucleotidic linkage in the core region is chiral, the core region has only one Rp, and each of the other internucleotidic linkages in the core region is Sp.
13 . A composition of any one of claims 1 - 12 , which composition displays reduced toxicity as compared with a reference composition comprising a plurality of oligonucleotides, each of which also has the common base sequence but which differs structurally from the oligonucleotides of the first plurality in that:
individual oligonucleotides within the reference plurality differ from one another in stereochemical structure; and/or
at least some oligonucleotides within the reference plurality have a structure different from a structure represented by the plurality of oligonucleotides of the composition; and/or
at least some oligonucleotides within the reference plurality do not comprise a wing region and a core region.
14 . A composition of any one of claims 1 - 12 , which composition displays reduced complement activation as compared with a reference composition comprising a plurality of oligonucleotides, each of which also has the common base sequence but which differs structurally from the oligonucleotides of the first plurality in that:
individual oligonucleotides within the reference plurality differ from one another in stereochemical structure; and/or
at least some oligonucleotides within the reference plurality have a structure different from a structure represented by the plurality of oligonucleotides of the composition; and/or
at least some oligonucleotides within the reference plurality do not comprise a wing region and a core region.
15 . A composition of claim 14 , wherein the reduced complement activation is observed in an assay that detects presence, absolute level and or relative levels of one or more complete-activation related product selected from the group consisting of C3a, Bb, C4a, C5a, C5b, C6, C7, C8 and C9.
16 . A composition of any one of claims 1 - 12 , which composition displays reduced injection site inflammation as compared with a reference composition comprising a plurality of oligonucleotides, each of which also has the common base sequence but which differs structurally from the oligonucleotides of the first plurality in that:
individual oligonucleotides within the reference plurality differ from one another in stereochemical structure; and/or
at least some oligonucleotides within the reference plurality have a structure different from a structure represented by the plurality of oligonucleotides of the composition; and/or
at least some oligonucleotides within the reference plurality do not comprise a wing region and a core region.
17 . A composition of any one of claims 1 - 12 , which composition displays altered protein binding as compared with a reference composition comprising a plurality of oligonucleotides, each of which also has the common base sequence but which differs structurally from the oligonucleotides of the first plurality in that:
individual oligonucleotides within the reference plurality differ from one another in stereochemical structure; and/or
at least some oligonucleotides within the reference plurality have a structure different from a structure represented by the plurality of oligonucleotides of the composition; and/or
at least some oligonucleotides within the reference plurality do not comprise a wing region and a core region.
18 . A composition of claim 17 , wherein the composition displays altered binding as compared with a reference composition to one or more proteins selected from serum proteins, heparin sulfate-binding proteins, and intracellular proteins.
19 . A composition of claim 17 , wherein the increased protein binding is observed in a BSA binding assay, wherein the first plurality of oligonucleotides have increased BSA binding that the reference plurality.
20 . A composition of any one of claims 1 - 12 , which the composition displays improved oligonucleotide delivery as compared with a reference composition comprising a plurality of oligonucleotides, each of which also has the common base sequence but which differs structurally from the oligonucleotides of the first plurality in that:
individual oligonucleotides within the reference plurality differ from one another in stereochemical structure; and/or
at least some oligonucleotides within the reference plurality have a structure different from a structure represented by the plurality of oligonucleotides of the composition; and/or
at least some oligonucleotides within the reference plurality do not comprise a wing region and a core region.
21 . A composition of any one of the preceding claims, comprising one or more lipids.
22 . A composition of any one of the preceding claims, comprising one or more targeting components.
23 . A method of administering an oligonucleotide composition comprising a first plurality of oligonucleotides having a common nucleotide sequence, comprising:
administering an oligonucleotide composition comprising the first plurality of oligonucleotides that is characterized by reduced toxicity relative to a reference oligonucleotide composition comprising a reference plurality of oligonucleotides of the same common nucleotide sequence.
24 . A method of administering an oligonucleotide composition comprising a first plurality of oligonucleotides having a common nucleotide sequence, comprising:
administering an oligonucleotide composition comprising the first plurality of oligonucleotides that is characterized by reduced complement activation relative to a reference oligonucleotide composition comprising a reference plurality of oligonucleotides of the same common nucleotide sequence.
25 . A method of administering an oligonucleotide composition comprising a first plurality of oligonucleotides having a common nucleotide sequence, comprising:
administering an oligonucleotide composition comprising the first plurality of oligonucleotides that is characterized by altered protein binding relative to a reference oligonucleotide composition comprising a reference plurality of oligonucleotides of the same common nucleotide sequence.
26 . The method of claim 25 , wherein the altered protein binding comprises improved binding to albumin.
27 . A method of administering an oligonucleotide composition comprising a first plurality of oligonucleotides having a common nucleotide sequence, comprising:
administering an oligonucleotide composition comprising the first plurality of oligonucleotides that is characterized by reduced injection site inflammation relative to a reference oligonucleotide composition comprising a reference plurality of oligonucleotides of the same common nucleotide sequence.
28 . The method of any one of claims 23 - 27 , wherein the first plurality of oligonucleotides have fewer sugar modifications than the reference plurality of oligonucleotides.
29 . The method of any one of claims 23 - 27 , wherein the first plurality of oligonucleotides, which comprise one or more modified internucleotidic linkages, have more natural phosphate linkages than the reference plurality of oligonucleotides.
30 . The method of claim 29 , wherein the oligonucleotide composition of the first plurality is chirally controlled, and the reference oligonucleotide composition of the reference plurality is not chirally controlled.
31 . The method of any one of claims 23 - 27 , wherein 1) the first plurality of oligonucleotides and the reference plurality of oligonucleotides have the same pattern of backbone linkages; 2) the oligonucleotide composition of the first plurality is chirally controlled; and 3) the reference oligonucleotide composition of the reference plurality is not chirally controlled.
32 . The method of claim 31 , wherein the first plurality of oligonucleotides and the reference plurality of oligonucleotides have the same pattern of modifications to bases, sugars, and internucleotidic linkages.
33 . The method of any one of claims 23 - 32 , wherein the composition of the first plurality of oligonucleotides is a composition of any one of claims 1 - 22 .
34 . A composition or method of any one of embodiments 1-322.