Oligonucleotide compositions and methods thereof
Oligonucleotides edit the I148M codon in PNPLA3 to V, addressing the toxicity and lipid accumulation issues of existing PNPLA3 knockdown technologies by enhancing polypeptide activity and stability, providing a more effective treatment for PNPLA3-related conditions.
Patent Information
- Application Number
- PCT/US2025/023326
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2025-03-12
- Filing Date
- 2025-04-04
- Publication Date
- 2025-10-09
AI Technical Summary
Existing technologies for knocking down or knocking out PNPLA3, particularly targeting the I148M mutation, often result in increased steatosis and lipid accumulation, and susceptibility to toxicity, such as ethanol and methotrexate toxicity, especially in homozygous and heterozygous genotypes.
Development of oligonucleotides that edit the I148M codon in PNPLA3 to a codon for V through base editing, utilizing A to I RNA editing and specific sugar and nucleobase modifications, enhancing the activity and stability of PNPLA3 polypeptides.
The oligonucleotides effectively convert A to I in PNPLA3 transcripts, resulting in improved lipase activity and reduced toxicity, offering a more effective treatment for conditions associated with PNPLA3 mutations.
Smart Images

Figure IMGF000007_0001 
Figure IMGF000013_0001 
Figure IMGF000013_0002
Abstract
Description
Attorney Docket No.: 2010581-1488 OLIGONUCLEOTIDE COMPOSITIONS AND METHODS THEREOF CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority to United States Provisional Application Nos. 63 / 575,619, filed on April 5, 2024, 63 / 714,113, filed on October 30, 2024, and 63 / 770,940, filed on March 12, 2025, the entirety of each of which is incorporated herein by reference. BACKGROUND
[0002] Oligonucleotides are useful in various applications, e.g., therapeutic, diagnostic, and / or research applications. For example, oligonucleotides targeting various genes can be useful for treatment of conditions, disorders or diseases related to such target genes, e.g., PNPLA3. SUMMARY
[0003] Many conditions, diseases or disorders are associated with PNPLA3 and / or mutations thereof. For example, various conditions, diseases or disorders are associated with I148M PNPLA3 mutation. Homozygous individuals with I148M PNPLA3 mutation can have higher risks of various conditions, diseases or disorders, and in some cases, of early death caused by liver conditions, diseases or disorders. Technologies have been developed to knockdown or knockout PNPLA3, in some cases, targeting both wild-type and mutant PNPLA3, and in some cases, selectively targeting mutant PNPLA3.
[0004] Among other things, the present disclosure encompasses the recognition that reported PNPLA3 knockdown or knockout technologies can suffer from various shortcomings. For example, in some embodiments, PNPLA3 knockdown or knockout can be worse than PNPLA3-I148M homozygous and / or heterozygous genotypes, e.g., in view of increased steatosis, increased lipid accumulation, and / or increased susceptibility to toxicity (e.g., to ethanol and / or methotrexate toxicity). Among other things, the present disclosure provides the insight that conversion of I148M PNPLA3 to I148V PNPLA3, e.g., through base editing of A·T to G·C in DNA (e.g., genomic DNA), through A to I RNA editing, etc., can provide PNPLA3 polypeptides with improved properties and / or activities, and can are useful for various applications including for treating various conditions, diseases or disorders.
[0005] Various technologies can be utilized in accordance with the present disclosure to edit an A in a codon for I148M in PNPLA3 to a codon for V. In some embodiments, a technology edits DNA. In some embodiments, a technology edits genomic DNA. In some embodiments, a technology edits an A genomic DNA. In some embodiments, a technology edits a transcript, e.g., a PNPLA3 RNA.
[0006] For example, in some embodiments, the present disclosure provides oligonucleotides that can edit the I148M codon in a PNPLA3 transcript to a codon for V. In some embodiments, the present disclosure provides PNPLA3 oligonucleotides and compositions thereof that have significantly improved properties and / or high activities. Among other things, the present disclosure provides technologies for designing, Page 1 of 743 12621738v1Attorney Docket No.: 2010581-1488 preparing, and utilizing such oligonucleotides and compositions. Particularly, in some embodiments, the present disclosure provides oligonucleotides comprising useful patterns of internucleotidic linkages and / or patterns of sugar modifications, which, when combined with one or more other structural elements, e.g., base sequence (or portion thereof), nucleobase modifications (and patterns thereof), additional chemical moieties, etc., can provide PNPLA3 oligonucleotides and compositions thereof with high activities and / or desired properties, including, but not limited to, effective and efficient site-directed editing of a PNPLA3 transcript. In some embodiments, PNPLA3 oligonucleotides and compositions modify one or more A residues, such as through conversion of A to I. In some embodiments, PNPLA3 oligonucleotides and compositions modify an A residue (e.g., converting an A to an I) in a PNPLA3 transcript, producing an alternative amino acid residue in PNPLA3 transcript.
[0007] In some embodiments, the present disclosure provides PNPLA3 nucleic acid sequences (e.g., RNA) comprising an A to I variation (e.g., at a target adenosine), wherein I is read as G during translation. In some embodiments, PNPLA3 nucleic acid sequences comprise an A to I variation that is read as a G, wherein G form encodes one or more proteins with higher desired activities and / or one or more better desired properties compared to those encoded by the corresponding A form. In some embodiments, a target adenosine is located at a position in a PNPLA3 nucleic acid that encodes for a methionine (e.g., corresponding to position 148 of SEQ ID NO: 2). In some embodiments, a target adenosine is located at a position in a PNPLA3 nucleic acid that encodes for an isoleucine (e.g., corresponding to position 148 of SEQ ID NO: 2). In some embodiments, a G form of a PNPLA3 nucleic acid sequence encodes for a valine (e.g., corresponding to position 148 of SEQ ID NO: 2). In some embodiments, a PNPLA3 nucleic acid sequence is GCUUCIUSCCUUUCUAC, wherein S is either G or C and each U can be optionally and independently replaced with T. In some embodiments, a PNPLA3 nucleic acid sequence has about or at least about 10%, 20%, 30%, 40%, or 50% sequence identity to GCUUCGUGCCUUUCUACAGUGGCCUUAUCC, wherein each U can be optionally and independently replaced with T. In some embodiments, a PNPLA3 nucleic acid sequence has about or at least about 10%, 20%, 30%, 40%, or 50% sequence identity to GCUUCGUCCCCUUCUACAGUGGCCUUAUCC, wherein each U can be optionally and independently replaced with T. In some embodiments, a PNPLA3 nucleic acid sequence is codon optimized for expression in a cell.. In some embodiments, a cell is a mammalian cell. In some embodiments, a cell is a human cell.
[0008] In some embodiments, a PNPLA3 nucleic acid sequence encodes VDALVCSCFVPF. In some embodiments, a PNPLA3 nucleic acid sequence comprises an amino acid sequence with about or at least about 10%, 20%, 30%, 40%, or 50% sequence identity to VDALVCSCFVPF. In some embodiments, a PNPLA3 nucleic acid sequence comprises an amino acid sequence with about or at least about 10%, 20%, 30%, 40%, or 50% sequence homology to VDALVCSCFVPF.
[0009] In some embodiments, the present disclosure provides PNPLA3 polypeptide sequences comprising a valine at a position corresponding to position 148 of SEQ ID NO: 2. In some embodiments, a PNPLA3 polypeptide comprises SEQ ID NO:2 or a characteristic portion thereof. In some embodiments, a Page 2 of 743 12621738v1Attorney Docket No.: 2010581-1488 PNPLA3 polypeptide is a characteristic portion of SEQ ID NO: 2 comprising V148. In some embodiments, a polypeptide comprises a characteristic portion of SEQ ID NO: 2, which characteristic portion comprises V148. In some embodiments, a characteristic portion can differentiate a PNPLA3 polypeptide from another polypeptide. In some embodiments, a characteristic portion can differentiate SEQ ID NO: 2 from another polypeptide. In some embodiments, a characteristic portion can differentiate SEQ ID NO: 2 from another polypeptide encoded by another gene. In some embodiments, a characteristic portion can differentiate SEQ ID NO: 2 from another polypeptide encoded by all other genes. In some embodiments, a polypeptide can provide one or more functions of a wild-type PNPLA3 polypeptide. In some embodiments, a polypeptide can provide high levels of functions, e.g., of a wild-type PNPLA3 polypeptide, compared to a reference polypeptide. In some embodiments, a reference polypeptide has M148 instead of V148 but is otherwise identical.
[0010] In some embodiments, the present disclosure provides cells comprising one or more PNPLA3 nucleic acids or polypeptides disclosed herein. In some embodiments, cells comprise a PNPLA3 nucleic acid comprising a sequence of GCTTCATGCCTTTCTACAGTGGCCTTATCC. In some embodiments, cells further comprise a PNPLA3 nucleic acid comprising a sequence of GCTTCATCCCCTTCTACAGTGGCCTTATCC. In transcripts (e.g., mRNA), T is typically U. In some embodiments, cells comprise a PNPLA3 nucleic acid comprising a sequence of GCUUCAUCCCCUUCUACAGUGGCCUUAUCC. In some embodiments, cells further comprise GCUUCAUGCCUUUCUACAGUGGCCUUAUCC. In some embodiments, cells further comprise a PNPLA3 polypeptide comprising a I148M variation, wherein position 148 is or corresponds to position 148 of SEQ ID NO: 2. In some embodiments, cells comprise a PNPLA3 polypeptide comprising an amino acid sequence of VDALVCSCFMPF. In some embodiments, a cell is a human cell.
[0011] In some embodiments, the present disclosure provides methods for increasing lipase activity of a PNPLA3 polypeptide or characteristic portion thereof, comprising modifying an amino acid residue at a position that is or correspond to position 148 of SEQ ID NO: 2. In some embodiments, methods comprise modification of a methionine. In some embodiments, methods comprise modification of an isoleucine. In some embodiments, increased lipase activity is about or at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 fold of that without a modification. In some embodiments, lipase activity is increased as compared to that of a PNPLA3 polypeptide comprising M148, wherein position 148 is or corresponds to position 148 of SEQ ID NO: 2. In some embodiments, lipase activity is increased as compared to that of a PNPLA3 polypeptide comprising I148, wherein position 148 is or corresponds to position 148 of SEQ ID NO: 2.
[0012] In some embodiments, the present disclosure provides oligonucleotides capable of editing a target adenosine in a nucleic acid encoding a PNPLA3 polypeptide to produce a PNPLA3 polypeptide variant that differs by at least one amino acid residue. In some embodiments, a target adenosine is at a position within a PNPLA3 nucleic acid corresponding to a codon encoding for an amino acid at position 148 of SEQ ID NO: 1 Page 3 of 743 12621738v1Attorney Docket No.: 2010581-1488 or 2. In some embodiments, an amino acid at position 148 is methionine. In some embodiments, an amino acid at position 148 is isoleucine.
[0013] In some embodiments, the present disclosure provides oligonucleotides capable of hybridizing to a target sequence comprising GCUUCAUSCCUUUCUAC, wherein S is either G or C. In some embodiments, oligonucleotides are capable of hybridizing to a target sequence comprising GCUUCAUGCCUUUCUAC. In some embodiments, oligonucleotides are capable of hybridizing to a target sequence comprising GCUUCAUCCCUUUCUAC. In some embodiments, a target sequence is a PNPLA3 transcript.
[0014] In some embodiments, the present disclosure provides oligonucleotides comprising a base sequence comprising at least 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 contiguous bases of a base sequence that is identical with or complementary to a base sequence of a PNPLA3 gene or a transcript thereof, wherein the oligonucleotide comprises one or more modified sugars, one or more modified nucleobases, and / or one or more modified internucleotidic linkages. In some embodiments, a base sequence of the oligonucleotide sequence comprises at least 17, 18, 19, 20, 21, 22, 23, 24, or 25 contiguous bases of a base sequence that is complementary to a PNPLA3 transcript. In some embodiments, a base sequence comprises at least 17, 18, 19, 20, 21, 22, 23, 24, or 25 contiguous bases of a base sequence that is complementary to a PNPLA3 mRNA. In some embodiments, oligonucleotides comprise a base sequence comprising at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 contiguous bases of GGAUAAGGCCACUGUAGAAGGGGAUGAAGC, GGGACACGGUGAUGGAGAAGGGCAUGAAGC, AUAAGGCCACUGUAGAAGGGGAUGAAGCAG, GGGAUAAGGCCACUGAGAAGGGGAUGAAGC, AGGGAUAAGGCCACUAGAAGGGGAUGAAGC, AGGAGGGAUAAGGCCAGAAGGGGAUGAAGC, GGAUAAGGCCACUGUAGAAGGGCAUGAAGC, GAUAAGGCCACUGUAGAAGGGCAUGAAGCA, AUAAGGCCACUGUAGAAGGGCAUGAAGCAG, GGGAUAAGGCCACUGAGAAGGGCAUGAAGC, AGGGAUAAGGCCACUAGAAGGGCAUGAAGC, AGGAGGGAUAAGGCCAGAAGGGCAUGAAGC, GGAUAAGGCCACUGUAGAAAGGCAUGAAGC, GAUAAGGCCACUGUAGAAAGGCAUGAAGCA, GAUAACGCCACUGUAGAAAGCCAUGAAGCA, GAUAACGCCTCUGUAGAAAGCCAUGAAGCA, GAUAACGCCACUGUAGAAAGCCAUGAAGCA, GAUAACGCCTCUGUAGAAAGCCAUGAAGCA, AUAAGGCCACUGUAGAAAGGCAUGAAGCAG, UAAGGCCACUGUAGAAAGGCAUGAAGCAGG, AAGGCCACUGUAGAAAGGCAUGAAGCAGGA, GGAUAAGGCCACUGUAGAAAGCCAUGAAGC, GGAUAAGGCCACUGUAGAAACGCAUGAAGC, GGAUAAGGCCACUGUAGAAUGGCAUGAAGC, GGAUAAGGCCACUGUAGAUAGGCAUGAAGC, GGAUAAGGCCACUGUAGUAAGGCAUGAAGC, GGAUAAGGCCACUGUACAAAGGCAUGAAGC, GGAUAAGGCCACUGUUGAAAGGCAUGAAGC, GGAUAAGGCCACUGUAGAAAGGCGUGAAGC, GGAUAAGGCCACUGUAGAGAGGCAUGAAGC, GGAUAAGGCCACUGUAGGAAGGCAUGAAGC, GGAUAAGGCCACUGUGGAAAGGCAUGAAGC, GGAUAAGGCCACUGUAGGGAGGCAUGAAGC, GGAUAAGGCCACUGUGGGGAGGCAUGAAGC, GGAUAAGGCCACUGUAGAAAGGUAUGAAGC, GGAUAAGGCCACUGUAGAAGGGUAUGAAGC, GGAUAAGGCCACUGUGGAAAGGUAUGAAGC, Page 4 of 743 12621738v1Attorney Docket No.: 2010581-1488 GGGAUAAGGCCACUGUAGAAAGGCAUGAAGCA, or GGAUAAGGCCACUGUAGAAAGGCAUGAAGCAG, wherein each T can be independently replaced with U and vice versa.
[0015] Among other things, the present disclosure provides designed oligonucleotides and compositions thereof which oligonucleotides comprise modifications (e.g., modifications to nucleobases sugars, and / or internucleotidic linkages, and patterns thereof) as described herein. In some embodiments, technologies (compounds (e.g., oligonucleotides), compositions, methods, etc.) of the present disclosure (e.g., oligonucleotides, oligonucleotide compositions, methods, etc.) are particularly useful for editing nucleic acids, e.g., site-directed editing in nucleic acids (e.g., editing of target adenosine). In some embodiments, as demonstrated herein, provided technologies can significantly improve efficiency of nucleic acid editing, e.g., modification of one or more A residues, such as conversion of A to I. In some embodiments, the present disclosure provides technologies for editing (e.g., for modifying an A residue, e.g., converting an A to I) in an RNA. In some embodiments, the present disclosure provides technologies for editing (e.g., for modifying an A residue, e.g., converting an A to an I) in a transcript, e.g., mRNA. Among other things, provided technologies provide the benefits of utilization of endogenous proteins such as ADAR (Adenosine Deaminases Acting on RNA) proteins (e.g., ADAR1 and / or ADAR2), for editing nucleic acids, e.g., for modifying an A. Those skilled in the art will appreciates that such utilization of endogenous proteins can avoid a number of challenges and / or provide various benefits compared to those technologies that require the delivery of exogenous components (e.g., proteins (e.g., those engineered to bind to oligonucleotides (and / or duplexes thereof with target nucleic acids) to provide desired activities), nucleic acids encoding proteins, viruses, etc.).
[0016] Particularly, in some embodiments, oligonucleotides of provided technologies comprise useful sugar modifications and / or patterns thereof (e.g., presence and / or absence of certain modifications), nucleobase modifications and / or patterns thereof (e.g., presence and / or absence of certain modifications), internucleotidic linkages modifications and / or stereochemistry and / or patterns thereof [e.g., types, modifications, and / or configuration (Rp or Sp) of chiral linkage phosphorus, etc.], etc., which, when combined with one or more other structural elements described herein (e.g., additional chemical moieties) can provide high activities and / or various desired properties, e.g., high efficiency of nucleic acid editing, high selectivity, high stability, high cellular uptake, low immune stimulation, low toxicity, improved distribution, improved affinity, etc. In some embodiments, provided oligonucleotides provide high stability, e.g., when compared to oligonucleotides having a high percentage of natural RNA sugars utilized for adenosine editing. In some embodiments, provided oligonucleotides provide high activities, e.g., adenosine editing activity. In some embodiments, provided oligonucleotides provide high selectivity, for example, in some embodiments, provided oligonucleotides provide selective modification of a target adenosine in a target nucleic acid over other adenosine in the same target nucleic acid (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 fold or more modification at the target adenosine than another adenosine, or all other adenosine, in a target nucleic acid). Page 5 of 743 12621738v1Attorney Docket No.: 2010581-1488
[0017] Among other things, the present disclosure provides designed oligonucleotides and compositions of improved properties and / or activities compared to reference oligonucleotides and compositions (e.g., those described herein or reported in the art). For example, in some embodiments, as demonstrated herein provided oligonucleotide and compositions can provide improved stability, pharmacokinetic properties, pharmacodynamic properties and / or improved activities (e.g., for A-to-I editing). Various designed oligonucleotides and compositions are described herein. For example, in some embodiments, the present disclosure provides oligonucleotides and compositions thereof, including chirally controlled oligonucleotide compositions thereof, wherein the oligonucleotides comprise several (e.g., 1, 2, 3, 4, or 5 or more; in some embodiments, 3 or more) nucleosides independently comprising sugar modifications (e.g., 2’-OR modifications wherein R is optionally substituted C1-6alkyl (e.g., 2’-OMe, 2’-MOE, etc.,), bicyclic sugars (e.g., LNA sugars, cEt sugars, etc.)) at their 5’- and 3’-ends. In some embodiments, the first several (e.g., 1, 2, 3, 4, or 5 or more; in some embodiments, 3 or more) nucleosides and / or the last several (e.g., 1, 2, 3, 4, or 5 or more; in some embodiments, 3 or more) nucleosides independently comprise sugar modifications. In some embodiments, the first 3 or more and the last 3 or more nucleosides independently comprise sugar modifications. In some embodiments, one or more internucleotidic linkages bonded to such nucleosides are non-negatively charged internucleotidic linkage such as phosphoryl guanidine internucleotidic linkages like n001. In some embodiments, both the first and the last internucleotidic linkages are independently non- negatively charged internucleotidic linkages. In some embodiments, both the first and the last internucleotidic linkages are independently phosphoryl guanidine internucleotidic linkages. In some embodiments, both the first and the last internucleotidic linkages are independently n001. In some embodiments, they are both chirally controlled and are Rp. In some embodiments, an oligonucleotide comprises a nucleoside N0which comprises a natural DNA sugar (two 2’-H), a natural RNA sugar or a 2’-F modified sugar. In some embodiments, N0is a nucleoside opposite to a target adenosine when an oligonucleotide is utilized for adenosine editing. In some embodiments, sugar of N0is a natural DNA sugar. In some embodiments, sugar of N1(“+” or nothing before a number indicates counting toward the 5’-direction (5’ …N1N0N-1… 3’)) is a 2’-Fmdified sugar, a natural DNA sugar, or a natural RNA sugar. In some embodiments, sugar of N1is a DNA sugar. In some embodiments, sugar of N-1(“-” indicates counting toward the 3’-direction (5’ …N1N0N-1… 3’)) is a 2’-F modified sugar, a natural DNA sugar, or a natural RNA sugar. In some embodiments, sugar of N-1is a DNA sugar. In some embodiments, sugar of N-3is a 2’-F modified sugar. In some embodiments, between N2and their 5’-ends oligonucleotides comprise multiple 2’-F modified sugars and multiple 2’-modified sugars (e.g., 2’-OR modified sugars wherein R is optionally substituted C1-6alkyl, bicyclic sugars such as LNA sugars, cEt sugars, etc.). In some embodiments, oligonucleotides comprise one or more (e.g., 1-20, 1-15, 1-10, 2-15, 2- 10, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more) 2’-F blocks and one or more (e.g., 1-20, 1-15, 1-10, 2-15, 2-10, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more) separating blocks from N2to their 5’-ends (e.g., first domains and first subdomains of second domains combined when first subdomains end with and include N2), wherein each nucleoside in a 2’-F block Page 6 of 743 12621738v1Attorney Docket No.: 2010581-1488 independently comprises a 2’-F modification, each nucleoside in a separating block independently comprises no 2’-F modification, and each block independently comprises one or more (e.g., 1-20, 1-15, 1-10, 2-15, 2-10, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more) nucleosides. In some embodiments, there are two or more such 2’-F blocks and two or more such separating blocks. In some embodiments, one or more or all such separating blocks are independently bonded to two 2’-F blocks. In some embodiments, each nucleoside in one or more or all separating blocks independently comprise a 2’-OR modification wherein R is optionally substituted C1-6alkyl or is a bicyclic sugar such as a LNA sugar, a cEt sugar, etc. In some embodiments, each nucleoside in one or more or all separating blocks independently comprise a 2’-OR modification wherein R is optionally substituted C1-6alkyl. In some embodiments, each nucleoside in one or more or all separating blocks independently comprise a 2’-OMe or 2’-MOE modification. In some embodiments, each of such 2’-F and separating blocks independently comprises 1, 2, 3, 4 or 5 nucleosides. In some embodiments, nucleosides close to N0, e.g., N2, N1, N0, N-1, N-2, etc., do not contain large 2’-modificatoins such as 2’-MOE. In some embodiments, sugars of N2, N1, N0, N-1, and N-2are independently natural DNA sugar, 2’-F modified sugar, or 2’-OMe modified sugar. In some embodiments, sugars of N1, N0, N-1are each a natural DNA sugar. In some embodiments, each chiral internucleotidic linkage is independently chirally controlled.
[0018] In some embodiments, the present disclosure provides an oligonucleotide comprising a first domain and a second domain, wherein the first domain comprises one or more 2’-F modifications, and the second domain comprises one or more sugars that do not have a 2’-F modification. In some embodiments, an oligonucleotide comprises a modified nucleobase, nucleoside, sugar or internucleotidic linkage as described in the present disclosure. In some embodiments, about or at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% of all sugars in an oligonucleotide are 2’-F modified sugars.
[0019] In some embodiments, a second domain comprises or consists of a first subdomain, a second subdomain and / or a third subdomain as described herein. In some embodiments, an oligonucleotide comprises a second subdomain.
[0020] In some embodiments, the present disclosure provides an oligonucleotide comprising one or more modified sugars and / or one or more modified internucleotidic linkages, wherein the oligonucleotide comprises a first domain and a second domain each independently comprising one or more nucleobases.
[0021] In some embodiments, when an oligonucleotide is contacted with a target PNPLA3 transcript comprising a target adenosine in a system, a target adenosine in the target PNPLA3 transcript is modified. In some embodiments, when an oligonucleotide is contacted with a target PNPLA3 transcript comprising a target adenosine in a system, level of the target PNPLA3 transcript is reduced compared to absence of the product or presence of a reference. In some embodiments, when an oligonucleotide is contacted with a target PNPLA3 transcript comprising a target adenosine in a system, level of a product of the target PNPLA3 transcript is altered compared to absence of the product or presence of a reference oligonucleotide. In some embodiments, a target PNPLA3 transcript is modified. In some embodiments, level of a product is increased, wherein the Page 7 of 743 12621738v1Attorney Docket No.: 2010581-1488 product is or is encoded by a PNPLA3 transcript which is otherwise identical to the target PNPLA3 transcript but the target adenosine is modified. In some embodiments, level of a product is increased, wherein the product is or is encoded by a PNPLA3 transcript which is otherwise identical to the target PNPLA3 transcript but the target adenosine is replaced with inosine. In some embodiments, level of a product is increased, wherein the product is or is encoded by a PNPLA3 transcript which is otherwise identical to the target PNPLA3 transcript but the adenine of the target adenosine is replaced with guanine. In some embodiments, a product is a protein. In some embodiments, a product is a PNPLA3 protein.
[0022] In some embodiments, a target adenosine is more associated with a condition, disorder or disease than a guanine at the same position. In some embodiments, an oligonucleotide is capable of forming a double- stranded complex with the target PNPLA3 transcript. In some embodiments, a target PNPLA3 transcript or a portion thereof is or comprises RNA. In some embodiments, a target adenosine is of an RNA. In some embodiments, a target adenosine is modified, and the modification is or comprises deamination of the target adenosine. In some embodiments, a target adenosine is modified and the modification is or comprises conversion of the target adenosine to an inosine. In some embodiments, a modification is promoted by an ADAR protein. In some embodiments, a system is an in vitro or ex vivo system comprising an ADAR protein. In some embodiments, a system is or comprises a cell that comprises or expresses an ADAR protein. In some embodiments, a system is a subject comprising a cell that comprises or expresses an ADAR protein. In some embodiments, a ADAR protein is ADAR1. In some embodiments, a ADAR protein is ADAR2.
[0023] In some embodiments, an oligonucleotide has a length of about 10-200 (e.g., about 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-120, 10-150, 20-30, 20-40, 20-50, 20-60, 20-70, 20-80, 20-90, 20-100, 20-120, 20-150, 20-200, 25-30, 25-40, 25-50, 25-60, 25-70, 25-80, 25-90, 25-100, 25-120, 25- 150, 25-200, 30-40, 30-50, 30-60, 30-70, 30-80, 30-90, 30-100, 30-120, 30-150, 30-200, 10, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, etc.) nucleobases. In some embodiments, a base sequence of an oligonucleotide is complementary to a base sequence of a portion of a target PNPLA3 transcript comprising the target adenosine with 0-10 (e.g., 0-1, 0-2, 0-3, 0-4, 0-5, 0-6, 0-7, 0-8, 0-9, 0-10, 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 2-3, 2-4, 2-5, 2-6, 2-7, 2-8, 2-9, 2-10, 3-4, 3-5, 3-6, 3-7, 3-8, 3-9, 3-10, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) mismatches which are not Watson-Crick base pairs. In some embodiments, one or more mismatches are independently a wobble base paring. In some embodiments, complementarity is about 50%-100% (e.g., about 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%- 95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%- 95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc.). In some embodiments, complementarity is about 90%-100% or about 95- 100%. In some embodiments, complementarity is 100%. In some embodiments, complementarity is 100% except at a nucleoside opposite to a target nucleoside (e.g., adenosine).
[0024] In some embodiments, an oligonucleotide can hybridize to a PNPLA3 transcript, wherein the Page 8 of 743 12621738v1Attorney Docket No.: 2010581-1488 portion the oligonucleotide hybridize to comprises a target adenosine. In some embodiments, an oligonucleotide can hybridize to a PNPLA3 transcript, wherein the portion the oligonucleotide hybridize to is, comprises, overlaps with, or is gcttcatccccttctacagtggccttatcc or gcttcatgcctttctacagtggccttatcc. In transcripts (e.g., mRNA) T is typically U. In some embodiments, an oligonucleotide can hybridize to a PNPLA3 transcript, wherein the portion the oligonucleotide hybridize to is, comprises, overlaps with, or is gcuucauccccuucuacaguggccuuaucc or gcuucaugccuuucuacaguggccuuaucc.
[0025] In some embodiments, an oligonucleotide consists of a first domain and a second domain. In some embodiments, a first domain has a length of about 2-50 (e.g., about 5, 6, 7, 8, 9, or 10 - about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, etc.) nucleobases. In some embodiments, a first domain has a length of about 10-25 nucleobases. In some embodiments, a first domain has a length of about 15 nucleobases. In some embodiments, a first domain comprises one or more (e.g., 1-10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) mismatches when the oligonucleotide is aligned with a target PNPLA3 transcript for complementarity. In some embodiments, a first domain comprises one or more (e.g., 1-10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) bulges when the oligonucleotide is aligned with a target PNPLA3 transcript for complementarity. In some embodiments, a first domain comprises one or more (e.g., 1-10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) wobble pairs when the oligonucleotide is aligned with a target PNPLA3 transcript for complementarity. In some embodiments, a first domain is fully complementary to a target PNPLA3 transcript. In some embodiments, a first domain comprises about 1-50 (e.g., about 5, 6, 7, 8, 9, or 10 − about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, etc., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, etc.) sugars with 2’-F modification. In some embodiments, about 5%-100% (e.g., about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%- 85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%- 95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc.) of sugars in a first domain independently comprise a 2’-F modification. In some embodiments, about 50%-100% (e.g., about 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%- 85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc.) of sugars in a first domain independently comprise a 2’-F modification. In some embodiments, about 30%-70% (e.g., about 30%-60%, 30%-50%, or about 30%, 40%, 50%, 60% or 70%) of sugars in a first domain independently comprise a 2’-F modification. In some embodiments, no more than about 1%-95% (e.g., no more than about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, etc.) of sugars in a first domain Page 9 of 743 12621738v1Attorney Docket No.: 2010581-1488 comprises 2’-OMe. In some embodiments, about 30%-70% (e.g., about 30%-60%, 30%-50%, or about 30%, 40%, 50%, 60% or 70%) of sugars in a first domain comprises 2’-OMe. In some embodiments, no more than about 50% of sugars in a first domain comprises 2’-OMe. In some embodiments, no more than about 1%-95% (e.g., no more than about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, etc.) of sugars in a first domain comprises 2’-OR, wherein R is optionally substituted C1-6aliphatic. In some embodiments, about 30%-70% (e.g., about 30%-60%, 30%-50%, or about 30%, 40%, 50%, 60% or 70%) of sugars in a first domain comprises 2’-OR, wherein R is optionally substituted C1-6aliphatic. In some embodiments, no more than about 50% of sugars in a first domain comprises 2’-OR, wherein R is optionally substituted C1-6aliphatic. In some embodiments, no more than about 1%-95% (e.g., no more than about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, etc.) of sugars in a first domain comprises 2’-OR. In some embodiments, about 30%- 70% (e.g., about 30%-60%, 30%-50%, or about 30%, 40%, 50%, 60% or 70%) of sugars in a first domain comprises 2’-OR, wherein R is not −H. In some embodiments, no more than about 50% of sugars in a first domain comprises 2’-OR. In some embodiments, a first domain comprises one or more (e.g., about 1-20, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, etc.) modified sugars comprising a 2’-OR modification, wherein R is optionally substituted C1-6aliphatic. In some embodiments, a first domain comprises one or more (e.g., about 1-20, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, etc.) modified sugars comprising a 2’-MOE modification. In some embodiments, a first domain comprises one or more (e.g., about 1-20, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, etc.) modified sugars comprising a 2’-OMe modification. In some embodiments, the first about 1-5, e.g., 1, 2, 3, 4, or 5 sugars from the 5’-end of a first domain is independently a 2’-OR modified sugar, wherein R is independently optionally substituted C1-6aliphatic. In some embodiments, the first about 1-5, e.g., 1, 2, 3, 4, or 5 sugars from the 5’-end of a first domain is independently a 2’-MOE modified sugar. In some embodiments, a first domain comprises a PS internucleotidic linkage and a PN internucleotidic linkage. In some embodiments, each internucleotidic linkage in a first domain is independently a PO internucleotidic linkage, a PS internucleotidic linkage or a PN internucleotidic linkage. In some embodiments, first domain comprises about 1-50 (e.g., about 5, 6, 7, 8, 9, or 10 − about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, etc., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, etc.) modified internucleotidic linkages. In some embodiments, about 5%- 100% (e.g., about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%- 100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%- 100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc.) of internucleotidic linkages in a first domain are modified internucleotidic linkages. In some embodiments, about 50%-100% (e.g., about 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%- Page 10 of 743 12621738v1Attorney Docket No.: 2010581-1488 95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%- 95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc.) of internucleotidic linkages in a first domain are modified internucleotidic linkages. In some embodiments, each modified internucleotidic linkage is independently a chiral internucleotidic linkage. In some embodiments, each modified internucleotidic linkage is independently a phosphorothioate internucleotidic linkage or a non-negatively charged internucleotidic linkage. In some embodiments, each modified internucleotidic linkages is independently a phosphorothioate internucleotidic linkage or a neutral internucleotidic linkage.
[0026] In some embodiments, a first domain comprises one or more phosphorothioate internucleotidic linkages. In some embodiments, a first domain comprises 1, 2, 3, 4, or 5 non-negatively charged internucleotidic linkages. In some embodiments, an internucleotidic linkage between the first and the second nucleosides of a first domain is a non-negatively charged internucleotidic linkage. In some embodiments, at least 5%-100% (e.g., about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%- 95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%- 95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc.) of chiral internucleotidic linkages in a first domain is Sp. In some embodiments, an internucleotidic linkage between the first and the second nucleosides of the first domain is Rp. In some embodiments, an internucleotidic linkage between the last and the second last nucleosides of the first domain is Rp. In some embodiments, each internucleotidic linkage in a first domain is independently a modified internucleotidic linkage. In some embodiments, a first domain can recruit, or promotes or contributes to recruitment of, an ADAR protein to a target PNPLA3 transcript.
[0027] In some embodiments, a second domain has a length of about 2-50 (e.g., about 5, 6, 7, 8, 9, or 10 - about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, etc.) nucleobases. In some embodiments, a second domain has a length of about 5-15 nucleobases. In some embodiments, a second domain comprises one or more (e.g., 1-10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) mismatches when the oligonucleotide is aligned with a target PNPLA3 transcript for complementarity. In some embodiments, a second domain comprises two or more mismatches when the oligonucleotide is aligned with a target PNPLA3 transcript for complementarity. In some embodiments, a second domain comprises one and no more than one mismatch when the oligonucleotide is aligned with a target PNPLA3 transcript for complementarity. In some embodiments, a second domain comprises two and no more than two mismatches when the oligonucleotide is aligned with a target PNPLA3 transcript for complementarity. In some embodiments, a second domain comprises one or more (e.g., 1-10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) bulges when the oligonucleotide is aligned with a target PNPLA3 transcript for Page 11 of 743 12621738v1Attorney Docket No.: 2010581-1488 complementarity. In some embodiments, each bulge independently comprises one or more base pairs that are not Watson-Crick or wobble pairs. In some embodiments, a second domain comprises one or more (e.g., 1-10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) wobble pairs when the oligonucleotide is aligned with a target PNPLA3 transcript for complementarity. In some embodiments, a second domain comprise a nucleoside opposite to a target adenosine when the oligonucleotide is aligned with a target PNPLA3 transcript for complementarity. In some embodiments, an opposite nucleobase is optionally substituted or protected U, or is an optionally substituted or protected tautomer of U. In some embodiments, an opposite nucleobase is U. In some embodiments, an oligonucleotide comprises a nucleobase BA, wherein BA is or comprises Ring BA or a tautomer thereof, wherein Ring BA is an optionally substituted, 5-20 membered, monocyclic, bicyclic or polycyclic ring having 0-10 heteroatoms. In some embodiments, Ring BA has the structure . In some embodiments, a second domain comprises about 1-50 (e.g., about 5, 6, 7, 8, 9, or 10 − about 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, etc., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, etc.) modified sugars independently with a modification that is not 2’-F. In some embodiments, a target adenosine is at a position within the PNPLA3 transcript encoding for an amino acid at position 148 of a PNPLA3 polypeptide. In some embodiments, a target adenosine is at a position within the PNPLA3 transcript encoding for an amino acid at position 148 of SEQ ID NO: 2. In some embodiments, an amino acid is methionine. In some embodiments, a second domain comprises a PS internucleotidic linkage and a PN internucleotidic linkage. In some embodiments, each internucleotidic linkage in a second domain is independently a PO internucleotidic linkage, a PS internucleotidic linkage or a PN internucleotidic linkage. In some embodiments, each PS internucleotidic linkage is independently a phosphorothioate internucleotidic linkage. In some embodiments, each PS internucleotidic linkage is independently a Sp phosphorothioate internucleotidic linkage. In some embodiments, each PN internucleotidic linkage is independently a phosphoryl guanidine internucleotidic linkage. In some embodiments, each PN internucleotidic linkage is independently a n001 internucleotidic linkage.
[0028] In some embodiments, an oligonucleotide comprises an additional chemical moiety. In some embodiments, an oligonucleotide comprises an asialoglycoprotein receptor ligand. In some embodiments, an oligonucleotide comprises GalNAc. In some embodiments, an oligonucleotide comprises Page 12 of 743 12621738v1Attorney Docket No.: 2010581-1488 . In some
[0029] In some embodiments, the number of chiral linkage phosphorus in the oligonucleotide is about or at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30. In some embodiments, each chiral linkage phosphorus independently has a diastereomeric purity of about or at least about 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%. In some embodiments, diastereomeric purity of the oligonucleotide is about or at least about (DS)nc, wherein DS is about 85%-100% (e.g., about or at least about 85%, 90%, 91%.92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%), and nc is the number of chiral linkage phosphorus in the oligonucleotide. In some embodiments, purity of the oligonucleotide is about 20%-100%, or is about or at least about 20%-95%, 30%-90%, 40%-85%, 40%-80%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, or 90% (e.g., peak area% at 260 nm).
[0030] In some embodiments, the present disclosure provides a pharmaceutical composition which comprises or delivers an effective amount of an oligonucleotide disclosed herein or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable carrier. In some embodiments, a composition comprising a plurality of oligonucleotides, wherein each oligonucleotides of the plurality is independently a particular oligonucleotide or a salt thereof, wherein the particular oligonucleotide is an oligonucleotide disclosed herein. In some embodiments, an oligonucleotide composition comprises a plurality of oligonucleotides, wherein oligonucleotides of the plurality share: 1) a common base sequence; and 2) the same linkage phosphorus stereochemistry independently at one or more (e.g., about 1-50, 1-40, 1-30, 1-25, 1-20, 1- 15, 1-10, 5-50, 5-40, 5-30, 5-25, 5-20, 5-15, 5-10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more) chiral internucleotidic linkages (“chirally controlled internucleotidic linkages”); wherein each oligonucleotide of the plurality is independently an oligonucleotide disclosed herein (e.g., in an acid, base, or salt form). In some embodiments, an oligonucleotide composition comprises a plurality of oligonucleotides, wherein oligonucleotides of the plurality share: 1) a common base sequence, and 2) the same linkage phosphorus stereochemistry independently at one or more (e.g., about 1-50, 1-40, 1-30, 1- 25, 1-20, 1-15, 1-10, 5-50, 5-40, 5-30, 5-25, 5-20, 5-15, 5-10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more) chiral internucleotidic linkages (“chirally controlled internucleotidic linkages”); wherein the common base sequence is complementary to a base sequence of a Page 13 of 743 12621738v1Attorney Docket No.: 2010581-1488 portion of PNPLA3 transcript which portion comprises a target adenosine. In some embodiments, a common base sequence is complementary to a base sequence of a portion of a PNPLA3 transcript with 0-10 (e.g., 0-1, 0-2, 0-3, 0-4, 0-5, 0-6, 0-7, 0-8, 0-9, 0-10, 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 2-3, 2-4, 2-5, 2-6, 2-7, 2- 8, 2-9, 2-10, 3-4, 3-5, 3-6, 3-7, 3-8, 3-9, 3-10, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) mismatches which are not Watson-Crick base pairs. In some embodiments, a common base sequence is complementary to a base sequence of a portion of a PNPLA3 transcript with 0-5 mismatches which are not Watson-Crick base pairs. In some embodiments, a common base sequence is 100% complementary to a base sequence of a portion of a PNPLA3 transcript across the length of the common base sequence except the nucleoside opposite to a target adenosine. In some embodiments, a common base sequence is 100% complementary to a base sequence of a portion of a PNPLA3 transcript across the length of the common base sequence. In some embodiments, a portion of a PNPLA3 transcript comprises a target adenosine in a codon encoding an amino acid at position 148 of SEQ ID NO: 1 or 2. In some embodiments, a portion of a PNPLA3 transcript comprises a target adenosine in a codon encoding an amino acid at position 148 of SEQ ID NO: 2. In some embodiments, a composition can edit a target A to I when contacted with a PNPLA3 transcript in a system expressing ADAR.
[0031] In some embodiments, oligonucleotides of the plurality share the same base and sugar modifications. In some embodiments, oligonucleotides of the plurality share the same pattern of backbone chiral centers. In some embodiments, a composition is enriched for oligonucleotides of the plurality compared to a stereorandom preparation of the oligonucleotides wherein no internucleotidic linkages are chirally controlled. In some embodiments, a non-random level of all oligonucleotides in a composition that share the common base sequence and the same base and sugar modifications are oligonucleotides of the plurality. In some embodiments, a non-random level of all oligonucleotides in a composition that share the common base sequence are oligonucleotides of the plurality. In some embodiments, oligonucleotides of the plurality are of the same oligonucleotide or one or more pharmaceutically acceptable salts thereof. In some embodiments, oligonucleotides of the plurality are one or more pharmaceutically acceptable salts of the same acid-form oligonucleotide. In some embodiments, oligonucleotides of the plurality are of the same constitution. In some embodiments, a non-random level of all oligonucleotides in the composition that share the same base sequence as oligonucleotides of the plurality are oligonucleotides of the plurality. In some embodiments, a non-random level of all oligonucleotides in the composition that share the same constitution are oligonucleotides of the plurality. In some embodiments, a level of oligonucleotides of a plurality in oligonucleotides in the composition that share the common constitution of the plurality is about or at least about (DS)nc, wherein DS is about 85%-100% (e.g., about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5% or more) and nc is the number of chiral linkage phosphorus. In some embodiments, a level of oligonucleotides of a plurality in oligonucleotides in the composition that share the common constitution of the plurality is about or at least about 20%-100%, or is about or at least about 20%-95%, 30%-90%, 40%-85%, 40%-80%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, or 90%. In some embodiments, oligonucleotides of the plurality are of the same structure. In some embodiments, oligonucleotides of the Page 14 of 743 12621738v1Attorney Docket No.: 2010581-1488 plurality are sodium salts. In some embodiments, oligonucleotides of the plurality share the same linkage phosphorus stereochemistry at 10 or more chiral internucleotidic linkages. In some embodiments, oligonucleotides of the plurality share the same linkage phosphorus stereochemistry at each phosphorothioate internucleotidic linkages. In some embodiments, oligonucleotides of the plurality do not share the same linkage phosphorus stereochemistry at one or more or any non-negatively charged internucleotidic linkages.
[0032] In some embodiments, the present disclosure provides a method for increasing lipase activity of a PNPLA3 polypeptide or characteristic portion thereof in a subject, comprising administering or delivering to the subject an effective amount of an oligonucleotide or composition disclosed herein. In some embodiments, the present disclosure provides a method for increasing lipase activity of a PNPLA3 polypeptide or characteristic portion thereof in a subject, comprising converting the amino acid at position 148 of the PNPLA3 polypeptide into a valine. In some embodiments, the present disclosure provides a method for producing a RNA encoding a PNPLA3 polypeptide that comprises I148V in a subject, comprising editing a target adenosine in PNPLA3 in the genome of the subject, wherein the target adenosine is in the codon encoding an amino acid at position 148 in the PNPLA3 polypeptide. In some embodiments, the present disclosure provides a method for producing a RNA encoding a PNPLA3 polypeptide that comprises I148V in a subject, comprising editing a target adenosine in a transcript encoding the PNPLA3 polypeptide, wherein the target adenosine is in the codon encoding an amino acid at position 148 in the PNPLA3 polypeptide. In some embodiments, the present disclosure provides a method for producing a RNA encoding a PNPLA3 polypeptide that comprises I148V in a subject, comprising administering or delivering to the subject an effective amount of an oligonucleotide or composition disclosed herein. In some embodiments, the present disclosure provides a method for producing a PNPLA3 polypeptide comprising I148V in a subject, comprising editing a target adenosine in PNPLA3 in the genome of the subject, wherein the target adenosine is in the codon encoding an amino acid at position 148 in the PNPLA3 polypeptide. In some embodiments, the present disclosure provides a method for producing a PNPLA3 polypeptide comprising I148V in a subject, comprising editing a target adenosine in a transcript encoding the PNPLA3 polypeptide, wherein the target adenosine is in the codon encoding an amino acid at position 148 in the PNPLA3 polypeptide. In some embodiments, the present disclosure provides a method for preventing or treating a condition, disorder or disease, comprising editing a target adenosine in PNPLA3 in the genome of a subject susceptible thereto or suffering therefrom, wherein the target adenosine is in the codon encoding an amino acid at position 148 of a PNPLA3 polypeptide. In some embodiments, the present disclosure provides a method for preventing or treating a condition, disorder or disease, comprising editing a target adenosine in PNPLA3 in the genome of a subject susceptible thereto or suffering therefrom, wherein the target adenosine is in the codon encoding an amino acid at position 148 of a PNPLA3 polypeptide. In some embodiments, the present disclosure provides a method for preventing or treating a condition, disorder or disease, comprising administering or delivering to a subject susceptible thereto or suffering therefrom an effective amount of an oligonucleotide or composition disclosed herein.
[0033] In some embodiments, a condition, disorder or disease is amenable to an A to G or A to I Page 15 of 743 12621738v1Attorney Docket No.: 2010581-1488 modification. In some embodiments, a condition, disease or disorder is associated with a PNPLA3 I148M mutation. In some embodiments, a subject comprises an I148M mutation in PNPLA3. In some embodiments, a subject is homozygous for the mutation. In some embodiments, a subject is heterozygous for the mutation. In some embodiments, a condition, disorder or disease is a liver condition, disorder or disease. In some embodiments, a condition, disorder or disease is a metabolic liver condition, disorder or disease. In some embodiments, a condition, disorder or disease is hepatitis. In some embodiments, a condition, disorder or disease is fibrosis. In some embodiments, a condition, disorder or disease is cirrhosis. In some embodiments, a condition, disorder or disease is HCC. In some embodiments, a condition, disorder or disease is liver failure. In some embodiments, oligonucleotides administered to a subject are GalNAc-conjugated oligonucleotides.
[0034] In some embodiments, the present disclosure provides use of an oligonucleotide or composition disclosed herein for editing a target adenosine in a codon. In some embodiments, sequence, expression, level and / or activity of a protein is altered.
[0035] In some embodiments, the present disclosure provides a method for modulating a protein interaction with an agent in a system wherein a protein is translated from its encoding RNA, comprising administering to the system an oligonucleotide or composition disclosed herein, wherein an adenosine in the encoding RNA is edited, wherein a protein is translated from the edited mRNA (“the edited protein”), wherein the edited protein differs from the unedited protein at an amino acid residue involving in the protein-agent interaction. In some embodiments, an agent is or comprises a small molecule. In some embodiments, an agent is or comprises a lipid. In some embodiments, an agent is or comprises a triglyceride. In some embodiments, a protein is PNPLA3 or a variant thereof. In some embodiments, an oligonucleotide is delivered by administering to the subject an effective amount of a conjugate of the oligonucleotide with an additional chemical moiety or a salt thereof.
[0036] In some embodiments, the present disclosure provides a method for delivering to a system an oligonucleotide, comprising administering to the system a conjugate of the oligonucleotide with an additional chemical moiety or a salt thereof. In some embodiments, a system is or comprises a cell. In some embodiments, a system is or comprises a tissue. In some embodiments, a system is or comprises an organ. In some embodiments, a system is a subject. In some embodiments, a system is a human. In some embodiments, an additional chemical moiety is or comprises a targeting moiety. In some embodiments, an additional chemical moiety is or comprises GalNAc. In some embodiments, an additional chemical moiety is or comprises optionally substituted Page 16 of 743 12621738v1Attorney Docket No.: 2010581-1488 me meembodiments, an additional chemical moiety is conjugated via a linker to oligonucleotide. In some embodiments, a linker is or comprises L001.
[0037] In some embodiments, as demonstrated herein chirally controlled oligonucleotide compositions provide a number of advantages, e.g., higher stability, activities, etc., compared to corresponding stereorandom oligonucleotide compositions. In some embodiments, it was observed that chirally controlled oligonucleotide compositions provide high levels of adenosine modifying (e.g., converting A to I) activities with various isoforms of an ADAR protein (e.g., p150 and p110 forms of ADAR1) while corresponding stereorandom compositions provide high levels of adenosine modifying (e.g., converting A to I) activities with only certain isoforms of an ADAR protein (e.g., p150 isoform of ADAR1).
[0038] In some embodiments, provided oligonucleotides comprise an additional moiety, e.g., a targeting moiety, a carbohydrate moiety, etc. In some embodiments, an additional moiety is or comprises a ligand for an asialoglycoprotein receptor. In some embodiments, an additional moiety is or comprises GalNAc or derivatives thereof. Among other things, additional moieties may facilitate delivery to certain target locations, e.g., cells, tissues, organs, etc. (e.g., locations comprising receptors that interact with additional moieties). In some embodiments, additional moieties facilitate delivery to liver.
[0039] In some embodiments, the present disclosure provides technologies for preparing oligonucleotides and compositions thereof, particularly chirally controlled oligonucleotide compositions. In some embodiments, provided oligonucleotides and compositions thereof are of high purity. In some embodiments, oligonucleotides of the present disclosure are at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% stereochemically pure at linkage phosphorus of chiral internucleotidic linkages. In some embodiments, oligonucleotides of the present disclosure are prepared stereoselectively and are substantially free of stereoisomers. In some embodiments, in provided compositions comprising a plurality of oligonucleotides which share the same base sequence of the same pattern of chiral linkage phosphorus stereochemistry (e.g., comprising one or more of Rp and / or Sp, wherein each chiral linkage phosphorus is independently Rp or Sp), at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% of all oligonucleotides in the composition that Page 17 of 743 12621738v1Attorney Docket No.: 2010581-1488 share the same base sequence as oligonucleotides of the plurality share the same pattern of chiral linkage phosphorus stereochemistry or are oligonucleotides of the plurality. In some embodiments, in provided compositions comprising a plurality of oligonucleotides which share the same base sequence of the same pattern of chiral linkage phosphorus stereochemistry, at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% of all oligonucleotides in the composition that share the same constitution as oligonucleotides of the plurality share the same pattern of chiral linkage phosphorus stereochemistry or are oligonucleotides of the plurality.
[0040] In some embodiments, the present disclosure describes useful technologies for assessing oligonucleotide and compositions thereof. For example, various technologies of the present disclosure are useful for assessing adenosine modification. As appreciated by those skilled in the art, in some embodiments, modification / editing of adenosine can be assessed through sequencing, mass spectrometry, assessment (e.g., levels, activities, etc.) of products (e.g., RNA, protein, etc.) of modified nucleic acids (e.g., wherein adenosines of target nucleic acids are converted to inosines), etc., optionally in view of other components (e.g., ADAR proteins) presence in modification systems (e.g., an in vitro system, an ex vivo system, cells, tissues, organs, organisms, subjects, etc.). Those skilled in the art will appreciate that oligonucleotides which provide adenosine modification of a target nucleic acid can also provide modified nucleic acid (e.g., wherein a target adenosine is converted into I) and one or more products thereof (e.g., mRNA, proteins, etc.). Certain useful technologies are described in the Examples.
[0041] As described herein, oligonucleotides and compositions of the present disclosure may be provided / utilized in various forms. In some embodiments, the present disclosure provides compositions comprising one or more forms of oligonucleotides, e.g., acid forms (e.g., in which natural phosphate linkages exist as –O(P(O)(OH)−O−, phosphorothioate internucleotidic linkages exist as –O(P(O)(SH)−O−), base forms, salt forms (e.g., in which natural phosphate linkages exist as salt forms (e.g., sodium salt (– O(P(O)(O−Na+)−O−), phosphorothioate internucleotidic linkages exist as salt forms (e.g., sodium salt (– O(P(O)(S−Na+)−O−) etc. As appreciated by those skilled in the art, oligonucleotides can exist in various salt forms, including pharmaceutically acceptable salts, and in solutions (e.g., various aqueous buffering system), cations may dissociate from anions. In some embodiments, the present disclosure provides a pharmaceutical composition comprising a provided oligonucleotide and / or one or more pharmaceutically acceptable salts thereof, and a pharmaceutically acceptable carrier. In some embodiments, pharmaceutical compositions are chirally controlled oligonucleotide compositions.
[0042] Provided technologies can be utilized for various purposes. For example, those skilled in the art will appreciate that provided technologies are useful for many purposes involving modification of adenosine, e.g., introduction of A to I variations that may be read as G during translation, modulate levels of certain nucleic acids and / or products encoded thereby (e.g., reducing levels of proteins by introducing A to I modifications), etc.
[0043] In some embodiments, the present disclosure provides technologies for preventing or treating a Page 18 of 743 12621738v1Attorney Docket No.: 2010581-1488 condition, disorder or disease that is amenable to an adenosine modification, e.g. conversion of A to I. As appreciated by those skilled in the art, I may perform one or more functions of G, e.g., in base pairing, translation, etc. In some embodiments, conversion of A to I may result in one or more products, e.g., proteins, of the G-version nucleic acid. In some embodiments, the present disclosure provides technologies for preventing or treating a condition, disorder or disease associated with a mutation, comprising administering to a subject susceptible thereto or suffering therefrom a provided oligonucleotide or composition thereof, which oligonucleotide or composition can mediate the effects of the mutation.
[0044] In some embodiments, the present disclosure provides technologies for preventing or treating a condition, disorder or disease associated with a C to G mutation, comprising administering to a subject susceptible thereto or suffering therefrom a provided oligonucleotide or composition thereof, which oligonucleotide or composition can modify an A in the same codon as the C to G mutation. In some embodiments, provided technologies modify an A in a transcript, e.g., RNA transcript to produce an alternative amino acid codon. In some embodiments, an A is converted into an I. In some embodiments, during translation protein synthesis machineries read I as G. In some embodiments, provided technologies modify an A to an I / G form to encodes one or more proteins that have one or more higher desired activities and / or one or more better desired properties compared those encoded by its corresponding A form. In some embodiments, a G form provides higher levels, compared to its corresponding A form, of one or more proteins that have one or more higher desired activities and / or one or more better desired properties. In some embodiments, products encoded by a G form are structurally different (e.g., longer, in some embodiments, full length proteins) from those encoded by its corresponding A form. In some embodiments, a G form provides structurally identical products (e.g., proteins) compared to its corresponding A form.
[0045] In some embodiments, the present disclosure provides technologies for modulating RNA / protein interactions by, e.g., editing target adenosines using oligonucleotides and composition described herein. In some embodiments, the present disclosure provides technologies for modulating levels of RNA and / or products encoded thereby by, e.g., editing a target adenosine. In some embodiments, the present disclosure provides technologies for increasing levels of RNA and / or products (e.g., polypeptides) encoded thereby by, e.g., editing a target adenosine. In some embodiments, a target adenosine is present in a RNA motif, e.g., an AU-rich element (ARE) motif.
[0046] In some embodiments, editing of an adenosine in a RNA modulates level of a RNA. In some embodiments, editing of an adenosine in a RNA modulates level of a product (e.g., a polypeptide) encoded thereby. In some embodiments, editing of an adenosine in a RNA increases level of the RNA. In some embodiments, editing of an adenosine in a RNA increases level of a product (e.g., a polypeptide) encoded thereby. In some embodiments, a RNA is a transcript. In some embodiments, a RNA is mRNA. In some embodiments, an adenosine is in a UTR region. In some embodiments, an adenosine is in a 5’-UTR region. In some embodiments, an adenosine is in a 3’-UTR region. In some embodiments, an adenosine is in a RNA motif. In some embodiments, the present disclosure provides technologies for preventing or treating a Page 19 of 743 12621738v1Attorney Docket No.: 2010581-1488 condition, disorder or disease associated with levels of a transcript and / or a product encoded thereby, comprising administering to a subject susceptible thereto or suffering therefrom a provided oligonucleotide or composition thereof, which oligonucleotide or composition can modify a target adenosine in the transcript. In some embodiments, the present disclosure provides technologies for preventing or treating a condition, disorder or disease, comprising administering to a subject susceptible thereto or suffering therefrom a provided oligonucleotide or composition thereof, which oligonucleotide or composition can modify a target adenosine in a RNA thereby modulating (e.g., increasing) levels of a RNA and / or a product encoded thereby. In some embodiments, a RNA is a transcript. In some embodiments, a transcript is a PNPLA3 transcript, e.g., a PNPLA3 mRNA. In some embodiments, a product encoded thereby is a PNPLA3 polypeptide, e.g., a PNPLA3 protein. In some embodiments, a RNA motif is in a PNPLA3 transcript, e.g., in 5’ UTR of a PNPLA3 mRNA. In some embodiments, a RNA motif is in a PNPLA3 transcript, e.g., in 3’ UTR of a PNPLA3 mRNA.
[0047] As those skilled in the art will appreciate, many conditions, disorders or diseases are associated with mutations that can be modified by provided technologies and can be prevented and / or treated using provided technologies. BRIEF DESCRIPTION OF THE DRAWINGS
[0048] Figure 1. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary wild-type (WT) human hepatocytes were dosed with 5uM of indicated oligonucleotides. Oligonucleotides targeted adenosine in I148 codon (i.e., AUC) of WT human PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUC). Cells were harvested after 48 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0049] Figure 2. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with 10 uM of indicated oligonucleotides. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 48 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0050] Figure 3. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes Page 20 of 743 12621738v1Attorney Docket No.: 2010581-1488 homozygous for M148 mutation were dosed with 0.1 uM of indicated oligonucleotides. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0051] Figure 4. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with 0.1 uM of indicated oligonucleotides. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0052] Figure 5. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with 0.01 uM of indicated oligonucleotides. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0053] Figure 6. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with 0.01 uM of indicated oligonucleotides. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0054] Figure 7. Various siRNA constructs targeting PNPLA3 were assessed for effects on lipid droplet formation. Primary human hepatocytes were dosed with indicated concentrations of indicated siRNAs. Cells were then treated with 250 uM linoleic acid (LA) lipid and lipid droplet formation was assessed by fluorescent microscopy.
[0055] Figure 8. Provided technologies can provide editing of target transcripts and produce functional protein product. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and Page 21 of 743 12621738v1Attorney Docket No.: 2010581-1488 assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with 3 uM of indicated oligonucleotides, including a non-targeting control (NTC, ADR-0108273), and an siRNA construct (DSR- 0105686). Cells were then treated with 250 uM linoleic acid (LA) lipid and lipid droplet formation was assessed by fluorescent microscopy.
[0056] Figure 9. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with indicated concentration of indicated oligonucleotides. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0057] Figure 10. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, m1d, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with 10 nM (left bar) or 50 nM (right bar) of indicated oligonucleotides via gymnotic uptake. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0058] Figure 11. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, m1d, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with 10 nM (left bar) or 50 nM (right bar) of indicated oligonucleotides via gymnotic uptake. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0059] Figure 12. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with 10 nM (left bar) or 50 nM (right bar) of indicated oligonucleotides via gymnotic uptake. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of Page 22 of 743 12621738v1Attorney Docket No.: 2010581-1488 mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0060] Figure 13. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with indicated concentration of indicated oligonucleotides via gymnotic uptake. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0061] Figure 14. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with indicated concentration of indicated oligonucleotides via gymnotic uptake. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0062] Figure 15. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation from two different donors were dosed with indicated concentration of indicated oligonucleotides via gymnotic uptake. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0063] Figure 16. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’-MOE, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with 50 nM (left bar) or 10 nM (right bar) of indicated oligonucleotides via gymnotic uptake. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of Page 23 of 743 12621738v1Attorney Docket No.: 2010581-1488 mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing.
[0064] Figure 17. Provided technologies can provide editing of target transcripts. Oligonucleotides comprising various modifications, such as base modifications (e.g., [3nU], [3nT]), linkage modifications (e.g., PS, PN (e.g., phosphoryl guanidine linkages such as n001), etc.), sugar modifications (e.g., 2’-F, 2’-OMe, 2’- MOE, natural DNA sugar, etc.), and stereochemistry and patterns thereof were designed and assessed. Primary human hepatocytes homozygous for M148 mutation were dosed with 50 nM (left bar) or 10 nM (right bar) of indicated oligonucleotides via gymnotic uptake. Oligonucleotides targeted adenosine in M148 codon (i.e., AUG) of mutant PNPLA3 to produce A-to-I editing, resulting in a codon that can be read as a valine codon (i.e., GUG). Cells were harvested after 72 hours and RNA was collected and reverse-transcribed into cDNA. Editing was quantified by Sanger sequencing. DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS
[0065] Technologies of the present disclosure may be understood more readily by reference to the following detailed description of certain embodiments. Definitions
[0066] As used herein, the following definitions shall apply unless otherwise indicated. For purposes of this disclosure, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed. Additionally, general principles of organic chemistry are described in "Organic Chemistry", Thomas Sorrell, University Science Books, Sausalito: 1999, and "March's Advanced Organic Chemistry", 5th Ed., Ed.: Smith, M.B. and March, J., John Wiley & Sons, New York: 2001.
[0067] As used herein in the present disclosure, unless otherwise clear from context, (i) the term “a” or “an” may be understood to mean “at least one”; (ii) the term “or” may be understood to mean “and / or”; (iii) the terms “comprising”, “comprise”, “including” (whether used with “not limited to” or not), and “include” (whether used with “not limited to” or not) may be understood to encompass itemized components or steps whether presented by themselves or together with one or more additional components or steps; (iv) the term “another” may be understood to mean at least an additional / second one or more; (v) the terms “about” and “approximately” may be understood to permit standard variation as would be understood by those of ordinary skill in the art; and (vi) where ranges are provided, endpoints are included.
[0068] Unless otherwise specified, description of oligonucleotides and elements thereof (e.g., base sequence, sugar modifications, internucleotidic linkages, linkage phosphorus stereochemistry, patterns thereof, etc.) is from 5’ to 3’. As those skilled in the art will appreciate, in some embodiments, oligonucleotides may be provided and / or utilized as salt forms, particularly pharmaceutically acceptable salt forms, e.g., sodium salts. As those skilled in the art will also appreciate, in some embodiments, individual oligonucleotides within Page 24 of 743 12621738v1Attorney Docket No.: 2010581-1488 a composition may be considered to be of the same constitution and / or structure even though, within such composition (e.g., a liquid composition), particular such oligonucleotides might be in different salt form(s) (and may be dissolved and the oligonucleotide chain may exist as an anion form when, e.g., in a liquid composition) at a particular moment in time. For example, those skilled in the art will appreciate that, at a given pH, individual internucleotidic linkages along an oligonucleotide chain may be in an acid (H) form, or in one of a plurality of possible salt forms (e.g., a sodium salt, or a salt of a different cation, depending on which ions might be present in the preparation or composition), and will understand that, so long as their acid forms (e.g., replacing all cations, if any, with H+) are of the same constitution and / or structure, such individual oligonucleotides may properly be considered to be of the same constitution and / or structure.
[0069] Aliphatic: As used herein, “aliphatic” means a straight-chain (i.e., unbranched) or branched, substituted or unsubstituted hydrocarbon chain that is completely saturated or that contains one or more units of unsaturation (but not aromatic), or a substituted or unsubstituted monocyclic, bicyclic, or polycyclic hydrocarbon ring that is completely saturated or that contains one or more units of unsaturation (but not aromatic), or combinations thereof. In some embodiments, aliphatic groups contain 1-50 aliphatic carbon atoms. In some embodiments, aliphatic groups contain 1-20 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-10 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-9 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-8 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-7 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-6 aliphatic carbon atoms. In still other embodiments, aliphatic groups contain 1-5 aliphatic carbon atoms, and in yet other embodiments, aliphatic groups contain 1, 2, 3, or 4 aliphatic carbon atoms. Suitable aliphatic groups include, but are not limited to, linear or branched, substituted or unsubstituted alkyl, alkenyl, alkynyl groups and hybrids thereof such as (cycloalkyl)alkyl, (cycloalkenyl)alkyl or (cycloalkyl)alkenyl.
[0070] Alkenyl: As used herein, the term “alkenyl” refers to an aliphatic group, as defined herein, having one or more double bonds.
[0071] Alkyl: As used herein, the term “alkyl” is given its ordinary meaning in the art and may include saturated aliphatic groups, including straight-chain alkyl groups, branched-chain alkyl groups, cycloalkyl (alicyclic) groups, alkyl substituted cycloalkyl groups, and cycloalkyl substituted alkyl groups. In some embodiments, alkyl has 1-100 carbon atoms. In certain embodiments, a straight chain or branched chain alkyl has about 1-20 carbon atoms in its backbone (e.g., C1-C20for straight chain, C2-C20for branched chain), and alternatively, about 1-10. In some embodiments, cycloalkyl rings have from about 3-10 carbon atoms in their ring structure where such rings are monocyclic, bicyclic, or polycyclic, and alternatively about 5, 6 or 7 carbons in the ring structure. In some embodiments, an alkyl group may be a lower alkyl group, wherein a lower alkyl group comprises 1-4 carbon atoms (e.g., C1-C4for straight chain lower alkyls).
[0072] Alkynyl: As used herein, the term “alkynyl” refers to an aliphatic group, as defined herein, having one or more triple bonds.
[0073] Analog: The term “analog” includes any chemical moiety which differs structurally from a Page 25 of 743 12621738v1Attorney Docket No.: 2010581-1488 reference chemical moiety or class of moieties, but which is capable of performing at least one function of such a reference chemical moiety or class of moieties. As non-limiting examples, a nucleotide analog differs structurally from a nucleotide but performs at least one function of a nucleotide; a nucleobase analog differs structurally from a nucleobase but performs at least one function of a nucleobase; etc.
[0074] Animal: As used herein, the term “animal” refers to any member of the animal kingdom. In some embodiments, “animal” refers to humans, at any stage of development. In some embodiments, “animal” refers to non-human animals, at any stage of development. In certain embodiments, the non-human animal is a mammal (e.g., a rodent, a mouse, a rat, a rabbit, a monkey, a dog, a cat, a sheep, cattle, a primate and / or a pig). In some embodiments, animals include, but are not limited to, mammals, birds, reptiles, amphibians, fish and / or worms. In some embodiments, an animal may be a transgenic animal, a genetically-engineered animal and / or a clone.
[0075] Aryl: The term “aryl", as used herein, used alone or as part of a larger moiety as in “aralkyl,” “aralkoxy,” or “aryloxyalkyl,” refers to monocyclic, bicyclic or polycyclic ring systems having a total of five to thirty ring members, wherein at least one ring in the system is aromatic. In some embodiments, an aryl group is a monocyclic, bicyclic or polycyclic ring system having a total of five to fourteen ring members, wherein at least one ring in the system is aromatic, and wherein each ring in the system contains 3 to 7 ring members. In some embodiments, each monocyclic ring unit is aromatic. In some embodiments, an aryl group is a biaryl group. The term “aryl” may be used interchangeably with the term “aryl ring.” In certain embodiments of the present disclosure, “aryl” refers to an aromatic ring system which includes, but is not limited to, phenyl, biphenyl, naphthyl, binaphthyl, anthracyl and the like, which may bear one or more substituents. Also included within the scope of the term “aryl,” as it is used herein, is a group in which an aromatic ring is fused to one or more non–aromatic rings, such as indanyl, phthalimidyl, naphthimidyl, phenanthridinyl, or tetrahydronaphthyl, and the like.
[0076] Characteristic portion: As used herein, the term “characteristic portion”, in the broadest sense, refers to a portion of a substance whose presence (or absence) correlates with presence (or absence) of a particular feature, attribute, or activity of the substance. In some embodiments, a characteristic portion of a substance is a portion that is found in the substance and in related substances that share the particular feature, attribute or activity, but not in those that do not share the particular feature, attribute or activity. In certain embodiments, a characteristic portion shares at least one functional characteristic with the intact substance. For example, in some embodiments, a “characteristic portion” of a protein or polypeptide is one that contains a continuous stretch of amino acids, or a collection of continuous stretches of amino acids, that together are characteristic of a protein or polypeptide. In some embodiments, each such continuous stretch generally contains at least 2, 5, 10, 15, 20, 50, or more amino acids. In general, a characteristic portion of a substance (e.g., of a protein, antibody, etc.) is one that, in addition to the sequence and / or structural identity specified above, shares at least one functional characteristic with the relevant intact substance. In some embodiments, a characteristic portion may be biologically active. Page 26 of 743 12621738v1Attorney Docket No.: 2010581-1488
[0077] Chiral control: As used herein, “chiral control” refers to control of the stereochemical designation of the chiral linkage phosphorus in a chiral internucleotidic linkage within an oligonucleotide. As used herein, a chiral internucleotidic linkage is an internucleotidic linkage whose linkage phosphorus is chiral. In some embodiments, a control is achieved through a chiral element that is absent from the sugar and base moieties of an oligonucleotide, for example, in some embodiments, a control is achieved through use of one or more chiral auxiliaries during oligonucleotide preparation, which chiral auxiliaries often are part of chiral phosphoramidites used during oligonucleotide preparation. In contrast to chiral control, a person having ordinary skill in the art will appreciate that conventional oligonucleotide synthesis which does not use chiral auxiliaries cannot control stereochemistry at a chiral internucleotidic linkage if such conventional oligonucleotide synthesis is used to form the chiral internucleotidic linkage. In some embodiments, the stereochemical designation of each chiral linkage phosphorus in each chiral internucleotidic linkage within an oligonucleotide is controlled.
[0078] Chirally controlled oligonucleotide composition: The terms “chirally controlled oligonucleotide composition”, “chirally controlled nucleic acid composition”, and the like, as used herein, refers to a composition that comprises a plurality of oligonucleotides (or nucleic acids) which share a common base sequence, wherein the plurality of oligonucleotides (or nucleic acids) share the same linkage phosphorus stereochemistry at one or more chiral internucleotidic linkages (chirally controlled or stereodefined internucleotidic linkages, whose chiral linkage phosphorus is Rp or Sp in the composition (“stereodefined”), not a random Rp and Sp mixture as non-chirally controlled internucleotidic linkages). In some embodiments, a chirally controlled oligonucleotide composition comprises a plurality of oligonucleotides (or nucleic acids) that share: 1) a common base sequence, 2) a common pattern of backbone linkages, and 3) a common pattern of backbone phosphorus modifications, wherein the plurality of oligonucleotides (or nucleic acids) share the same linkage phosphorus stereochemistry at one or more chiral internucleotidic linkages (chirally controlled or stereodefined internucleotidic linkages, whose chiral linkage phosphorus is Rp or Sp in the composition (“stereodefined”), not a random Rp and Sp mixture as non-chirally controlled internucleotidic linkages). Level of the plurality of oligonucleotides (or nucleic acids) in a chirally controlled oligonucleotide composition is pre-determined / controlled or enriched (e.g., through chirally controlled oligonucleotide preparation to stereoselectively form one or more chiral internucleotidic linkages) compared to a random level in a non- chirally controlled oligonucleotide composition. In some embodiments, about 1%-100%, (e.g., about 5%- 100%, 10%-100%, 20%-100%, 30%-100%, 40%-100%, 50%-100%, 60%-100%, 70%-100%, 80-100%, 90- 100%, 95-100%, 50%-90%, or about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%, or at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) of all oligonucleotides in a chirally controlled oligonucleotide composition are oligonucleotides of the plurality. In some embodiments, about 1%- 100%, (e.g., about 5%-100%, 10%-100%, 20%-100%, 30%-100%, 40%-100%, 50%-100%, 60%-100%, 70%- 100%, 80-100%, 90-100%, 95-100%, 50%-90%, or about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, Page 27 of 743 12621738v1Attorney Docket No.: 2010581-1488 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%, or at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) of all oligonucleotides in a chirally controlled oligonucleotide composition that share the common base sequence, the common pattern of backbone linkages, and the common pattern of backbone phosphorus modifications are oligonucleotides of the plurality. In some embodiments, a level is about 1%-100%, (e.g., about 5%-100%, 10%-100%, 20%-100%, 30%-100%, 40%-100%, 50%-100%, 60%-100%, 70%-100%, 80-100%, 90-100%, 95-100%, 50%-90%, or about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%, or at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) of all oligonucleotides in a composition, or of all oligonucleotides in a composition that share a common base sequence (e.g., of a plurality of oligonucleotide or an oligonucleotide type), or of all oligonucleotides in a composition that share a common base sequence, a common pattern of backbone linkages, and a common pattern of backbone phosphorus modifications, or of all oligonucleotides in a composition that share a common base sequence, a common patter of base modifications, a common pattern of sugar modifications, a common pattern of internucleotidic linkage types, and / or a common pattern of internucleotidic linkage modifications. In some embodiments, the plurality of oligonucleotides share the same stereochemistry at about 1-50 (e.g., about 1-10, 1-20, 5-10, 5-20, 10-15, 10- 20, 10-25, 10-30, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) chiral internucleotidic linkages. In some embodiments, the plurality of oligonucleotides share the same stereochemistry at about 1%-100% (e.g., about 5%-100%, 10%-100%, 20%-100%, 30%-100%, 40%-100%, 50%-100%, 60%-100%, 70%-100%, 80-100%, 90-100%, 95-100%, 50%-90%, about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, or at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99%) of chiral internucleotidic linkages. In some embodiments, oligonucleotides (or nucleic acids) of a plurality share the same pattern of sugar and / or nucleobase modifications, in any. In some embodiments, oligonucleotides (or nucleic acids) of a plurality are various forms of the same oligonucleotide (e.g., acid and / or various salts of the same oligonucleotide). In some embodiments, oligonucleotides (or nucleic acids) of a plurality are of the same constitution. In some embodiments, level of the oligonucleotides (or nucleic acids) of the plurality is about 1%-100%, (e.g., about 5%-100%, 10%-100%, 20%-100%, 30%-100%, 40%-100%, 50%-100%, 60%-100%, 70%-100%, 80-100%, 90-100%, 95-100%, 50%-90%, or about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%, or at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) of all oligonucleotides (or nucleic acids) in a composition that share the same constitution as the oligonucleotides (or nucleic acids) of the plurality. In some embodiments, each chiral internucleotidic linkage is a chiral controlled internucleotidic linkage, and the composition is a completely chirally controlled oligonucleotide composition. In some embodiments, oligonucleotides (or nucleic acids) of a plurality are structurally identical. In some Page 28 of 743 12621738v1Attorney Docket No.: 2010581-1488 embodiments, a chirally controlled internucleotidic linkage has a diastereopurity of at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5%, typically at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5%. In some embodiments, a chirally controlled internucleotidic linkage has a diastereopurity of at least 95%. In some embodiments, a chirally controlled internucleotidic linkage has a diastereopurity of at least 96%. In some embodiments, a chirally controlled internucleotidic linkage has a diastereopurity of at least 97%. In some embodiments, a chirally controlled internucleotidic linkage has a diastereopurity of at least 98%. In some embodiments, a chirally controlled internucleotidic linkage has a diastereopurity of at least 99%. In some embodiments, a percentage of a level is or is at least (DS)nc, wherein DS is a diastereopurity as described in the present disclosure (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5% or more) and nc is the number of chiral linkage phosphorus as described in the present disclosure (e.g., 1-50, 1-40, 1-30, 1-25, 1-20, 5-50, 5-40, 5-30, 5-25, 5-20, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more). In some embodiments, a percentage of a level is or is at least (DS)nc, wherein DS is a diastereopurity as described in the present disclosure (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5% or more) and nc is the number of chirally controlled internucleotidic linkages as described in the present disclosure (e.g., 1-50, 1-40, 1-30, 1-25, 1-20, 5-50, 5-40, 5-30, 5-25, 5-20, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more). In some embodiments, a percentage of a level is or is at least (DS)nc, wherein DS is 95%-100%. For example, when DS is 99% and nc is 10, the percentage is or is at least 90% ((99%)100.90 = 90%). In some embodiments, level of a plurality of oligonucleotides in a composition is represented as the product of the diastereopurity of each chiral linkage phosphorus. In some embodiments, level of a plurality of oligonucleotides in a composition is represented as the product of the diastereopurity of each chirally controlled internucleotidic linkage in the oligonucleotides. In some embodiments, diastereopurity of an internucleotidic linkage connecting two nucleosides in an oligonucleotide (or nucleic acid) is represented by the diastereopurity of an internucleotidic linkage of a dimer connecting the same two nucleosides, wherein the dimer is prepared using comparable conditions, in some instances, identical synthetic cycle conditions (e.g., for the linkage between Nx and Ny in an oligonucleotide ….NxNy….., the dimer is NxNy). In some embodiments, not all chiral internucleotidic linkages are chiral controlled internucleotidic linkages, and the composition is a partially chirally controlled oligonucleotide composition. In some embodiments, a non-chirally controlled internucleotidic linkage has a diastereopurity of less than about 80%, 75%, 70%, 65%, 60%, 55%, or of about 50%, as typically observed in stereorandom oligonucleotide compositions (e.g., as appreciated by those skilled in the art, from traditional oligonucleotide synthesis, e.g., the phosphoramidite method). In some embodiments, oligonucleotides (or nucleic acids) of a plurality are of the same type. In some embodiments, a chirally controlled oligonucleotide composition comprises non-random or controlled levels of individual oligonucleotide or nucleic acids types. For instance, in some embodiments a chirally controlled oligonucleotide composition comprises one and no more than one oligonucleotide type. In some embodiments, Page 29 of 743 12621738v1Attorney Docket No.: 2010581-1488 a chirally controlled oligonucleotide composition comprises more than one oligonucleotide type. In some embodiments, a chirally controlled oligonucleotide composition comprises multiple oligonucleotide types. In some embodiments, a chirally controlled oligonucleotide composition is a composition of oligonucleotides of an oligonucleotide type, which composition comprises a non-random or controlled level of a plurality of oligonucleotides of the oligonucleotide type.
[0079] Comparable: The term “comparable” is used herein to describe two (or more) sets of conditions or circumstances that are sufficiently similar to one another to permit comparison of results obtained or phenomena observed. In some embodiments, comparable sets of conditions or circumstances are characterized by a plurality of substantially identical features and one or a small number of varied features. Those of ordinary skill in the art will appreciate that sets of conditions are comparable to one another when characterized by a sufficient number and type of substantially identical features to warrant a reasonable conclusion that differences in results obtained or phenomena observed under the different sets of conditions or circumstances are caused by or indicative of the variation in those features that are varied.
[0080] Cycloaliphatic: The term “cycloaliphatic,” “carbocycle,” “carbocyclyl,” “carbocyclic radical,” and “carbocyclic ring,” are used interchangeably, and as used herein, refer to saturated or partially unsaturated, but non-aromatic, cyclic aliphatic monocyclic, bicyclic, or polycyclic ring systems, as described herein, having, unless otherwise specified, from 3 to 30 ring members. Cycloaliphatic groups include, without limitation, cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, cycloheptenyl, cyclooctyl, cyclooctenyl, norbornyl, adamantyl, and cyclooctadienyl. In some embodiments, a cycloaliphatic group has 3–6 carbons. In some embodiments, a cycloaliphatic group is saturated and is cycloalkyl. The term “cycloaliphatic” may also include aliphatic rings that are fused to one or more aromatic or nonaromatic rings, such as decahydronaphthyl or tetrahydronaphthyl. In some embodiments, a cycloaliphatic group is bicyclic. In some embodiments, a cycloaliphatic group is tricyclic. In some embodiments, a cycloaliphatic group is polycyclic. In some embodiments, “cycloaliphatic” refers to C3-C6monocyclic hydrocarbon, or C8-C10bicyclic or polycyclic hydrocarbon, that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic, that has a single point of attachment to the rest of the molecule, or a C9-C16polycyclic hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic, that has a single point of attachment to the rest of the molecule.
[0081] Heteroaliphatic: The term “heteroaliphatic”, as used herein, is given its ordinary meaning in the art and refers to aliphatic groups as described herein in which one or more carbon atoms are independently replaced with one or more heteroatoms (e.g., oxygen, nitrogen, sulfur, silicon, phosphorus, and the like). In some embodiments, one or more units selected from C, CH, CH2, and CH3are independently replaced by one or more heteroatoms (including oxidized and / or substituted forms thereof). In some embodiments, a heteroaliphatic group is heteroalkyl. In some embodiments, a heteroaliphatic group is heteroalkenyl.
[0082] Heteroalkyl: The term “heteroalkyl”, as used herein, is given its ordinary meaning in the art and refers to alkyl groups as described herein in which one or more carbon atoms are independently replaced with Page 30 of 743 12621738v1Attorney Docket No.: 2010581-1488 one or more heteroatoms (e.g., oxygen, nitrogen, sulfur, silicon, phosphorus, and the like). Examples of heteroalkyl groups include, but are not limited to, alkoxy, poly(ethylene glycol)-, alkyl-substituted amino, tetrahydrofuranyl, piperidinyl, morpholinyl, etc.
[0083] Heteroaryl: The terms “heteroaryl” and “heteroar–”, as used herein, used alone or as part of a larger moiety, e.g., “heteroaralkyl,” or “heteroaralkoxy,” refer to monocyclic, bicyclic or polycyclic ring systems having a total of five to thirty ring members, wherein at least one ring in the system is aromatic and at least one aromatic ring atom is a heteroatom. In some embodiments, a heteroaryl group is a group having 5 to 10 ring atoms (i.e., monocyclic, bicyclic or polycyclic), in some embodiments 5, 6, 9, or 10 ring atoms. In some embodiments, each monocyclic ring unit is aromatic. In some embodiments, a heteroaryl group has 6, 10, or 14 π electrons shared in a cyclic array; and having, in addition to carbon atoms, from one to five heteroatoms. Heteroaryl groups include, without limitation, thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, indolizinyl, purinyl, naphthyridinyl, and pteridinyl. In some embodiments, a heteroaryl is a heterobiaryl group, such as bipyridyl and the like. The terms “heteroaryl” and “heteroar–”, as used herein, also include groups in which a heteroaromatic ring is fused to one or more aryl, cycloaliphatic, or heterocyclyl rings, where the radical or point of attachment is on the heteroaromatic ring. Non-limiting examples include indolyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzthiazolyl, quinolyl, isoquinolyl, cinnolinyl, phthalazinyl, quinazolinyl, quinoxalinyl, 4H–quinolizinyl, carbazolyl, acridinyl, phenazinyl, phenothiazinyl, phenoxazinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and pyrido[2,3–b]–1,4–oxazin–3(4H)–one. A heteroaryl group may be monocyclic, bicyclic or polycyclic. The term “heteroaryl” may be used interchangeably with the terms “heteroaryl ring,” “heteroaryl group,” or “heteroaromatic,” any of which terms include rings that are optionally substituted. The term “heteroaralkyl” refers to an alkyl group substituted by a heteroaryl group, wherein the alkyl and heteroaryl portions independently are optionally substituted.
[0084] Heteroatom: The term “heteroatom", as used herein, means an atom that is not carbon or hydrogen. In some embodiments, a heteroatom is boron, oxygen, sulfur, nitrogen, phosphorus, or silicon (including oxidized forms of nitrogen, sulfur, phosphorus, or silicon; charged forms of nitrogen (e.g., quaternized forms, forms as in iminium groups, etc.), phosphorus, sulfur, oxygen; etc.). In some embodiments, a heteroatom is silicon, phosphorus, oxygen, sulfur or nitrogen. In some embodiments, a heteroatom is silicon, oxygen, sulfur or nitrogen. In some embodiments, a heteroatom is oxygen, sulfur or nitrogen.
[0085] Heterocycle: As used herein, the terms “heterocycle,” “heterocyclyl,” “heterocyclic radical,” and “heterocyclic ring", as used herein, are used interchangeably and refer to a monocyclic, bicyclic or polycyclic ring moiety (e.g., 3-30 membered) that is saturated or partially unsaturated and has one or more heteroatom ring atoms. In some embodiments, a heterocyclyl group is a stable 5– to 7–membered monocyclic or 7– to 10– membered bicyclic heterocyclic moiety that is either saturated or partially unsaturated, and having, in addition to carbon atoms, one or more, preferably one to four, heteroatoms, as defined above. When used in reference Page 31 of 743 12621738v1Attorney Docket No.: 2010581-1488 to a ring atom of a heterocycle, the term "nitrogen" includes substituted nitrogen. As an example, in a saturated or partially unsaturated ring having 0–3 heteroatoms selected from oxygen, sulfur and nitrogen, the nitrogen may be N (as in 3,4–dihydro–2H–pyrrolyl), NH (as in pyrrolidinyl), or+NR (as in N–substituted pyrrolidinyl). A heterocyclic ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure and any of the ring atoms can be optionally substituted. Examples of such saturated or partially unsaturated heterocyclic radicals include, without limitation, tetrahydrofuranyl, tetrahydrothienyl, pyrrolidinyl, piperidinyl, pyrrolinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, morpholinyl, and quinuclidinyl. The terms “heterocycle,” “heterocyclyl,” “heterocyclyl ring,” “heterocyclic group,” “heterocyclic moiety,” and “heterocyclic radical,” are used interchangeably herein, and also include groups in which a heterocyclyl ring is fused to one or more aryl, heteroaryl, or cycloaliphatic rings, such as indolinyl, 3H–indolyl, chromanyl, phenanthridinyl, or tetrahydroquinolinyl. A heterocyclyl group may be monocyclic, bicyclic or polycyclic. The term “heterocyclylalkyl” refers to an alkyl group substituted by a heterocyclyl, wherein the alkyl and heterocyclyl portions independently are optionally substituted.
[0086] Identity: As used herein, the term “identity” refers to the overall relatedness between polymeric molecules, e.g., between nucleic acid molecules (e.g., oligonucleotides, DNA, RNA, etc.) and / or between polypeptide molecules. In some embodiments, polymeric molecules are considered to be “substantially identical” to one another if their sequences are at least 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% identical. Calculation of the percent identity of two nucleic acid or polypeptide sequences, for example, can be performed by aligning the two sequences for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second sequences for optimal alignment and non-identical sequences can be disregarded for comparison purposes). In certain embodiments, the length of a sequence aligned for comparison purposes is at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or substantially 100% of the length of a reference sequence. The nucleotides at corresponding positions are then compared. When a position in the first sequence is occupied by the same residue (e.g., nucleotide or amino acid) as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which needs to be introduced for optimal alignment of the two sequences. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. For example, the percent identity between two nucleotide sequences can be determined using the algorithm of Meyers and Miller (CABIOS, 1989, 4: 11-17), which has been incorporated into the ALIGN program (version 2.0). In some exemplary embodiments, nucleic acid sequence comparisons made with the ALIGN program use a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. The percent identity between two nucleotide sequences can, alternatively, be determined using the GAP program in the GCG software package using an NWSgapdna.CMP matrix. Page 32 of 743 12621738v1Attorney Docket No.: 2010581-1488
[0087] Internucleotidic linkage: As used herein, the phrase “internucleotidic linkage” refers generally to a linkage linking nucleoside units of an oligonucleotide or a nucleic acid. In some embodiments, an internucleotidic linkage is a phosphodiester linkage, as extensively found in naturally occurring DNA and RNA molecules (natural phosphate linkage (−OP(=O)(OH)O−), which as appreciated by those skilled in the art may exist as a salt form). In some embodiments, an internucleotidic linkage is a modified internucleotidic linkage (not a natural phosphate linkage). In some embodiments, an internucleotidic linkage is a “modified internucleotidic linkage” wherein at least one oxygen atom or −OH of a phosphodiester linkage is replaced by a different organic or inorganic moiety. In some embodiments, such an organic or inorganic moiety is selected from =S, =Se, =NR’, –SR’, –SeR’, –N(R’)2, B(R’)3,–S–, –Se–, and –N(R’)–, wherein each R’ is independently as defined and described in the present disclosure. In some embodiments, an internucleotidic linkage is a phosphotriester linkage, phosphorothioate linkage (or phosphorothioate diester linkage, −OP(=O)(SH)O−, which as appreciated by those skilled in the art may exist as a salt form), or phosphorothioate triester linkage. In some embodiments, a modified internucleotidic linkage is a phosphorothioate linkage. In some embodiments, an internucleotidic linkage is one of, e.g., PNA (peptide nucleic acid) or PMO (phosphorodiamidate Morpholino oligomer) linkage. In some embodiments, a modified internucleotidic linkage is a non-negatively charged internucleotidic linkage. In some embodiments, a modified internucleotidic linkage is a neutral internucleotidic linkage (e.g., n001 in certain provided oligonucleotides). It is understood by a person of ordinary skill in the art that an internucleotidic linkage may exist as an anion or cation at a given pH due to the existence of acid or base moieties in the linkage. In some embodiments, a modified internucleotidic linkages is a modified internucleotidic linkages designated as s, s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15, s16, s17 and s18 as described in WO 2017 / 210647.
[0088] In vitro: As used herein, the term “in vitro” refers to events that occur in an artificial environment, e.g., in a test tube or reaction vessel, in cell culture, etc., rather than within an organism (e.g., animal, plant and / or microbe).
[0089] In vivo: As used herein, the term “in vivo” refers to events that occur within an organism (e.g., animal, plant and / or microbe).
[0090] Linkage phosphorus: as defined herein, the phrase “linkage phosphorus” is used to indicate that the particular phosphorus atom being referred to is the phosphorus atom present in the internucleotidic linkage, which phosphorus atom corresponds to the phosphorus atom of a phosphodiester internucleotidic linkage as occurs in naturally occurring DNA and RNA. In some embodiments, a linkage phosphorus atom is in a modified internucleotidic linkage, wherein each oxygen atom of a phosphodiester linkage is optionally and independently replaced by an organic or inorganic moiety. In some embodiments, a linkage phosphorus atom is chiral (e.g., as in phosphorothioate internucleotidic linkages). In some embodiments, a linkage phosphorus atom is achiral (e.g., as in natural phosphate linkages).
[0091] Modified nucleobase: The terms "modified nucleobase", "modified base" and the like refer to a chemical moiety which is chemically distinct from a nucleobase, but which is capable of performing at least Page 33 of 743 12621738v1Attorney Docket No.: 2010581-1488 one function of a nucleobase. In some embodiments, a modified nucleobase is a nucleobase which comprises a modification. In some embodiments, a modified nucleobase is capable of at least one function of a nucleobase, e.g., forming a moiety in a polymer capable of base-pairing to a nucleic acid comprising an at least complementary sequence of bases. In some embodiments, a modified nucleobase is substituted A, T, C, G, or U, or a substituted tautomer of A, T, C, G, or U. In some embodiments, a modified nucleobase in the context of oligonucleotides refer to a nucleobase that is not A, T, C, G or U.
[0092] Modified nucleoside: The term "modified nucleoside" refers to a moiety derived from or chemically similar to a natural nucleoside, but which comprises a chemical modification which differentiates it from a natural nucleoside. Non-limiting examples of modified nucleosides include those which comprise a modification at the base and / or the sugar. Non-limiting examples of modified nucleosides include those with a 2’ modification at a sugar. Non-limiting examples of modified nucleosides also include abasic nucleosides (which lack a nucleobase). In some embodiments, a modified nucleoside is capable of at least one function of a nucleoside, e.g., forming a moiety in a polymer capable of base-pairing to a nucleic acid comprising an at least complementary sequence of bases.
[0093] Modified nucleotide: The term “modified nucleotide” includes any chemical moiety which differs structurally from a natural nucleotide but is capable of performing at least one function of a natural nucleotide. In some embodiments, a modified nucleotide comprises a modification at a sugar, base and / or internucleotidic linkage. In some embodiments, a modified nucleotide comprises a modified sugar, modified nucleobase and / or modified internucleotidic linkage. In some embodiments, a modified nucleotide is capable of at least one function of a nucleotide, e.g., forming a subunit in a polymer capable of base-pairing to a nucleic acid comprising an at least complementary sequence of bases.
[0094] Modified sugar: The term “modified sugar” refers to a moiety that can replace a sugar. A modified sugar mimics the spatial arrangement, electronic properties, or some other physicochemical property of a sugar. In some embodiments, as described in the present disclosure, a modified sugar is substituted ribose or deoxyribose. In some embodiments, a modified sugar comprises a 2’-modification. Examples of useful 2’- modification are widely utilized in the art and described herein. In some embodiments, a 2’-modification is 2’-F. In some embodiments, a 2’-modification is 2’-OR, wherein R is optionally substituted C1-10aliphatic. In some embodiments, a 2’-modification is 2’-OMe. In some embodiments, a 2’-modification is 2’-MOE. In some embodiments, a modified sugar is a bicyclic sugar (e.g., a sugar used in LNA, BNA, etc.). In some embodiments, in the context of oligonucleotides, a modified sugar is a sugar that is not ribose or deoxyribose as typically found in natural RNA or DNA.
[0095] Nucleic acid: The term “nucleic acid”, as used herein, includes any nucleotides and polymers thereof. The term “polynucleotide”, as used herein, refers to a polymeric form of nucleotides of any length, either ribonucleotides (RNA) or deoxyribonucleotides (DNA) or a combination thereof. These terms refer to the primary structure of the molecules and, thus, include double- and single-stranded DNA, and double- and single-stranded RNA. These terms include, as equivalents, analogs of either RNA or DNA comprising Page 34 of 743 12621738v1Attorney Docket No.: 2010581-1488 modified nucleotides and / or modified polynucleotides, such as, though not limited to, methylated, protected and / or capped nucleotides or polynucleotides. The terms encompass poly- or oligo-ribonucleotides (RNA) and poly- or oligo-deoxyribonucleotides (DNA); RNA or DNA derived from N-glycosides or C-glycosides of nucleobases and / or modified nucleobases; nucleic acids derived from sugars and / or modified sugars; and nucleic acids derived from phosphate bridges and / or modified internucleotidic linkages. The term encompasses nucleic acids containing any combinations of nucleobases, modified nucleobases, sugars, modified sugars, phosphate bridges or modified internucleotidic linkages. Examples include, and are not limited to, nucleic acids containing ribose moieties, nucleic acids containing deoxy-ribose moieties, nucleic acids containing both ribose and deoxyribose moieties, nucleic acids containing ribose and modified ribose moieties. Unless otherwise specified, the prefix poly- refers to a nucleic acid containing 2 to about 10,000 nucleotide monomer units and wherein the prefix oligo- refers to a nucleic acid containing 2 to about 200 nucleotide monomer units.
[0096] Nucleobase: The term “nucleobase” refers to the parts of nucleic acids that are involved in the hydrogen-bonding that binds one nucleic acid strand to another complementary strand in a sequence specific manner. The most common naturally-occurring nucleobases are adenine (A), guanine (G), uracil (U), cytosine (C), and thymine (T). In some embodiments, a naturally-occurring nucleobases are modified adenine, guanine, uracil, cytosine, or thymine. In some embodiments, a naturally-occurring nucleobases are methylated adenine, guanine, uracil, cytosine, or thymine. In some embodiments, a nucleobase comprises a heteroaryl ring wherein a ring atom is nitrogen, and when in a nucleoside, the nitrogen is bonded to a sugar moiety. In some embodiments, a nucleobase comprises a heterocyclic ring wherein a ring atom is nitrogen, and when in a nucleoside, the nitrogen is bonded to a sugar moiety. In some embodiments, a nucleobase is a “modified nucleobase,” a nucleobase other than adenine (A), guanine (G), uracil (U), cytosine (C), and thymine (T). In some embodiments, a modified nucleobase is substituted A, T, C, G or U. In some embodiments, a modified nucleobase is a substituted tautomer of A, T, C, G, or U. In some embodiments, a modified nucleobases is methylated adenine, guanine, uracil, cytosine, or thymine. In some embodiments, a modified nucleobase mimics the spatial arrangement, electronic properties, or some other physicochemical property of the nucleobase and retains the property of hydrogen-bonding that binds one nucleic acid strand to another in a sequence specific manner. In some embodiments, a modified nucleobase can pair with all of the five naturally occurring bases (uracil, thymine, adenine, cytosine, or guanine) without substantially affecting the melting behavior, recognition by intracellular enzymes or activity of the oligonucleotide duplex. As used herein, the term “nucleobase” also encompasses structural analogs used in lieu of natural or naturally-occurring nucleotides, such as modified nucleobases and nucleobase analogs. In some embodiments, a nucleobase is optionally substituted A, T, C, G, or U, or an optionally substituted tautomer of A, T, C, G, or U. In some embodiments, a “nucleobase” refers to a nucleobase unit in an oligonucleotide or a nucleic acid (e.g., A, T, C, G or U as in an oligonucleotide or a nucleic acid).
[0097] Nucleoside: The term “nucleoside” refers to a moiety wherein a nucleobase or a modified Page 35 of 743 12621738v1Attorney Docket No.: 2010581-1488 nucleobase is covalently bound to a sugar or a modified sugar. In some embodiments, a nucleoside is a natural nucleoside, e.g., adenosine, deoxyadenosine, guanosine, deoxyguanosine, thymidine, uridine, cytidine, or deoxycytidine. In some embodiments, a nucleoside is a modified nucleoside, e.g., a substituted natural nucleoside selected from adenosine, deoxyadenosine, guanosine, deoxyguanosine, thymidine, uridine, cytidine, and deoxycytidine. In some embodiments, a nucleoside is a modified nucleoside, e.g., a substituted tautomer of a natural nucleoside selected from adenosine, deoxyadenosine, guanosine, deoxyguanosine, thymidine, uridine, cytidine, and deoxycytidine. In some embodiments, a “nucleoside” refers to a nucleoside unit in an oligonucleotide or a nucleic acid.
[0098] Nucleotide: The term “nucleotide” as used herein refers to a monomeric unit of a polynucleotide that consists of a nucleobase, a sugar, and one or more internucleotidic linkages (e.g., phosphate linkages in natural DNA and RNA). The naturally occurring bases [guanine, (G), adenine, (A), cytosine, (C), thymine, (T), and uracil (U)] are derivatives of purine or pyrimidine, though it should be understood that naturally and non-naturally occurring base analogs are also included. The naturally occurring sugar is the pentose (five- carbon sugar) deoxyribose (which forms DNA) or ribose (which forms RNA), though it should be understood that naturally and non-naturally occurring sugar analogs are also included. Nucleotides are linked via internucleotidic linkages to form nucleic acids, or polynucleotides. Many internucleotidic linkages are known in the art (such as, though not limited to, phosphate, phosphorothioates, boranophosphates and the like). Artificial nucleic acids include PNAs (peptide nucleic acids), phosphotriesters, phosphorothionates, H- phosphonates, phosphoramidates, boranophosphates, methylphosphonates, phosphonoacetates, thiophosphonoacetates and other variants of the phosphate backbone of native nucleic acids, such as those described herein. In some embodiments, a natural nucleotide comprises a naturally occurring base, sugar and internucleotidic linkage. As used herein, the term “nucleotide” also encompasses structural analogs used in lieu of natural or naturally-occurring nucleotides, such as modified nucleotides and nucleotide analogs. In some embodiments, a “nucleotide” refers to a nucleotide unit in an oligonucleotide or a nucleic acid.
[0099] Oligonucleotide: The term "oligonucleotide" refers to a polymer or oligomer of nucleotides, and may contain any combination of natural and non-natural nucleobases, sugars, and internucleotidic linkages.
[0100] Oligonucleotides can be single-stranded or double-stranded. A single-stranded oligonucleotide can have double-stranded regions (formed by two portions of the single-stranded oligonucleotide) and a double-stranded oligonucleotide, which comprises two oligonucleotide chains, can have single-stranded regions for example, at regions where the two oligonucleotide chains are not complementary to each other. Example oligonucleotides include, but are not limited to structural genes, genes including control and termination regions, self-replicating systems such as viral or plasmid DNA, single-stranded and double- stranded RNAi agents and other RNA interference reagents (RNAi agents or iRNA agents), shRNA, antisense oligonucleotides, ribozymes, microRNAs, microRNA mimics, supermirs, aptamers, antimirs, antagomirs, Ul adaptors, triplex-forming oligonucleotides, G-quadruplex oligonucleotides, RNA activators, immuno- stimulatory oligonucleotides, and decoy oligonucleotides. Page 36 of 743 12621738v1Attorney Docket No.: 2010581-1488
[0101] Oligonucleotides of the present disclosure can be of various lengths. In particular embodiments, oligonucleotides can range from about 2 to about 200 nucleosides in length. In various related embodiments, oligonucleotides, single-stranded, double-stranded, or triple-stranded, can range in length from about 4 to about 10 nucleosides, from about 10 to about 50 nucleosides, from about 20 to about 50 nucleosides, from about 15 to about 30 nucleosides, from about 20 to about 30 nucleosides in length. In some embodiments, an oligonucleotide is from about 9 to about 39 nucleosides in length. In some embodiments, an oligonucleotide is from about 25 to about 70 nucleosides in length. In some embodiments, an oligonucleotide is from about 26 to about 70 nucleosides in length. In some embodiments, an oligonucleotide is from about 27 to about 70 nucleosides in length. In some embodiments, an oligonucleotide is from about 28 to about 70 nucleosides in length. In some embodiments, an oligonucleotide is from about 29 to about 70 nucleosides in length. In some embodiments, an oligonucleotide is from about 30 to about 70 nucleosides in length. In some embodiments, an oligonucleotide is from about 31 to about 70 nucleosides in length. In some embodiments, an oligonucleotide is from about 32 to about 70 nucleosides in length. In some embodiments, an oligonucleotide is from about 25 to about 60 nucleosides in length. In some embodiments, an oligonucleotide is from about 25 to about 50 nucleosides in length. In some embodiments, an oligonucleotide is from about 25 to about 40 nucleosides in length. In some embodiments, an oligonucleotide is from about 30 to about 40 nucleosides in length. In some embodiments, the oligonucleotide is at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleosides in length. In some embodiments, an oligonucleotide is at least 4 nucleosides in length. In some embodiments, an oligonucleotide is at least 5 nucleosides in length. In some embodiments, an oligonucleotide is at least 6 nucleosides in length. In some embodiments, an oligonucleotide is at least 7 nucleosides in length. In some embodiments, an oligonucleotide is at least 8 nucleosides in length. In some embodiments, an oligonucleotide is at least 9 nucleosides in length. In some embodiments, an oligonucleotide is at least 10 nucleosides in length. In some embodiments, an oligonucleotide is at least 11 nucleosides in length. In some embodiments, an oligonucleotide is at least 12 nucleosides in length. In some embodiments, an oligonucleotide is at least 15 nucleosides in length. In some embodiments, an oligonucleotide is at least 15 nucleosides in length. In some embodiments, an oligonucleotide is at least 16 nucleosides in length. In some embodiments, an oligonucleotide is at least 17 nucleosides in length. In some embodiments, an oligonucleotide is at least 18 nucleosides in length. In some embodiments, an oligonucleotide is at least 19 nucleosides in length. In some embodiments, an oligonucleotide is at least 20 nucleosides in length. In some embodiments, an oligonucleotide is at least 25 nucleosides in length. In some embodiments, an oligonucleotide is at least 26 nucleosides in length. In some embodiments, an oligonucleotide is at least 27 nucleosides in length. In some embodiments, an oligonucleotide is at least 28 nucleosides in length. In some embodiments, an oligonucleotide is at least 29 nucleosides in length. In some embodiments, an oligonucleotide is at least 30 nucleosides in length. In some embodiments, an oligonucleotide is at least 31 nucleosides in length. In some embodiments, an oligonucleotide is at least 32 nucleosides in length. In some embodiments, an oligonucleotide is at least 33 nucleosides in length. In some embodiments, an oligonucleotide is at least 34 nucleosides in Page 37 of 743 12621738v1Attorney Docket No.: 2010581-1488 length. In some embodiments, an oligonucleotide is at least 35 nucleosides in length. In some embodiments, an oligonucleotide is at least 36 nucleosides in length. In some embodiments, an oligonucleotide is at least 37 nucleosides in length. In some embodiments, an oligonucleotide is at least 38 nucleosides in length. In some embodiments, an oligonucleotide is at least 39 nucleosides in length. In some embodiments, an oligonucleotide is at least 40 nucleosides in length. In some embodiments, an oligonucleotide is 25 nucleosides in length. In some embodiments, an oligonucleotide is 26 nucleosides in length. In some embodiments, an oligonucleotide is 27 nucleosides in length. In some embodiments, an oligonucleotide is 28 nucleosides in length. In some embodiments, an oligonucleotide is 29 nucleosides in length. In some embodiments, an oligonucleotide is 30 nucleosides in length. In some embodiments, an oligonucleotide is 31 nucleosides in length. In some embodiments, an oligonucleotide is 32 nucleosides in length. In some embodiments, an oligonucleotide is 33 nucleosides in length. In some embodiments, an oligonucleotide is 34 nucleosides in length. In some embodiments, an oligonucleotide is 35 nucleosides in length. In some embodiments, an oligonucleotide is 36 nucleosides in length. In some embodiments, an oligonucleotide is 37 nucleosides in length. In some embodiments, an oligonucleotide is 38 nucleosides in length. In some embodiments, an oligonucleotide is 39 nucleosides in length. In some embodiments, an oligonucleotide is 40 nucleosides in length. In some embodiments, each nucleoside counted in an oligonucleotide length independently comprises a nucleobase comprising a ring having at least one nitrogen ring atom. In some embodiments, each nucleoside counted in an oligonucleotide length independently comprises A, T, C, G, or U, or optionally substituted A, T, C, G, or U, or an optionally substituted tautomer of A, T, C, G or U.
[0102] Oligonucleotide type: As used herein, the phrase “oligonucleotide type” is used to define an oligonucleotide that has a particular base sequence, pattern of backbone linkages (i.e., pattern of internucleotidic linkage types, for example, phosphate, phosphorothioate, phosphorothioate triester, etc.), pattern of backbone chiral centers [i.e., pattern of linkage phosphorus stereochemistry (Rp / Sp)], and pattern of backbone phosphorus modifications. In some embodiments, oligonucleotides of a common designated “type” are structurally identical to one another.
[0103] One of skill in the art will appreciate that synthetic methods of the present disclosure provide for a degree of control during the synthesis of an oligonucleotide strand such that each nucleotide unit of the oligonucleotide strand can be designed and / or selected in advance to have a particular stereochemistry at the linkage phosphorus and / or a particular modification at the linkage phosphorus, and / or a particular base, and / or a particular sugar. In some embodiments, an oligonucleotide strand is designed and / or selected in advance to have a particular combination of stereocenters at the linkage phosphorus. In some embodiments, an oligonucleotide strand is designed and / or determined to have a particular combination of modifications at the linkage phosphorus. In some embodiments, an oligonucleotide strand is designed and / or selected to have a particular combination of bases. In some embodiments, an oligonucleotide strand is designed and / or selected to have a particular combination of one or more of the above structural characteristics. In some embodiments, the present disclosure provides compositions comprising or consisting of a plurality of oligonucleotide Page 38 of 743 12621738v1Attorney Docket No.: 2010581-1488 molecules (e.g., chirally controlled oligonucleotide compositions). In some embodiments, all such molecules are of the same type (i.e., are structurally identical to one another). In some embodiments, however, provided compositions comprise a plurality of oligonucleotides of different types, typically in pre-determined relative amounts.
[0104] Optionally Substituted: As described herein, compounds of the disclosure may contain optionally substituted, substituted and / or unsubstituted moieties. In general, the term “substituted,” means that one or more hydrogens of the designated moiety are independently replaced with a substituent. Unless otherwise indicated, an “optionally substituted” group may independently have a substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with two or more substituents, the substituents may be either the same or different at every position. In some embodiments, an optionally substituted group is unsubstituted. In some embodiments, an optionally substituted group is substituted. Various substituents are described below.
[00105] Monovalent substituents are independently halogen; –(CH2)0–4R ; –(CH2)0–4OR ; −O(CH2)0-4Ro, –O–(CH2)0–4C(O)OR°; –(CH2)0–4CH(OR )2; –(CH2)0–4Ph, which may be substituted with R°; −(CH2)0–4O(CH2)0–1Ph which may be substituted with R°; –CH=CHPh, which may be substituted with R°; –(CH2)0–4O(CH2)0–1-pyridyl which may be substituted with R°; –NO2; –CN; –N3; -(CH2)0–4N(R )2; –(CH2)0–4N(R )C(O)R ; –N(R )C(S)R ; –(CH2)0–4N(R )C(O)N(R )2; −N(R )C(S)N(R )2; –(CH2)0–4N(R )C(O)OR ; –N(R )N(R )C(O)R ; −N(R )N(R )C(O)N(R )2; −N(R )N(R )C(O)OR ; –(CH2)0–4C(O)R ; –C(S)R ; –(CH2)0–4C(O)OR ; –(CH2)0–4C(O)SR ; −(CH2)0–4C(O)OSi(R )3; –(CH2)0–4OC(O)R ; –OC(O)(CH2)0–4SR°,−SC(S)SR°; −(CH2)0–4SC(O)R ; –(CH2)0–4C(O)N(R )2; –C(S)N(R )2; –C(S)SR°; −SC(S)SR°, -(CH2)0–R R R R H R − R R H R H2)0–4S(O)2R ; –(CH2)0–4S(O)2OR ; –(CH2)0–4OS(O)2R ; −S(O)2N(R )2; -(CH2)0–4S(O)R ; –N(R )S(O)2N(R )2; –N(R )S(O)2R ; –N(OR )R ; −C(NH)N(R )2; –Si(R )3; –OSi(R )3; −P(R )2; −P(OR )2; −OP(R )2;−OP(OR )2; −N(R )P(R )2; −B(R )2; −OB(R )2; −P(O)(R )2; −OP(O)(R )2; −N(R )P(O)(R )2; –(C1-4 straightor branched alkylene)O–N(R )2; or –(C1-4 straight or branched alkylene)C(O)O–N(R )2; wherein each R maybe independently substituted as defined below and is independently hydrogen, C1-10(e.g., C1-6, C1-4, etc.) aliphatic, C1-10(e.g., C1-6, C1-4, etc.) heteroaliphatic having 1-5 heteroatoms independently selected from nitrogen, oxygen, sulfur, silicon and phosphorus, C6-10(e.g., C6, C10, etc.) aryl, 5-10 (e.g., 5-9, 5-6, 5, 6, 9, 10, etc.) membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen and sulfur, −CH2−(C6-10(e.g., C6, C10, etc.) aryl), −O(CH2)0-1(C6-10(e.g., C6, C10, etc.) aryl), −CH2−(5-10 (e.g., 5-9, 5-6, 5, 6, 9, 10, etc.) membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen and sulfur), −O(CH2)0-1(5-10 (e.g., 5-9, 5-6, 5, 6, 9, 10, etc.) membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen and sulfur), a 3-10 (e.g., 3-6, 5-6, 3, 4, 5, 6, 7, 8, 9, 10, etc.) membered, monocyclic, bicyclic, or polycyclic, saturated, or partially unsaturated ring having 0-5 heteroatoms independently selected from nitrogen, oxygen, sulfur, silicon and phosphorus, or, notwithstanding the Page 39 of 743 12621738v1Attorney Docket No.: 2010581-1488 definition above, two independent occurrences of R , taken together with their intervening atom(s), form a 3-10 (e.g., 3-6, 5-6, 3, 4, 5, 6, 7, 8, 9, 10, etc.) membered, monocyclic, bicyclic, or polycyclic, saturated, partially unsaturated or aromatic ring (for aromatic ring, 5-10 (e.g., 5-9, 5-6, 5, 6, 9, 10, etc.) membered) having, in addition to the intervening atom(s), 0-5 heteroatoms independently selected from nitrogen, oxygen, sulfur, silicon and phosphorus, which may be substituted as defined below.
[00106] Monovalent substituents on R (or the ring formed by taking two independent occurrences of Rtogether with their intervening atoms), are independently halogen, –(CH2)0–2R , –(haloR ), –(CH2)0–2OH, –(CH2)0–2OR , –(CH2)0–2CH(OR )2; –O(haloR ), –CN, –N3, –(CH2)0–2C(O)R , –(CH2)0–2C(O)OH, –(CH2)0–2C(O)OR , –(CH2)0–2SR , –(CH2)0–2SH, –(CH2)0–2NH2, –(CH2)0–2NHR , –(CH2)0–2NR 2, –NO2, –SiR 3, –tedor where preceded by halo is substituted only with one or more halogens, and is independently selected from C1–4aliphatic, –CH2Ph, –O(CH2)0–1Ph, or a 3-6 (e.g., 3-5, 5-6, etc.)-membered saturated, partially unsaturated, or aromatic ring (for aromatic ring, 5- or 6-membered) having 0-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. Divalent substituents on a saturated carbon atom of R are independently =O or=S.
[0107] Divalent substituents are independently the following: =O, =S, =NNR*2, =NNHC(O)R*, =NNHC(O)OR*, =NNHS(O)2R*, =NR*, =NOR*, −O(C(R*2))2–3O−, or −S(C(R*2))2–3S−, wherein each independent occurrence of R*is selected from hydrogen, C1-6aliphatic which may be substituted as defined below, or an unsubstituted 3-6 (e.g., 3-5, 5-6, etc.)-membered saturated, partially unsaturated, or aromatic ring (for aromatic ring, 5- or 6-membered) having 0-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur. Divalent substituents that are bound to vicinal substitutable carbons of an “optionally substituted” group are independently −O(CR*2)2–3O−, wherein each independent occurrence of R*is selected from hydrogen, C1-6aliphatic which may be substituted as defined below, or an unsubstituted 3-6 (e.g., 3-5, 5-6, etc.)-membered saturated, partially unsaturated, or aromatic ring (for aromatic ring, 5- or 6-membered) having 0-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
[00108] Substituents on the aliphatic group of R* are independently halogen, –R , -(haloR ), –OH, −OR ,–O(haloR ), –CN, –C(O)OH, –C(O)OR , –NH2, –NHR , –NR 2, or –NO2, wherein each R is unsubstitutedor where preceded by “halo” is substituted only with one or more halogens, and is independently C1–4aliphatic, –CH2Ph, –O(CH2)0–1Ph, or a 3-6 (e.g., 3-5, 5-6, etc.)-membered saturated, partially unsaturated, or aromatic ring (for aromatic ring, 5- or 6-membered) having 0-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
[0109] Substituents on a substitutable nitrogen are independently –R†, −NR†2, −C(O)R†, –C(O)OR†, – C(O)C(O)R†, –C(O)CH2C(O)R†, –S(O)2R†, –S(O)2NR†2, −C(S)NR†2, –C(NH)NR†2, or –N(R†)S(O)2R†; wherein each R†is independently hydrogen, C1–6 aliphatic which may be substituted as defined below, unsubstituted –OPh, or an unsubstituted 3-6 (e.g., 3-5, 5-6, etc.)-membered saturated, partially unsaturated, or Page 40 of 743 12621738v1Attorney Docket No.: 2010581-1488 aromatic ring (for aromatic ring, 5- or 6-membered) having 0-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, or, notwithstanding the definition above, two independent occurrences of R†, taken together with their intervening atom(s) form an unsubstituted 3–12 (e.g., 3-10, 3-6, 5-10, 5-6, 3, 4, 5, 6, 7, 8, 9, 10, etc.) membered saturated, partially unsaturated, or aryl mono– or bicyclic ring having 0–4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
[0110] Substituents on the aliphatic group of R† are independently halogen, −R , -(haloR ), −OH, –OR ,–O(haloR ), –CN, –C(O)OH, –C(O)OR , –NH2, –NHR , –NR 2, or –NO2, wherein each R is unsubstitutedor where preceded by “halo” is substituted only with one or more halogens, and is independently C1–4aliphatic, –CH2Ph, –O(CH2)0–1Ph, or a 3-6 (e.g., 3-5, 5-6, etc.)-membered saturated, partially unsaturated, or aromatic ring (for aromatic ring, 5- or 6-membered) having 0-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
[0111] P-modification: as used herein, the term “P-modification” refers to any modification at the linkage phosphorus other than a stereochemical modification. In some embodiments, a P-modification comprises addition, substitution, or removal of a pendant moiety covalently attached to a linkage phosphorus.
[0112] Partially unsaturated: As used herein, the term “partially unsaturated” refers to a ring moiety that includes at least one double or triple bond. The term “partially unsaturated” is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aryl or heteroaryl moieties, as herein defined.
[0113] Pharmaceutical composition: As used herein, the term “pharmaceutical composition” refers to an active agent, formulated together with one or more pharmaceutically acceptable carriers. In some embodiments, an active agent is present in unit dose amount appropriate for administration in a therapeutic regimen that shows a statistically significant probability of achieving a predetermined therapeutic effect when administered to a relevant population. In some embodiments, pharmaceutical compositions may be specially formulated for administration in solid or liquid form, including those adapted for the following: oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; topical application, for example, as a cream, ointment, or a controlled-release patch or spray applied to the skin, lungs, or oral cavity; intravaginally or intrarectally, for example, as a pessary, cream, or foam; sublingually; ocularly; transdermally; or nasally, pulmonary, and to other mucosal surfaces.
[0114] Pharmaceutically acceptable: As used herein, the phrase “pharmaceutically acceptable” refers to those compounds, materials, compositions and / or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit / risk ratio. Page 41 of 743 12621738v1Attorney Docket No.: 2010581-1488
[0115] Pharmaceutically acceptable carrier: As used herein, the term “pharmaceutically acceptable carrier” means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient. Some examples of materials which can serve as pharmaceutically-acceptable carriers include: sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen- free water; isotonic saline; Ringer’s solution; ethyl alcohol; pH buffered solutions; polyesters, polycarbonates and / or polyanhydrides; and other non-toxic compatible substances employed in pharmaceutical formulations.
[0116] Pharmaceutically acceptable salt: The term “pharmaceutically acceptable salt”, as used herein, refers to salts of such compounds that are appropriate for use in pharmaceutical contexts, i.e., salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit / risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge, et al. describes pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 66: 1-19 (1977). In some embodiments, pharmaceutically acceptable salt include, but are not limited to, nontoxic acid addition salts, which are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. In some embodiments, pharmaceutically acceptable salts include, but are not limited to, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2- hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. In some embodiments, a provided compound comprises one or more acidic groups, e.g., an oligonucleotide, and a pharmaceutically acceptable salt is an alkali, alkaline earth metal, or ammonium (e.g., an ammonium salt of N(R)3, wherein each R is independently defined and described in the present disclosure) salt. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. In some embodiments, a Page 42 of 743 12621738v1Attorney Docket No.: 2010581-1488 pharmaceutically acceptable salt is a sodium salt. In some embodiments, a pharmaceutically acceptable salt is a potassium salt. In some embodiments, a pharmaceutically acceptable salt is a calcium salt. In some embodiments, pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, alkyl having from 1 to 6 carbon atoms, sulfonate and aryl sulfonate. In some embodiments, a provided compound comprises more than one acid groups, for example, an oligonucleotide may comprise two or more acidic groups (e.g., in natural phosphate linkages and / or modified internucleotidic linkages). In some embodiments, a pharmaceutically acceptable salt, or generally a salt, of such a compound comprises two or more cations, which can be the same or different. In some embodiments, in a pharmaceutically acceptable salt (or generally, a salt), all ionizable hydrogen (e.g., in an aqueous solution with a pKa no more than about 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2; in some embodiments, no more than about 7; in some embodiments, no more than about 6; in some embodiments, no more than about 5; in some embodiments, no more than about 4; in some embodiments, no more than about 3) in the acidic groups are replaced with cations. In some embodiments, each phosphorothioate and phosphate group independently exists in its salt form (e.g., if sodium salt, −O−P(O)(SNa)−O− and −O−P(O)(ONa)−O−, respectively). In some embodiments, each phosphorothioate and phosphate internucleotidic linkage independently exists in its salt form (e.g., if sodium salt, −O−P(O)(SNa)−O− and −O−P(O)(ONa)−O−, respectively). In some embodiments, a pharmaceutically acceptable salt is a sodium salt of an oligonucleotide. In some embodiments, a pharmaceutically acceptable salt is a sodium salt of an oligonucleotide, wherein each acidic phosphate and modified phosphate group (e.g., phosphorothioate, phosphate, etc.), if any, exists as a salt form (all sodium salt).
[0117] Predetermined: By predetermined (or pre-determined) is meant deliberately selected or non- random or controlled, for example as opposed to randomly occurring, random, or achieved without control. Those of ordinary skill in the art, reading the present specification, will appreciate that the present disclosure provides technologies that permit selection of particular chemistry and / or stereochemistry features to be incorporated into oligonucleotide compositions, and further permits controlled preparation of oligonucleotide compositions having such chemistry and / or stereochemistry features. Such provided compositions are “predetermined” as described herein. Compositions that may contain certain oligonucleotides because they happen to have been generated through a process that are not controlled to intentionally generate the particular chemistry and / or stereochemistry features are not “predetermined” compositions. In some embodiments, a predetermined composition is one that can be intentionally reproduced (e.g., through repetition of a controlled process). In some embodiments, a predetermined level of a plurality of oligonucleotides in a composition means that the absolute amount, and / or the relative amount (ratio, percentage, etc.) of the plurality of oligonucleotides in the composition is controlled. In some embodiments, a predetermined level of a plurality of oligonucleotides in a composition is achieved through chirally controlled oligonucleotide preparation.
[0118] Protecting group: The term “protecting group,” as used herein, is well known in the art and includes those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, Page 43 of 743 12621738v1Attorney Docket No.: 2010581-1488 3rdedition, John Wiley & Sons, 1999, the entirety of which is incorporated herein by reference. Also included are those protecting groups specially adapted for nucleoside and nucleotide chemistry described in Current Protocols in Nucleic Acid Chemistry, edited by Serge L. Beaucage et al.06 / 2012, the entirety of Chapter 2 is incorporated herein by reference. Suitable amino–protecting groups include methyl carbamate, ethyl carbamante, 9–fluorenylmethyl carbamate (Fmoc), 9–(2–sulfo)fluorenylmethyl carbamate, 9–(2,7– dibromo)fluoroenylmethyl carbamate, 2,7–di–t–butyl–[9–(10,10–dioxo–10,10,10,10– tetrahydrothioxanthyl)]methyl carbamate (DBD–Tmoc), 4–methoxyphenacyl carbamate (Phenoc), 2,2,2– trichloroethyl carbamate (Troc), 2–trimethylsilylethyl carbamate (Teoc), 2–phenylethyl carbamate (hZ), 1–(1– adamantyl)–1–methylethyl carbamate (Adpoc), 1,1–dimethyl–2–haloethyl carbamate, 1,1–dimethyl–2,2– dibromoethyl carbamate (DB–t–BOC), 1,1–dimethyl–2,2,2–trichloroethyl carbamate (TCBOC), 1–methyl–1– (4–biphenylyl)ethyl carbamate (Bpoc), 1–(3,5–di–t–butylphenyl)–1–methylethyl carbamate (t–Bumeoc), 2– (2’– and 4’–pyridyl)ethyl carbamate (Pyoc), 2–(N,N–dicyclohexylcarboxamido)ethyl carbamate, t–butyl carbamate (BOC), 1–adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl carbamate (Alloc), 1– isopropylallyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4–nitrocinnamyl carbamate (Noc), 8–quinolyl carbamate, N–hydroxypiperidinyl carbamate, alkyldithio carbamate, benzyl carbamate (Cbz), p– methoxybenzyl carbamate (Moz), p–nitobenzyl carbamate, p–bromobenzyl carbamate, p–chlorobenzyl carbamate, 2,4–dichlorobenzyl carbamate, 4–methylsulfinylbenzyl carbamate (Msz), 9–anthrylmethyl carbamate, diphenylmethyl carbamate, 2–methylthioethyl carbamate, 2–methylsulfonylethyl carbamate, 2–(p– toluenesulfonyl)ethyl carbamate, [2–(1,3–dithianyl)]methyl carbamate (Dmoc), 4–methylthiophenyl carbamate (Mtpc), 2,4–dimethylthiophenyl carbamate (Bmpc), 2–phosphonioethyl carbamate (Peoc), 2– triphenylphosphonioisopropyl carbamate (Ppoc), 1,1–dimethyl–2–cyanoethyl carbamate, m–chloro–p– acyloxybenzyl carbamate, p–(dihydroxyboryl)benzyl carbamate, 5–benzisoxazolylmethyl carbamate, 2– (trifluoromethyl)–6–chromonylmethyl carbamate (Tcroc), m–nitrophenyl carbamate, 3,5–dimethoxybenzyl carbamate, o–nitrobenzyl carbamate, 3,4–dimethoxy–6–nitrobenzyl carbamate, phenyl(o–nitrophenyl)methyl carbamate, phenothiazinyl–(10)–carbonyl derivative, N’–p–toluenesulfonylaminocarbonyl derivative, N’– phenylaminothiocarbonyl derivative, t–amyl carbamate, S–benzyl thiocarbamate, p–cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl carbamate, p– decyloxybenzyl carbamate, 2,2–dimethoxycarbonylvinyl carbamate, o–(N,N–dimethylcarboxamido)benzyl carbamate, 1,1–dimethyl–3–(N,N–dimethylcarboxamido)propyl carbamate, 1,1–dimethylpropynyl carbamate, di(2–pyridyl)methyl carbamate, 2–furanylmethyl carbamate, 2–iodoethyl carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p–(p’–methoxyphenylazo)benzyl carbamate, 1–methylcyclobutyl carbamate, 1–methylcyclohexyl carbamate, 1–methyl–1–cyclopropylmethyl carbamate, 1–methyl–1–(3,5– dimethoxyphenyl)ethyl carbamate, 1–methyl–1–(p–phenylazophenyl)ethyl carbamate, 1–methyl–1– phenylethyl carbamate, 1–methyl–1–(4–pyridyl)ethyl carbamate, phenyl carbamate, p–(phenylazo)benzyl carbamate, 2,4,6–tri–t–butylphenyl carbamate, 4–(trimethylammonium)benzyl carbamate, 2,4,6– trimethylbenzyl carbamate, formamide, acetamide, chloroacetamide, trichloroacetamide, trifluoroacetamide, Page 44 of 743 12621738v1Attorney Docket No.: 2010581-1488 phenylacetamide, 3–phenylpropanamide, picolinamide, 3–pyridylcarboxamide, N–benzoylphenylalanyl derivative, benzamide, p–phenylbenzamide, o–nitophenylacetamide, o–nitrophenoxyacetamide, acetoacetamide, (N’–dithiobenzyloxycarbonylamino)acetamide, 3–(p–hydroxyphenyl)propanamide, 3–(o– nitrophenyl)propanamide, 2–methyl–2–(o–nitrophenoxy)propanamide, 2–methyl–2–(o– phenylazophenoxy)propanamide, 4–chlorobutanamide, 3–methyl–3–nitrobutanamide, o–nitrocinnamide, N– acetylmethionine derivative, o–nitrobenzamide, o–(benzoyloxymethyl)benzamide, 4,5–diphenyl–3–oxazolin– 2–one, N–phthalimide, N–dithiasuccinimide (Dts), N–2,3–diphenylmaleimide, N–2,5–dimethylpyrrole, N– 1,1,4,4–tetramethyldisilylazacyclopentane adduct (STABASE), 5–substituted 1,3–dimethyl–1,3,5– triazacyclohexan–2–one, 5–substituted 1,3–dibenzyl–1,3,5–triazacyclohexan–2–one, 1–substituted 3,5– dinitro–4–pyridone, N–methylamine, N–allylamine, N–[2–(trimethylsilyl)ethoxy]methylamine (SEM), N–3– acetoxypropylamine, N–(1–isopropyl–4–nitro–2–oxo–3–pyroolin–3–yl)amine, quaternary ammonium salts, N–benzylamine, N–di(4–methoxyphenyl)methylamine, N–5–dibenzosuberylamine, N–triphenylmethylamine (Tr), N–[(4–methoxyphenyl)diphenylmethyl]amine (MMTr), N–9–phenylfluorenylamine (PhF), N–2,7– dichloro–9–fluorenylmethyleneamine, N–ferrocenylmethylamino (Fcm), N–2–picolylamino N’–oxide, N– 1,1–dimethylthiomethyleneamine, N–benzylideneamine, N–p–methoxybenzylideneamine, N– diphenylmethyleneamine, N–[(2–pyridyl)mesityl]methyleneamine, N–(N’,N’– dimethylaminomethylene)amine, N,N’–isopropylidenediamine, N–p–nitrobenzylideneamine, N– salicylideneamine, N–5–chlorosalicylideneamine, N–(5–chloro–2–hydroxyphenyl)phenylmethyleneamine, N–cyclohexylideneamine, N–(5,5–dimethyl–3–oxo–1–cyclohexenyl)amine, N–borane derivative, N– diphenylborinic acid derivative, N–[phenyl(pentacarbonylchromium– or tungsten)carbonyl]amine, N–copper chelate, N–zinc chelate, N–nitroamine, N–nitrosoamine, amine N–oxide, diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt), diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzyl phosphoramidate, diphenyl phosphoramidate, benzenesulfenamide, o–nitrobenzenesulfenamide (Nps), 2,4– dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2–nitro–4–methoxybenzenesulfenamide, triphenylmethylsulfenamide, 3–nitropyridinesulfenamide (Npys), p–toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6,–trimethyl–4–methoxybenzenesulfonamide (Mtr), 2,4,6– trimethoxybenzenesulfonamide (Mtb), 2,6–dimethyl–4–methoxybenzenesulfonamide (Pme), 2,3,5,6– tetramethyl–4–methoxybenzenesulfonamide (Mte), 4–methoxybenzenesulfonamide (Mbs), 2,4,6– trimethylbenzenesulfonamide (Mts), 2,6–dimethoxy–4–methylbenzenesulfonamide (iMds), 2,2,5,7,8– pentamethylchroman–6–sulfonamide (Pmc), methanesulfonamide (Ms), β–trimethylsilylethanesulfonamide (SES), 9–anthracenesulfonamide, 4–(4’,8’–dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS), benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide.
[0119] Suitably protected carboxylic acids further include, but are not limited to, silyl–, alkyl–, alkenyl– , aryl–, and arylalkyl–protected carboxylic acids. Examples of suitable silyl groups include trimethylsilyl, triethylsilyl, t–butyldimethylsilyl, t–butyldiphenylsilyl, triisopropylsilyl, and the like. Examples of suitable alkyl groups include methyl, benzyl, p–methoxybenzyl, 3,4–dimethoxybenzyl, trityl, t–butyl, tetrahydropyran– Page 45 of 743 12621738v1Attorney Docket No.: 2010581-1488 2–yl. Examples of suitable alkenyl groups include allyl. Examples of suitable aryl groups include optionally substituted phenyl, biphenyl, or naphthyl. Examples of suitable arylalkyl groups include optionally substituted benzyl (e.g., p–methoxybenzyl (MPM), 3,4–dimethoxybenzyl, O–nitrobenzyl, p–nitrobenzyl, p–halobenzyl, 2,6–dichlorobenzyl, p–cyanobenzyl), and 2– and 4–picolyl.
[0120] Suitable hydroxyl protecting groups include methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t–butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM), p– methoxybenzyloxymethyl (PMBM), (4–methoxyphenoxy)methyl (p–AOM), guaiacolmethyl (GUM), t– butoxymethyl, 4–pentenyloxymethyl (POM), siloxymethyl, 2–methoxyethoxymethyl (MEM), 2,2,2– trichloroethoxymethyl, bis(2–chloroethoxy)methyl, 2–(trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3–bromotetrahydropyranyl, tetrahydrothiopyranyl, 1–methoxycyclohexyl, 4– methoxytetrahydropyranyl (MTHP), 4–methoxytetrahydrothiopyranyl, 4–methoxytetrahydrothiopyranyl S,S– dioxide, 1–[(2–chloro–4–methyl)phenyl]–4–methoxypiperidin–4–yl (CTMP), 1,4–dioxan–2–yl, tetrahydrofuranyl, tetrahydrothiofuranyl, 2,3,3a,4,5,6,7,7a–octahydro–7,8,8–trimethyl–4,7– methanobenzofuran–2–yl, 1–ethoxyethyl, 1–(2–chloroethoxy)ethyl, 1–methyl–1–methoxyethyl, 1–methyl–1– benzyloxyethyl, 1–methyl–1–benzyloxy–2–fluoroethyl, 2,2,2–trichloroethyl, 2–trimethylsilylethyl, 2– (phenylselenyl)ethyl, t–butyl, allyl, p–chlorophenyl, p–methoxyphenyl, 2,4–dinitrophenyl, benzyl, p– methoxybenzyl, 3,4–dimethoxybenzyl, o–nitrobenzyl, p–nitrobenzyl, p–halobenzyl, 2,6–dichlorobenzyl, p– cyanobenzyl, p–phenylbenzyl, 2–picolyl, 4–picolyl, 3–methyl–2–picolyl N–oxido, diphenylmethyl, p,p’– dinitrobenzhydryl, 5–dibenzosuberyl, triphenylmethyl, α–naphthyldiphenylmethyl, p– methoxyphenyldiphenylmethyl, di(p–methoxyphenyl)phenylmethyl, tri(p–methoxyphenyl)methyl, 4–(4’– bromophenacyloxyphenyl)diphenylmethyl, 4,4’,4’’–tris(4,5–dichlorophthalimidophenyl)methyl, 4,4’,4’’– tris(levulinoyloxyphenyl)methyl, 4,4’,4’’–tris(benzoyloxyphenyl)methyl, 3–(imidazol–1–yl)bis(4’,4’’– dimethoxyphenyl)methyl, 1,1–bis(4–methoxyphenyl)–1’–pyrenylmethyl, 9–anthryl, 9–(9–phenyl)xanthenyl, 9–(9–phenyl–10–oxo)anthryl, 1,3–benzodithiolan–2–yl, benzisothiazolyl S,S–dioxido, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl (TIPS), dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS), dimethylthexylsilyl, t–butyldimethylsilyl (TBDMS), t–butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri–p– xylylsilyl, triphenylsilyl, diphenylmethylsilyl (DPMS), t–butylmethoxyphenylsilyl (TBMPS), formate, benzoylformate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p–chlorophenoxyacetate, 3–phenylpropionate, 4–oxopentanoate (levulinate), 4,4–(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4– methoxycrotonate, benzoate, p–phenylbenzoate, 2,4,6–trimethylbenzoate (mesitoate), alkyl methyl carbonate, 9–fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl 2,2,2–trichloroethyl carbonate (Troc), 2– (trimethylsilyl)ethyl carbonate (TMSEC), 2–(phenylsulfonyl) ethyl carbonate (Psec), 2–(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutyl carbonate, alkyl vinyl carbonate alkyl allyl carbonate, alkyl p– nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p–methoxybenzyl carbonate, alkyl 3,4–dimethoxybenzyl carbonate, alkyl o–nitrobenzyl carbonate, alkyl p–nitrobenzyl carbonate, alkyl S–benzyl thiocarbonate, 4– Page 46 of 743 12621738v1Attorney Docket No.: 2010581-1488 ethoxy–1–napththyl carbonate, methyl dithiocarbonate, 2–iodobenzoate, 4–azidobutyrate, 4–nitro–4– methylpentanoate, o–(dibromomethyl)benzoate, 2–formylbenzenesulfonate, 2–(methylthiomethoxy)ethyl, 4– (methylthiomethoxy)butyrate, 2–(methylthiomethoxymethyl)benzoate, 2,6–dichloro–4– methylphenoxyacetate, 2,6–dichloro–4–(1,1,3,3–tetramethylbutyl)phenoxyacetate, 2,4–bis(1,1– dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, isobutyrate, monosuccinoate, (E)–2–methyl–2– butenoate, o–(methoxycarbonyl)benzoate, α–naphthoate, nitrate, alkyl N,N,N’,N’– tetramethylphosphorodiamidate, alkyl N–phenylcarbamate, borate, dimethylphosphinothioyl, alkyl 2,4– dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts). For protecting 1,2– or 1,3–diols, the protecting groups include methylene acetal, ethylidene acetal, 1–t– butylethylidene ketal, 1–phenylethylidene ketal, (4–methoxyphenyl)ethylidene acetal, 2,2,2– trichloroethylidene acetal, acetonide, cyclopentylidene ketal, cyclohexylidene ketal, cycloheptylidene ketal, benzylidene acetal, p–methoxybenzylidene acetal, 2,4–dimethoxybenzylidene ketal, 3,4– dimethoxybenzylidene acetal, 2–nitrobenzylidene acetal, methoxymethylene acetal, ethoxymethylene acetal, dimethoxymethylene ortho ester, 1–methoxyethylidene ortho ester, 1–ethoxyethylidine ortho ester, 1,2– dimethoxyethylidene ortho ester, α–methoxybenzylidene ortho ester, 1–(N,N–dimethylamino)ethylidene derivative, α–(N,N’–dimethylamino)benzylidene derivative, 2–oxacyclopentylidene ortho ester, di–t– butylsilylene group (DTBS), 1,3–(1,1,3,3–tetraisopropyldisiloxanylidene) derivative (TIPDS), tetra–t– butoxydisiloxane–1,3–diylidene derivative (TBDS), cyclic carbonates, cyclic boronates, ethyl boronate, and phenyl boronate.
[0121] In some embodiments, a hydroxyl protecting group is acetyl, t-butyl, tbutoxymethyl, methoxymethyl, tetrahydropyranyl, 1 -ethoxyethyl, 1 -(2-chloroethoxy)ethyl, 2- trimethylsilylethyl, p- chlorophenyl, 2,4-dinitrophenyl, benzyl, benzoyl, p-phenylbenzoyl, 2,6- dichlorobenzyl, diphenylmethyl, p- nitrobenzyl, triphenylmethyl (trityl), 4,4'-dimethoxytrityl, trimethylsilyl, triethylsilyl, t-butyldimethylsilyl, t- butyldiphenylsilyl, triphenylsilyl, triisopropylsilyl, benzoylformate, chloroacetyl, trichloroacetyl, trifiuoroacetyl, pivaloyl, 9- fluorenylmethyl carbonate, mesylate, tosylate, triflate, trityl, monomethoxytrityl (MMTr), 4,4'-dimethoxytrityl, (DMTr) and 4,4',4''-trimethoxytrityl (TMTr), 2-cyanoethyl (CE or Cne), 2- (trimethylsilyl)ethyl (TSE), 2-(2-nitrophenyl)ethyl, 2-(4-cyanophenyl)ethyl 2-(4-nitrophenyl)ethyl (NPE), 2- (4-nitrophenylsulfonyl)ethyl, 3,5-dichlorophenyl, 2,4-dimethylphenyl, 2-nitrophenyl, 4-nitrophenyl, 2,4,6- trimethylphenyl, 2-(2-nitrophenyl)ethyl, butylthiocarbonyl, 4,4',4''-tris(benzoyloxy)trityl, diphenylcarbamoyl, levulinyl, 2-(dibromomethyl)benzoyl (Dbmb), 2-(isopropylthiomethoxymethyl)benzoyl (Ptmt), 9- phenylxanthen-9-yl (pixyl) or 9-(p-methoxyphenyl)xanthine-9-y1 (MOX). In some embodiments, each of the hydroxyl protecting groups is, independently selected from acetyl, benzyl, t- butyldimethylsilyl, t- butyldiphenylsilyl and 4,4'-dimethoxytrityl. In some embodiments, the hydroxyl protecting group is selected from the group consisting of trityl, monomethoxytrityl and 4,4'-dimethoxytrityl group. In some embodiments, a phosphorous linkage protecting group is a group attached to the phosphorous linkage (e.g., an internucleotidic linkage) throughout oligonucleotide synthesis. In some embodiments, a protecting group is attached to a sulfur Page 47 of 743 12621738v1Attorney Docket No.: 2010581-1488 atom of an phosphorothioate group. In some embodiments, a protecting group is attached to an oxygen atom of an internucleotide phosphorothioate linkage. In some embodiments, a protecting group is attached to an oxygen atom of the internucleotide phosphate linkage. In some embodiments a protecting group is 2- cyanoethyl (CE or Cne), 2-trimethylsilylethyl, 2-nitroethyl, 2-sulfonylethyl, methyl, benzyl, o-nitrobenzyl, 2- (p-nitrophenyl)ethyl (NPE or Npe), 2-phenylethyl, 3-(N-tert-butylcarboxamido)-1-propyl, 4-oxopentyl, 4- methylthio-l-butyl, 2-cyano-1,1-dimethylethyl, 4-N-methylaminobutyl, 3-(2-pyridyl)-1-propyl, 2-[N-methyl- N-(2-pyridyl)]aminoethyl, 2-(N-formyl,N-methyl)aminoethyl, or 4-[N-methyl-N-(2,2,2- trifluoroacetyl)amino]butyl.
[0122] Subject: As used herein, the term “subject” or “test subject” refers to any organism to which a compound (e.g., an oligonucleotide) or composition is administered in accordance with the present disclosure e.g., for experimental, diagnostic, prophylactic and / or therapeutic purposes. Typical subjects include animals (e.g., mammals such as mice, rats, rabbits, non-human primates, and humans; insects; worms; etc.) and plants. In some embodiments, a subject is a human. In some embodiments, a subject may be suffering from and / or susceptible to a disease, disorder and / or condition.
[0123] Substantially: As used herein, the term “substantially” refers to the qualitative condition of exhibiting total or near-total extent or degree of a characteristic or property of interest. A base sequence which is substantially identical or complementary to a second sequence is not fully identical or complementary to the second sequence, but is mostly or nearly identical or complementary to the second sequence. In some embodiments, an oligonucleotide with a substantially complementary sequence to another oligonucleotide or nucleic acid forms duplex with the oligonucleotide or nucleic acid in a similar fashion as an oligonucleotide with a fully complementary sequence. In addition, one of ordinary skill in the biological and / or chemical arts will understand that biological and chemical phenomena rarely, if ever, go to completion and / or proceed to completeness or achieve or avoid an absolute result. The term “substantially” is therefore used herein to capture the potential lack of completeness inherent in many biological and / or chemical phenomena.
[0124] Sugar: The term “sugar” refers to a monosaccharide or polysaccharide in closed and / or open form. In some embodiments, sugars are monosaccharides. In some embodiments, sugars are polysaccharides. Sugars include, but are not limited to, ribose, deoxyribose, pentofuranose, pentopyranose, and hexopyranose moieties. As used herein, the term “sugar” also encompasses structural analogs used in lieu of conventional sugar molecules, such as glycol, polymer of which forms the backbone of the nucleic acid analog, glycol nucleic acid (“GNA”), etc. As used herein, the term “sugar” also encompasses structural analogs used in lieu of natural or naturally-occurring nucleotides, such as modified sugars and nucleotide sugars. In some embodiments, a sugar is a RNA or DNA sugar (ribose or deoxyribose). In some embodiments, a sugar is a modified ribose or deoxyribose sugar, e.g., 2’-modified, 5’-modified, etc. As described herein, in some embodiments, when used in oligonucleotides and / or nucleic acids, modified sugars may provide one or more desired properties, activities, etc. In some embodiments, a sugar is optionally substituted ribose or deoxyribose. In some embodiments, a “sugar” refers to a sugar unit in an oligonucleotide or a nucleic acid. Page 48 of 743 12621738v1Attorney Docket No.: 2010581-1488
[0125] Susceptible to: An individual who is “susceptible to” a disease, disorder and / or condition is one who has a higher risk of developing the disease, disorder and / or condition than does a member of the general public. In some embodiments, an individual who is susceptible to a disease, disorder and / or condition is predisposed to have that disease, disorder and / or condition. In some embodiments, an individual who is susceptible to a disease, disorder and / or condition may not have been diagnosed with the disease, disorder and / or condition. In some embodiments, an individual who is susceptible to a disease, disorder and / or condition may exhibit symptoms of the disease, disorder and / or condition. In some embodiments, an individual who is susceptible to a disease, disorder and / or condition may not exhibit symptoms of the disease, disorder and / or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and / or condition will develop the disease, disorder, and / or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and / or condition will not develop the disease, disorder, and / or condition.
[0126] Therapeutic agent: As used herein, the term “therapeutic agent” in general refers to any agent that elicits a desired effect (e.g., a desired biological, clinical, or pharmacological effect) when administered to a subject. In some embodiments, an agent is considered to be a therapeutic agent if it demonstrates a statistically significant effect across an appropriate population. In some embodiments, an appropriate population is a population of subjects suffering from and / or susceptible to a disease, disorder or condition. In some embodiments, an appropriate population is a population of model organisms. In some embodiments, an appropriate population may be defined by one or more criterion such as age group, gender, genetic background, preexisting clinical conditions, prior exposure to therapy. In some embodiments, a therapeutic agent is a substance that alleviates, ameliorates, relieves, inhibits, prevents, delays onset of, reduces severity of, and / or reduces incidence of one or more symptoms or features of a disease, disorder, and / or condition in a subject when administered to the subject in an effective amount. In some embodiments, a “therapeutic agent” is an agent that has been or is required to be approved by a government agency before it can be marketed for administration to humans. In some embodiments, a “therapeutic agent” is an agent for which a medical prescription is required for administration to humans. In some embodiments, a therapeutic agent is a provided compound, e.g., a provided oligonucleotide.
[0127] Therapeutically effective amount: As used herein, the term “therapeutically effective amount” means an amount of a substance (e.g., a therapeutic agent, composition, and / or formulation) that elicits a desired biological response when administered as part of a therapeutic regimen. In some embodiments, a therapeutically effective amount of a substance is an amount that is sufficient, when administered to a subject suffering from or susceptible to a disease, disorder, and / or condition, to treat, diagnose, prevent, and / or delay the onset of the disease, disorder, and / or condition. As will be appreciated by those of ordinary skill in this art, the effective amount of a substance may vary depending on such factors as the desired biological endpoint, the substance to be delivered, the target cell or tissue, etc. For example, the effective amount of compound in a formulation to treat a disease, disorder, and / or condition is the amount that alleviates, ameliorates, relieves, inhibits, prevents, delays onset of, reduces severity of and / or reduces incidence of one or more symptoms or Page 49 of 743 12621738v1Attorney Docket No.: 2010581-1488 features of the disease, disorder, and / or condition. In some embodiments, a therapeutically effective amount is administered in a single dose; in some embodiments, multiple unit doses are required to deliver a therapeutically effective amount.
[0128] Treat: As used herein, the term “treat,” “treatment,” or “treating” refers to any method used to partially or completely alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of, and / or reduce incidence of one or more symptoms or features of a disease, disorder, and / or condition. Treatment may be administered to a subject who does not exhibit signs of a disease, disorder, and / or condition. In some embodiments, treatment may be administered to a subject who exhibits only early signs of the disease, disorder, and / or condition, for example for the purpose of decreasing the risk of developing pathology associated with the disease, disorder, and / or condition.
[0129] Unsaturated: The term "unsaturated," as used herein, means that a moiety has one or more units of unsaturation.
[0130] Wild-type: As used herein, the term “wild-type” has its art-understood meaning that refers to an entity having a structure and / or activity as found in nature in a “normal” (as contrasted with mutant, diseased, altered, etc.) state or context. Those of ordinary skill in the art will appreciate that wild type genes and polypeptides often exist in multiple different forms (e.g., alleles).
[0131] As those skilled in the art will appreciate, methods and compositions described herein relating to provided compounds (e.g., oligonucleotides) generally also apply to pharmaceutically acceptable salts of such compounds. Description of Certain Embodiments
[0132] Oligonucleotides are useful in various therapeutic, diagnostic, and research applications. For example, PNPLA3 oligonucleotides are useful in therapeutic and research applications, including the treatment of a variety of PNPLA3-associated conditions, disorders, and diseases, including but not limited to non- alcoholic fatty liver disease (NAFLD), also referred to as metabolic dysfunction-associated steatotic liver disease (MASLD), steatosis, non-alcoholic steatohepatitis (NASH), also referred to as metabolic dysfunction- associated steatohepatitis (MASH),cirrhosis, and hepatocellular carcinoma (HCC). Use of naturally occurring nucleic acids is limited, for example, by their susceptibility to endo- and exo-nucleases. As such, various synthetic counterparts have been developed to circumvent these shortcomings and / or to further improve various properties and activities. These include synthetic oligonucleotides that contain chemical modifications, e.g., base modifications, sugar modifications, backbone modifications, etc., which, among other things, render these molecules less susceptible to degradation and improve other properties and / or activities.
[0133] From a structural point of view, modifications to internucleotidic linkages can introduce chirality, and certain properties and activities may be affected by configurations of linkage phosphorus atoms of oligonucleotides. For example, binding affinity, sequence specific binding to complementary RNA, stability to nucleases, activities, delivery, pharmacokinetics, etc. can be affected by, inter alia, chirality of backbone Page 50 of 743 12621738v1Attorney Docket No.: 2010581-1488 linkage phosphorus atoms.
[0134] Among other things, the present disclosure utilizes technologies for controlling various structural elements, e.g., sugar modifications and patterns thereof, nucleobase modifications and patterns thereof, modified internucleotidic linkages and patterns thereof, linkage phosphorus stereochemistry and patterns thereof, additional chemical moieties (moieties that are not typically in an oligonucleotide chain) and patterns thereof, etc. With the capability to fully control structural elements of oligonucleotides, the present disclosure provides oligonucleotides with improved and / or new properties and / or activities for various applications, e.g., as therapeutic agents, probes, etc. For example, as demonstrated herein, provided oligonucleotides and compositions thereof are particularly powerful for editing target adenosine in target nucleic acids to, in some embodiments, correct a G to A mutation by converting A to I.
[0135] In some embodiments, an oligonucleotide comprises a sequence that is identical to or is completely or substantially complementary to 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, typically 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60 or more, contiguous bases of a PNPLA3 genomic sequence or transcript therefrom (e.g., DNA, pre-mRNA, mRNA, etc.). In some embodiments, a oligonucleotide comprises a sequence that is completely complementary to 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, typically 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60 or more, contiguous bases of a PNPLA3 transcript. In some embodiments, a PNPLA3 transcript is a target PNPLA3 transcript comprising one or more target adenosine. In some embodiments, a target PNPLA3 transcript comprises one and no more than one target adenosine. In some embodiments, an oligonucleotide can hybridize with a target PNPLA3 transcript. In some embodiments, such hybridization facilitates modification of A (e.g., conversion of A to I) by, e.g., ADAR1, ADAR2, etc., in a target PNPLA3 transcript.
[0136] In some embodiments, the present disclosure provides a oligonucleotide as disclosed herein, wherein the oligonucleotide has a base sequence which is, or comprises about 10-40, about 15-40, about 20- 40, or at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34 contiguous bases of, an oligonucleotide or nucleic acid disclosed herein (e.g., in a Table), or a sequence that is complementary to a target RNA sequence gene, transcript, etc. disclosed herein, and wherein each T can be optionally and independently replaced with U and vice versa. In some embodiments, the present disclosure provides an oligonucleotide or oligonucleotide composition as disclosed herein, e.g., in a Table. In some embodiments, the present disclosure provides a oligonucleotide comprising a base sequence disclosed herein, wherein the oligonucleotide is stereorandom or not chirally controlled, and wherein each T can be optionally and independently replaced with U and vice versa. Page 51 of 743 12621738v1Attorney Docket No.: 2010581-1488
[0137] In some embodiments, a oligonucleotide is a single-stranded oligonucleotide for site-directed editing of a nucleoside (e.g., a target adenosine) in a target PNPLA3 nucleic acid, e.g., RNA.
[0138] As described herein, oligonucleotides may contain one or more modified internucleotidic linkages (non-natural phosphate linkages). In some embodiments, a modified internucleotidic linkage is a chiral internucleotidic linkage whose linkage phosphorus is chiral. In some embodiments, a modified internucleotidic linkage is a phosphorothioate internucleotidic linkage. In some embodiments, oligonucleotides comprise one or more negatively charged internucleotidic linkages (e.g., phosphorothioate internucleotidic linkages, natural phosphate linkages, etc.). In some embodiments, oligonucleotides comprise one or more non-negatively charged internucleotidic linkages. In some embodiments, oligonucleotides comprise one or more neutral internucleotidic linkages. In some embodiments, the present disclosure provides a oligonucleotide composition wherein the oligonucleotides are stereorandom or not chirally controlled. In some embodiments, a oligonucleotide comprises at least one stereorandom internucleotidic linkage and at least one chirally controlled internucleotidic linkage.
[0139] In some embodiments, oligonucleotides are chirally controlled. In some embodiments, oligonucleotides are chirally pure (or “stereopure”, “stereochemically pure”), wherein the oligonucleotide exists as a single stereoisomeric form (in many cases a single diastereoisomeric (or “diastereomeric”) form as multiple chiral centers may exist in an oligonucleotide, e.g., at linkage phosphorus, sugar carbon, etc.). As appreciated by those skilled in the art, a chirally pure oligonucleotide is separated from its other stereoisomeric forms (to the extent that some impurities may exist as chemical and biological processes, selectivities and / or purifications etc. rarely, if ever, go to absolute completeness). In a chirally pure oligonucleotide, each chiral center is independently defined with respect to its configuration (for a chirally pure oligonucleotide, each internucleotidic linkage is independently stereodefined or chirally controlled). In contrast to chirally controlled and chirally pure oligonucleotides which comprise stereodefined linkage phosphorus, racemic (or “stereorandom”, “non-chirally controlled”) oligonucleotides comprising chiral linkage phosphorus, e.g., from traditional phosphoramidite oligonucleotide synthesis without stereochemical control during coupling steps in combination with traditional sulfurization (creating stereorandom phosphorothioate internucleotidic linkages), refer to a random mixture of various stereoisomers (typically diastereoisomers (or “diastereomers”) as there are multiple chiral centers in an oligonucleotide; e.g., from traditional oligonucleotide preparation using reagents containing no chiral elements other than those in nucleosides and linkage phosphorus). For example, for A*A*A wherein * is a phosphorothioate internucleotidic linkage (which comprises a chiral linkage phosphorus), a racemic oligonucleotide preparation includes four diastereomers [22= 4, considering the two chiral linkage phosphorus, each of which can exist in either of two configurations (Sp or Rp)]: A *S A *S A, A *S A *R A, A *R A *S A, and A *R A *R A, wherein *S represents a Sp phosphorothioate internucleotidic linkage and *R represents a Rp phosphorothioate internucleotidic linkage. For a chirally pure oligonucleotide, e.g., A *S A *S A, it exists in a single stereoisomeric form and it is separated from the other stereoisomers (e.g., the diastereomers A *S A *R A, A *R A *S A, and A *R A *R A). Page 52 of 743 12621738v1Attorney Docket No.: 2010581-1488
[0140] In some embodiments, oligonucleotides comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more stereorandom internucleotidic linkages (mixture of Rp and Sp linkage phosphorus at the internucleotidic linkage, e.g., from traditional non-chirally controlled oligonucleotide synthesis). In some embodiments, oligonucleotides comprise one or more (e.g., 1-60, 1-50, 1-40, 1-30, 1-25, 1-20, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60 or more) chirally controlled internucleotidic linkages (Rp or Sp linkage phosphorus at the internucleotidic linkage, e.g., from chirally controlled oligonucleotide synthesis). In some embodiments, an internucleotidic linkage is a phosphorothioate internucleotidic linkage. In some embodiments, an internucleotidic linkage is a stereorandom phosphorothioate internucleotidic linkage. In some embodiments, an internucleotidic linkage is a chirally controlled phosphorothioate internucleotidic linkage.
[0141] Among other things, the present disclosure provides technologies for preparing chirally controlled (in some embodiments, stereochemically pure) oligonucleotides. In some embodiments, oligonucleotides are stereochemically pure. In some embodiments, oligonucleotides of the present disclosure are about 5%-100%, 10%-100%, 20%-100%, 30%-100%, 40%-100%, 50%-100%, 60%-100%, 70%-100%, 80-100%, 90-100%, 95-100%, 50%-90%, or about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, or at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% stereochemically pure.
[0142] In some embodiments, the present disclosure provides various oligonucleotide compositions. In some embodiments, oligonucleotide compositions are stereorandom or not chirally controlled. In some embodiments, there are no chirally controlled internucleotidic linkages in oligonucleotides of provided compositions. In some embodiments, internucleotidic linkages of oligonucleotides in compositions comprise one or more chirally controlled internucleotidic linkages (e.g.,, chirally controlled oligonucleotide compositions).
[0143] In some embodiments, a oligonucleotide composition comprises a plurality of oligonucleotides sharing a common base sequence, wherein one or more internucleotidic linkages in the oligonucleotides are chirally controlled and one or more internucleotidic linkages are stereorandom (not chirally controlled). In some embodiments, a oligonucleotide composition comprises a plurality of oligonucleotides sharing a common base sequence, wherein each internucleotidic linkage comprising chiral linkage phosphorus in the oligonucleotides is independently a chirally controlled internucleotidic linkage. In some embodiments, a plurality of oligonucleotides share the same base sequence, and the same base and sugar modification. In some embodiments, a plurality of oligonucleotides share the same base sequence, and the same base, sugar and internucleotidic linkage modification. In some embodiments, a oligonucleotide composition comprises oligonucleotides of the same constitution, wherein one or more internucleotidic linkages are chirally controlled and one or more internucleotidic linkages are stereorandom (not chirally controlled). In some embodiments, a oligonucleotide composition comprises oligonucleotides of the same constitution, wherein each Page 53 of 743 12621738v1Attorney Docket No.: 2010581-1488 internucleotidic linkage comprising chiral linkage phosphorus is independently a chirally controlled internucleotidic linkage. In some embodiments, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90% or 95% of all oligonucleotides, or all oligonucleotides of the common base sequence, are oligonucleotides of the plurality.
[0144] In some embodiments, the present disclosure provides technologies for preparing, assessing and / or utilizing provided oligonucleotides and compositions thereof.
[0145] As used in the present disclosure, in some embodiments, “one or more” is 1-200, 1-150, 1-100, 1- 90, 1-80, 1-70, 1-60, 1-50, 1-40, 1-30, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60. In some embodiments, “one or more” is one. In some embodiments, “one or more” is two. In some embodiments, “one or more” is three. In some embodiments, “one or more” is four. In some embodiments, “one or more” is five. In some embodiments, “one or more” is six. In some embodiments, “one or more” is seven. In some embodiments, “one or more” is eight. In some embodiments, “one or more” is nine. In some embodiments, “one or more” is ten. In some embodiments, “one or more” is at least one. In some embodiments, “one or more” is at least two. In some embodiments, “one or more” is at least three. In some embodiments, “one or more” is at least four. In some embodiments, “one or more” is at least five. In some embodiments, “one or more” is at least six. In some embodiments, “one or more” is at least seven. In some embodiments, “one or more” is at least eight. In some embodiments, “one or more” is at least nine. In some embodiments, “one or more” is at least ten.
[0146] As used in the present disclosure, in some embodiments, “at least one” is one or more.
[0147] Various embodiments are described for variables, e.g., R, RL, L, etc., as examples. Embodiments described for a variable, e.g., R, are generally applicable to all variables that can be such a variable (e.g., R’, R”, RL, RL1, etc.). PNPLA3
[0148] In some embodiments, PNPLA3 refers to a gene or a gene product thereof (including but not limited to a DNA or RNA, a transcript, a protein encoded thereby and can be from any form of PNPLA3, e.g., wild-type or mutant alleles) from any species, which may be known as: PNPLA3, adiponutrin, IPLA2 epsilon, C22orf20, or ADPN. In some embodiments, it refers to the gene and product thereof in a human. In some embodiments, it refers to the gene and product thereof in a non-human primate. Various PNPLA3 sequences, including variants thereof, from human, mouse, rat, monkey, etc. are readily available to those of skill in the art. In some embodiments, PNPLA3 is a human or mouse PNPLA3, which is wild-type or mutant. It has been reported that PNPLA3 can have a number of functions. Various technologies, e.g., assays, cells, animal models, etc. have also been reported and can be utilized for characterization and / or assessment of provided technologies (e.g., oligonucleotides, compositions, methods, etc.) in accordance with the present disclosure.
[0149] In some embodiments, a PNPLA3 gene, transcript (e.g., mRNA or pre-mRNA), or protein variant or isoform comprises a mutation. In some embodiments, a PNPLA3 gene, transcript, or protein is or comprises Page 54 of 743 12621738v1Attorney Docket No.: 2010581-1488 a mutation at position corresponding to position 148 of SEQ ID NO: 2. In some embodiments, a PNPLA3 gene, transcript, or protein is or comprises a I148M mutation. Table A. Example PNPLA3 amino acid sequences. SEQ ID Description Sequence NO 1 Wild PNPLA3 MYDAERGWSLSFAGCGFLGFYHVGATRCLSEHAPHLLRDA I E L S I E G L SPNPLA3-Associated Conditions, Disorders, or Diseases
[0150] Various conditions, disorders, or diseases are reported to be associated with PNPLA3. Generally, a disease, disorder, or condition is associated with PNPLA3 if the presence, level, activity, and / or form of PNPLA3 and / or products (e.g., transcripts, encoded proteins, etc.) thereof correlates with incidence of and / or susceptibility to the disease, disorder, or condition (e.g., across a relevant population). In some embodiments, a condition, disorder, or disease associated with PNPLA3 may be treated and / or prevented by reducing expression, level, and / or activity of PNPLA3 transcripts and / or proteins. In some embodiments, a condition, disorder, or disease associated with PNPLA3 may be treated and / or prevented by reducing expression, level, and / or activity of mutant PNPLA3 transcripts and / or proteins (e.g., I148M mutant PNPLA3 or variant thereof).
[0151] Various PNPLA3-associated conditions, disorders, or diseases have been reported.
[0152] In some embodiments, a PNPLA3-associated condition, disorder, or disease is non-alcoholic fatty liver disease (NAFLD), also referred to as metabolic dysfunction-associated steatotic liver disease (MASLD) (e.g., hepatic steatosis, NASH, MASH etc.). In some embodiments, a PNPLA3-associated condition, disorder, or disease is cirrhosis. NAFLD / MASLD are reportedly marked by, e.g., the buildup of excess fat in the liver Page 55 of 743 12621738v1Attorney Docket No.: 2010581-1488 (Krawczyk et al., Best Pract. Res. Clin. Gastroenterol., 2010). In some embodiments, NAFLD / MASLD comprises nonalcoholic fatty liver (NAFL). NAFL is reportedly marked by, e.g., the buildup of excess fat in the liver, enlargement of the liver, and potential pain. In some embodiments, NAFLD comprises nonalcoholic steatohepatitis (NASH), also referred to as metabolic dysfunction-associated steatohepatitis (MASH). NASH / MASH is reportedly marked by, e.g., the buildup of excess fat in the liver, inflammation of the liver, and potential liver damage. NASH / MASH may also be marked by liver fibrosis (e.g., scarring of the liver) and / or cirrhosis (e.g., scarring, degeneration of liver cells, and / or permanent damage of the liver). Reports indicate that development of NAFLD / MASLD may be associated with risk factors including obesity.
[0153] In some embodiments, a PNPLA3-associated condition, disorder, or disease is cancer. In some embodiments, a PNPLA3-associated condition, disorder, or disease is liver cancer. In some embodiments, a PNPLA3-associated condition, disorder, or disease is hepatocellular carcinoma (HCC). Hepatocellular carcinoma (HCC) is reportedly a type of liver cancer, and further the most common type of liver cancer (Llovet et al., Nat. Rev. Dis. Primers, 2021). In some embodiments, HCC may be associated with chronic liver disease such as alcoholic liver disease, NAFLD, MASLD, NAFL, NASH, MASH, liver fibrosis, and / or liver cirrhosis.
[0154] It has been reported that a SNP (rs738409) in a PNPLA3 gene that results in an I148M mutation in a PNPLA3 protein is associated with the development of various PNPLA3-associated conditions, disorders, or diseases including NAFLD, MASLD, NAFL, NASH, MASH, and HCC (Falleti et al., Liver Int., 2011; Sookoian and Pirola, Hepatology, 2011). In some embodiments, a mutant PNPLA3 transcript comprises a SNP. In some embodiments, a mutant PNPLA3 transcript comprises a SNP corresponding to rs738409. In some embodiments, a PNPLA3 transcript comprises a SNP resulting in a I148M mutation in an encoded PNPLA3 protein.
[0155] In some embodiments, a PNPLA3-associated condition, disorder, or disease is liver fat accumulation. In some embodiments, a PNPLA3-associated condition, disorder, or disease is liver inflammation. In some embodiments, a PNPLA3-associated condition, disorder, or disease is liver fibrosis. In some embodiments, a PNPLA3-associated condition, disorder, or disease is liver cirrhosis. In some embodiments, a PNPLA3-associated condition, disorder, or disease is hyperlipidemia. In some embodiments, a PNPLA3-associated condition, disorder, or disease is Type I diabetes. In some embodiments, a PNPLA3- associated condition, disorder, or disease is Type II diabetes mellitus. In some embodiments, a PNPLA3- associated condition, disorder, or disease is idiopathic Type I diabetes (Type Ib). In some embodiments, a PNPLA3-associated condition, disorder, or disease is latent autoimmune diabetes in adults (LADA). In some embodiments, a PNPLA3-associated condition, disorder, or disease is early-onset Type 2 diabetes (EOD). In some embodiments, a PNPLA3-associated condition, disorder, or disease is youth-onset atypical diabetes (YOAD). In some embodiments, a PNPLA3-associated condition, disorder, or disease is maturity onset diabetes of the young (MODY). In some embodiments, a PNPLA3-associated condition, disorder, or disease is malnutrition-related diabetes. In some embodiments, a PNPLA3-associated condition, disorder, or disease is gestational diabetes. In some embodiments, a PNPLA3-associated condition, disorder, or disease is coronary Page 56 of 743 12621738v1Attorney Docket No.: 2010581-1488 heart disease. In some embodiments, a PNPLA3-associated condition, disorder, or disease is ischemic stroke. In some embodiments, a PNPLA3-associated condition, disorder, or disease is restenosis after angioplasty. In some embodiments, a PNPLA3-associated condition, disorder, or disease is peripheral vascular disease. In some embodiments, a PNPLA3-associated condition, disorder, or disease is intermittent claudication. In some embodiments, a PNPLA3-associated condition, disorder, or disease is myocardial infarction. In some embodiments, a PNPLA3-associated condition, disorder, or disease is dyslipidemia. In some embodiments, a PNPLA3-associated condition, disorder, or disease is post-prandial lipemia. In some embodiments, a PNPLA3- associated condition, disorder, or disease is a impaired glucose tolerance (IGT). In some embodiments, a PNPLA3-associated condition, disorder, or disease is impaired fasting plasma glucose. In some embodiments, a PNPLA3-associated condition, disorder, or disease is metabolic acidosis. In some embodiments, a PNPLA3- associated condition, disorder, or disease is ketosis. In some embodiments, a PNPLA3-associated condition, disorder, or disease is arthritis. In some embodiments, a PNPLA3-associated condition, disorder, or disease is obesity. In some embodiments, a PNPLA3-associated condition, disorder, or disease is osteoporosis. In some embodiments, a PNPLA3-associated condition, disorder, or disease is hypertension. congestive heart failure. In some embodiments, a PNPLA3-associated condition, disorder, or disease is left ventricular hypertrophy. In some embodiments, a PNPLA3-associated condition, disorder, or disease is peripheral arterial disease. In some embodiments, a PNPLA3-associated condition, disorder, or disease is diabetic retinopathy. In some embodiments, a PNPLA3-associated condition, disorder, or disease is macular degeneration. In some embodiments, a PNPLA3-associated condition, disorder, or disease is cataract. In some embodiments, a PNPLA3-associated condition, disorder, or disease is diabetic nephropathy. In some embodiments, a PNPLA3- associated condition, disorder, or disease is glomerulosclerosis. In some embodiments, a PNPLA3-associated condition, disorder, or disease is chronic renal failure. In some embodiments, a PNPLA3-associated condition, disorder, or disease is diabetic neuropathy. In some embodiments, a PNPLA3-associated condition, disorder, or disease is metabolic syndrome. In some embodiments, a PNPLA3-associated condition, disorder, or disease is syndrome X. In some embodiments, a PNPLA3-associated condition, disorder, or disease is premenstrual syndrome. In some embodiments, a PNPLA3-associated condition, disorder, or disease is angina pectoris. In some embodiments, a PNPLA3-associated condition, disorder, or disease is thrombosis. In some embodiments, a PNPLA3-associated condition, disorder, or disease is atherosclerosis. In some embodiments, a PNPLA3- associated condition, disorder, or disease is transient ischemic attacks. In some embodiments, a PNPLA3- associated condition, disorder, or disease is stroke. vascular restenosis. In some embodiments, a PNPLA3- associated condition, disorder, or disease is hyperglycemia. In some embodiments, a PNPLA3-associated condition, disorder, or disease is hyperinsulinemia. In some embodiments, a PNPLA3-associated condition, disorder, or disease is hypertriglyceridemia. In some embodiments, a PNPLA3-associated condition, disorder, or disease is insulin resistance. In some embodiments, a PNPLA3-associated condition, disorder, or disease is impaired glucose metabolism. In some embodiments, a PNPLA3-associated condition, disorder, or disease is erectile dysfunction. In some embodiments, a PNPLA3-associated condition, disorder, or disease is a skin and Page 57 of 743 12621738v1Attorney Docket No.: 2010581-1488 connective tissue disorder. In some embodiments, a PNPLA3-associated condition, disorder, or disease is a foot ulceration. In some embodiments, a PNPLA3-associated condition, disorder, or disease is ulcerative colitis. In some embodiments, a PNPLA3-associated condition, disorder, or disease is endothelial dysfunction. In some embodiments, a PNPLA3-associated condition, disorder, or disease is impaired vascular compliance. In some embodiments, a PNPLA3-associated condition, disorder, or disease is hyper apo B lipoproteinemia. In some embodiments, a PNPLA3-associated condition, disorder, or disease is Alzheimer’s disease. In some embodiments, a PNPLA3-associated condition, disorder, or disease is schizophrenia. In some embodiments, a PNPLA3-associated condition, disorder, or disease is impaired cognition. In some embodiments, a PNPLA3- associated condition, disorder, or disease is inflammatory bowel disease. In some embodiments, a PNPLA3- associated condition, disorder, or disease is Crohn’s disease. In some embodiments, a PNPLA3-associated condition, disorder, or disease is irritable bowel syndrome. In some embodiments, a PNPLA3-associated condition, disorder, or disease is alcoholic liver disease. In some embodiments, a PNPLA3-associated condition, disorder, or disease is alcoholic steatosis. In some embodiments, a PNPLA3-associated condition, disorder, or disease is steatosis. In some embodiments, a PNPLA3-associated condition, disorder, or disease is alcoholic cirrhosis.
[0156] Among other things, provided technologies are useful for treating or preventing a condition, disorder, or disease associated with PNPLA3, e.g., non-alcoholic fatty liver disease (NAFLD), also referred to as metabolic dysfunction-associated steatotic liver disease (MASLD) (e.g., hepatic steatosis, NASH / MASH, etc.), cirrhosis, hepatocellular carcinoma (HCC), etc.
[0157] In some embodiments, provide technologies may be used to treat NAFLD / MASLD. In some embodiments, treatment comprises administration of an oligonucleotide or composition disclosed herein. In some embodiments, treatment comprises reduction of reduction of signs and / or symptoms associated with NAFLD / MASLD (e.g., fatigue, abdominal swelling, shortness of breath, edema, itchy skin, ascites, enlarged spleen, red palms, jaundice, etc.).
[0158] In some embodiments, provide technologies may be used to treat cirrhosis. In some embodiments, treatment comprises administration of an oligonucleotide or composition disclosed herein. In some embodiments, treatment comprises reduction of reduction of signs and / or symptoms associated with cirrhosis (e.g., fatigue, loss of appetite, nausea, edema, weight loss, itchy skin, jaundice, ascites, red palms, etc.).
[0159] In some embodiments, provided technologies (e.g., oligonucleotides, compositions, methods, etc.) reduce expression, level functions, and / or activities of mutant PNPLA3 transcripts (e.g., I148M PNPLA3 mutant) and proteins encoded thereby. In some embodiments, such reduction further comprises increased levels of alternative PNPLA3 transcripts (e.g., I148V PNPLA3) that encodes a PNPLA3 protein with improved lipase activity. In some embodiments, such alternative PNPLA3 transcripts and proteins encoded thereby can reduce symptoms or characteristics of one or more PNPLA3-associated conditions, disorders, or diseases.
[0160] In some embodiments, the present disclosure provides methods for reducing a level, function, and / or activity of mutant PNPLA3 transcripts (e.g., I148M PNPLA3 mutant), comprising contacting the Page 58 of 743 12621738v1Attorney Docket No.: 2010581-1488 mutant PNPLA3 transcript with an oligonucleotide or a composition of the present disclosure. In some embodiments, such reduction further comprises increased levels of alternative PNPLA3 transcripts (e.g., I148V PNPLA3) that encodes a PNPLA3 protein with improved lipase activity.
[0161] In some embodiments, treatment or prevention with provided technologies increases lipase activity of a PNPLA3 protein, through reducing level of mutant PNPLA3 transcripts (e.g., I148M PNPLA3 mutant) and increasing levels of alternative PNPLA3 transcripts (e.g., I148V PNPLA3) that encodes a PNPLA3 protein with improved lipase activity. In some embodiments, treatment or prevention with provided technologies reduces the rate of clinical decline, or delays or prevents onset of a condition, disorder, or disease.
[0162] As appreciated by those skilled in the art, mechanisms, genotypes, symptoms, biomarkers, etc. of such conditions, disorders, or diseases may be utilized in accordance with the present disclosure to characterize / assess provided technologies.
[0163] In some embodiments, a condition, disease or disorder is associated with I148M mutation in PNPLA3. In some embodiments, a subject is homozygous with respect to I148M mutation in PNPLA3. In some embodiments, a condition, disease or disorder is less associated with I148V in PNPLA3 compared to I148M in PNPLA3.
[0164] Among other things, the present disclosure encompasses the recognition that I148M mutation in PNPLA3 increases risks for various conditions, diseases or disorders. For example, homozygous I148M patients can have significantly higher risk of HCC which can be liver-related. In some embodiments, PNPLA3 knockdown or knockout may result in worse conditions compared to PNPLA3-I148M homozygous and heterozygous genotypes (e.g., increased steatosis, increased lipid accumulation, increased susceptibility to ethanol and methotrexate toxicity, etc.). In some embodiments, the present disclosure encompasses the recognition that conversion of I148M to I148V (e.g., via genome DNA editing, RNA editing, etc.) in PNPLA3 can provide various benefits and advantages compared to reference technologies (e.g., knockdown, knockout, etc.). In some embodiments, provided technologies increases or restores certain PNPLA3 functions. In some embodiments, provided technologies increases or restores certain PNPLA3 activities, e.g., lipase activity. In some embodiments, provided technologies can reduce levels of various markers, e.g., triglyceride. In some embodiments, provided technologies reduce triglyceride level in liver which has been reported to be associated with liver PNPLA3 abundance. Oligonucleotides
[0165] Among other things, the present disclosure provides PNPLA3 oligonucleotides of various designs, which may comprise various nucleobases and patterns thereof, sugars and patterns thereof, internucleotidic linkages and patterns thereof, and / or additional chemical moieties and patterns thereof as described in the present disclosure. In some embodiments, provided oligonucleotides can direct A to I editing in target PNPLA3 transcripts. In some embodiments, oligonucleotides of the present disclosure are single-stranded oligonucleotides capable of site-directed editing of an adenosine (conversion of A into I) in a target PNPLA3 RNA sequence. Page 59 of 743 12621738v1Attorney Docket No.: 2010581-1488
[0166] In some embodiments, oligonucleotides are of suitable lengths and sequence complementarity to specifically hybridize with target PNPLA3 transcripts. In some embodiments, oligonucleotides are sufficiently long and are sufficiently complementary to target PNPLA3 transcripts to distinguish target PNPLA3 transcripts from other nucleic acids to reduce off-target effects. In some embodiments, oligonucleotides are sufficiently short to facilitate delivery, reduce manufacture complexity and / or cost which maintaining desired properties and activities (e.g., editing of adenosine).
[0167] In some embodiments, a oligonucleotide has a length of about 10-200 (e.g., about 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-120, 10-150, 20-30, 20-40, 20-50, 20-60, 20-70, 20-80, 20-90, 20-100, 20-120, 20-150, 20-200, 25-30, 25-40, 25-50, 25-60, 25-70, 25-80, 25-90, 25-100, 25-120, 25- 150, 25-200, 30-40, 30-50, 30-60, 30-70, 30-80, 30-90, 30-100, 30-120, 30-150, 30-200, 10, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, etc.) nucleobases. In some embodiments, the base sequence of a oligonucleotide is about 10-60 nucleobases in length. In some embodiments, a base sequence is about 15-50 nucleobases in length. In some embodiments, a base sequence is from about 15 to about 35 nucleobases in length. In some embodiments, a base sequence is from about 25 to about 34 nucleobases in length. In some embodiments, a base sequence is from about 26 to about 35 nucleobases in length. In some embodiments, a base sequence is from about 27 to about 32 nucleobases in length. In some embodiments, a base sequence is from about 29 to about 35 nucleobases in length. In some embodiments, a base sequence is about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 nucleobases in length. In some other embodiments, a base sequence is or is at least 35 nucleobases in length. In some other embodiments, a base sequence is or is at least 34 nucleobases in length. In some other embodiments, a base sequence is or is at least 33 nucleobases in length. In some other embodiments, a base sequence is or is at least 32 nucleobases in length. In some other embodiments, a base sequence is or is at least 31 nucleobases in length. In some other embodiments, a base sequence is or is at least 30 nucleobases in length. In some other embodiments, a base sequence is or is at least 29 nucleobases in length. In some other embodiments, a base sequence is or is at least 28 nucleobases in length. In some other embodiments, a base sequence is or is at least 27 nucleobases in length. In some other embodiments, a base sequence is or is at least 26 nucleobases in length. In some other embodiments, the base sequence of the complementary portion in a duplex is at least 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35 or more nucleobases in length. In some other embodiments, it is at least 18 nucleobases in length. In some other embodiments, it is at least 19 nucleobases in length. In some other embodiments, it is at least 20 nucleobases in length. In some other embodiments, it is at least 21 nucleobases in length. In some other embodiments, it is at least 22 nucleobases in length. In some other embodiments, it is at least 23 nucleobases in length. In some other embodiments, it is at least 24 nucleobases in length. In some other embodiments, it is at least 25 nucleobases in length. Among other things, the present disclosure provides oligonucleotides of comparable or better properties and / or comparable or higher activities but of shorter lengths compared to prior reported adenosine editing Page 60 of 743 12621738v1Attorney Docket No.: 2010581-1488 oligonucleotides.
[0168] In some embodiments, a base sequence of an oligonucleotide is complementary to a base sequence of a target PNPLA3 transcript (e.g., complementarity to a portion of the target nucleic acid comprising the target adenosine) with 0-10 (e.g., 0-1, 0-2, 0-3, 0-4, 0-5, 0-6, 0-7, 0-8, 0-9, 0-10, 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1- 8, 1-9, 1-10, 2-3, 2-4, 2-5, 2-6, 2-7, 2-8, 2-9, 2-10, 3-4, 3-5, 3-6, 3-7, 3-8, 3-9, 3-10, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) mismatches which are not Watson-Crick base pairs (AT, AU and CG). In some embodiments, there are no mismatches. In some embodiments, there is 1 mismatch. In some embodiments, there are 2 mismatches. In some embodiments, there are 3 mismatches. In some embodiments, there are 4 mismatches. In some embodiments, there are 5 mismatches. In some embodiments, there are 6 mismatches. In some embodiments, there are 7 mismatches. In some embodiments, there are 8 mismatches. In some embodiments, there are 9 mismatches. In some embodiments, there are 10 mismatches. In some embodiments, oligonucleotides may contain portions that are not designed for complementarity (e.g., loops, protein binding sequences, etc., for recruiting of proteins, e.g., ADAR). As those skilled in the art will appreciate, when calculating mismatches and / or complementarity, such portions may be properly excluded. In some embodiments, complementarity, e.g., between oligonucleotides and target nucleic acids, is about 50%-100% (e.g., about 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%- 100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%- 100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc.). In some embodiments, complementarity is at least about 60%. In some embodiments, complementarity is at least about 65%. In some embodiments, complementarity is at least about 70%. In some embodiments, complementarity is at least about 75%. In some embodiments, complementarity is at least about 80%. In some embodiments, complementarity is at least about 85%. In some embodiments, complementarity is at least about 90%. In some embodiments, complementarity is at least about 95%. In some embodiments, complementarity is 100% across the length of an oligonucleotide. In some embodiments, complementarity is 100% except at a nucleoside opposite to a target nucleoside (e.g., adenosine) across the length of an oligonucleotide. Typically, complementarity is based on Watson-Crick base pairs AT, AU and CG. Those skilled in the art will appreciate that when assessing complementarity of two sequences of different lengths (e.g., a provided oligonucleotide and a target nucleic acid) complementarity may be properly based on the length of the shorter sequence and / or maximum complementarity between the two sequences. In many embodiments, oligonucleotides and target nucleic acids are of sufficient complementarity such that modifications are selectively directed to target adenosine sites.
[0169] In some embodiments, one or more mismatches are independently wobbles. In some embodiments, each mismatch is a wobble. In some embodiments, there are 0-10 (e.g., 0-1, 0-2, 0-3, 0-4, 0-5, 0-6, 0-7, 0-8, 0-9, 0-10, 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 2-3, 2-4, 2-5, 2-6, 2-7, 2-8, 2-9, 2-10, 3-4, 3-5, 3-6, 3-7, 3-8, 3-9, 3-10, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) wobbles. In some embodiments, the number Page 61 of 743 12621738v1Attorney Docket No.: 2010581-1488 is 0. In some embodiments, the number is 1. In some embodiments, the number is 2. In some embodiments, the number is 3. In some embodiments, the number is 4. In some embodiments, the number is 5. In some embodiments, a wobble is G-U, I-A, G-A, I-U, I-C, I-T, A-A, or reverse A-T. In some embodiments, a wobble is G-U, I-A, G-A, I-U, or I-C. In some embodiments, I-C may be considered a match when I is a 3’ immediate nucleoside next to a nucleoside opposite to a target nucleoside. In some embodiments, a base that forms a wobble pair (e.g., U which can form a G-U wobble) may replace a base that forms a match pair (e.g., C which matches G) and can provide a oligonucleotide with editing activity.
[0170] In some embodiments, N9produces a mismatch or a wobble base pairing when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N9produces a G-U wobble base pairing aligned with a target nucleic acid. In some embodiments, N9produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a nucleobase of N9is optionally substituted C and produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a nucleobase of N9is optionally substituted U and produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a 16thnucleoside from the 5’-end of an oligonucleotide produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a nucleobase of a 16thnucleoside from the 5’-end of an oligonucleotide is C. In some embodiments, a nucleobase of a 16thnucleoside from the 5’-end of an oligonucleotide is U. In some embodiments, N16produces a mismatch or a wobble base pairing when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N16produces a G-U wobble base pairing when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a nucleobase of N16is U. In some embodiments, a 9thnucleoside from the 5’-end of an oligonucleotide produces a mismatch or a wobble base pairing when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a 9thnucleoside from the 5’-end of an oligonucleotide produces a G-U wobble base pairing when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a nucleobase of a 9thnucleoside from the 5’-end of an oligonucleotide is U. In some embodiments, N16produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a nucleobase of N16is optionally substituted A and produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a 9thnucleoside from the 5’-end of an oligonucleotide produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a nucleobase of a 9thnucleoside from the 5’-end of an oligonucleotide is A. In some embodiments, N20produces a mismatch or a wobble base pairing when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N20produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a nucleobase of N20is optionally substituted T and produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a nucleobase of N20is optionally substituted U and produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a nucleobase of N20is optionally substituted C and produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a 5thnucleoside from the 5’-end of an oligonucleotide produces a mismatch Page 62 of 743 12621738v1Attorney Docket No.: 2010581-1488 or a wobble base pairing when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a 5thnucleoside from the 5’-end of an oligonucleotide produces a mismatch when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, a nucleobase of a 5thnucleoside from the 5’-end of an oligonucleotide is T. In some embodiments, a nucleobase of a 5thnucleoside from the 5’-end of an oligonucleotide is U. In some embodiments, a nucleobase of a 5thnucleoside from the 5’-end of an oligonucleotide is A. In some embodiments, a nucleobase of a 5thnucleoside from the 5’-end of an oligonucleotide is C.
[0171] In some embodiments, oligonucleotides comprise multiple mismatches and / or wobble-base pairings when aligned with a target nucleic acid. In some embodiments, oligonucleotides comprise two or more mismatches and / or wobble-base pairings when aligned with a target nucleic acid. In some embodiments, oligonucleotides comprise three or more mismatches and / or wobble-base pairings when aligned with a target nucleic acid. In some embodiments, oligonucleotides comprise four or more mismatches and / or wobble-base pairings when aligned with a target nucleic acid. In some embodiments, oligonucleotides comprise five or more mismatches and / or wobble-base pairings when aligned with a target nucleic acid. In some embodiments, oligonucleotides comprise two mismatches and / or wobble-base pairings when aligned with a target nucleic acid. In some embodiments, oligonucleotides comprise three mismatches and / or wobble-base pairings when aligned with a target nucleic acid. In some embodiments, oligonucleotides comprise four mismatches and / or wobble-base pairings when aligned with a target nucleic acid. In some embodiments, oligonucleotides comprise five mismatches and / or wobble-base pairings when aligned with a target nucleic acid. In some embodiments, N21and N20produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N20and N19produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N19and N18produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N18and N17produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N17and N16produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N16and N15produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N15and N14produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N14and N13produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N13and N12produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N12and N11produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N11and N10produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N10and N9produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N9and N8Page 63 of 743 12621738v1Attorney Docket No.: 2010581-1488 produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N8 and N7 produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N7and N6produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N6and N5produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N5and N4produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N4and N3produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid. In some embodiments, N3and N2produce mismatches and / or wobble-base pairings when the oligonucleotide is aligned with a target nucleic acid.
[0172] In some embodiments, duplexes of oligonucleotides and target PNPLA3 transcripts comprise one or more bulges each of which independently comprise one or more mismatches that are not wobbles. In some embodiments, there are 0-10 (e.g., 0-1, 0-2, 0-3, 0-4, 0-5, 0-6, 0-7, 0-8, 0-9, 0-10, 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 2-3, 2-4, 2-5, 2-6, 2-7, 2-8, 2-9, 2-10, 3-4, 3-5, 3-6, 3-7, 3-8, 3-9, 3-10, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) bulges. In some embodiments, the number is 0. In some embodiments, the number is 1. In some embodiments, the number is 2. In some embodiments, the number is 3. In some embodiments, the number is 4. In some embodiments, the number is 5.
[0173] In some embodiments, distances between two mismatches, mismatches and one or both ends of oligonucleotides (or a portion thereof, e.g., first domain, second domain, first subdomain, second subdomain, third subdomain), and / or mismatches and nucleosides opposite to target adenosine can independently be 0-50, 0-40, 0-30, 0-25, 0-20, 0-15, 0-10 (e.g., 0-1, 0-2, 0-3, 0-4, 0-5, 0-6, 0-7, 0-8, 0-9, 0-10, 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 2-3, 2-4, 2-5, 2-6, 2-7, 2-8, 2-9, 2-10, 3-4, 3-5, 3-6, 3-7, 3-8, 3-9, 3-10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 nucleobases (not including mismatches, end nucleosides and nucleosides opposite to target adenosine). In some embodiments, a number is 0-30. In some embodiments, a number is 0-20. In some embodiments, a number is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20. In some embodiments, a distance between two mismatches is 0-20. In some embodiments, a distance between two mismatches is 1-10. In some embodiments, a distance between a mismatch and a 5’-end nucleoside of an oligonucleotide is 0-20. In some embodiments, a distance between a mismatch and a 5’-end nucleoside of an oligonucleotide is 5-20. In some embodiments, a distance between a mismatch and a 3’-end nucleoside of an oligonucleotide is 0-40. In some embodiments, a distance between a mismatch and a 3’-end nucleoside of an oligonucleotide is 5-20. In some embodiments, a distance between a mismatch and a nucleoside opposite to a target adenosine is 0-20. In some embodiments, a distance between a mismatch and a nucleoside opposite to a target adenosine is 1-10. In some embodiments, the number of nucleobases for a distance is 0. In some embodiments, it is 1. In some embodiments, it is 2. In some embodiments, it is 3. In some embodiments, it is 4. In some embodiments, it is 5. In some embodiments, it is 6. In some embodiments, it is 7. In some embodiments, it is 8. In some Page 64 of 743 12621738v1Attorney Docket No.: 2010581-1488 embodiments, it is 9. In some embodiments, it is 10. In some embodiments, it is 11. In some embodiments, it is 12. In some embodiments, it is 13. In some embodiments, it is 14. In some embodiments, it is 15. In some embodiments, it is 16. In some embodiments, it is 17. In some embodiments, it is 18. In some embodiments, it is 19. In some embodiments, it is 20. In some embodiments, a mismatch is at an end, e.g., a 5’-end or 3’-end of a first domain, second domain, first subdomain, second subdomain, or third subdomain. In some embodiments, a mismatch is at a nucleoside opposite to a target adenosine.
[0174] In some embodiments, provided oligonucleotides can direct adenosine editing (e.g.,, converting A to I) in a target PNPLA3 transcript and have a base sequence which consists of, comprises, or comprises a portion (e.g., a span of 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or more contiguous bases) of the base sequence of a oligonucleotide disclosed herein, wherein each T can be independently replaced with U and vice versa, and the oligonucleotide comprises at least one non-naturally-occurring modification of a base, sugar and / or internucleotidic linkage.
[0175] In some embodiments, a provided oligonucleotide comprises one or more carbohydrate moieties. In some embodiments, a provided oligonucleotide comprises one or more GalNAc moieties. In some embodiments, a provided oligonucleotide comprises one or more targeting moieties. Non-limiting examples of such additional chemical moieties which can be conjugated to oligonucleotide chain are described herein.
[0176] In some embodiments, provided PNPLA3 oligonucleotides can direct a modification of an A in a in a target PNPLA3 transcript, wherein the A is in the same codon as a C to G mutation. In some embodiments, a modification of an A in a PNPLA3 transcript is or comprises conversion of A to I, which can be read as G during translation or other biological processes. In some embodiments, modification of an A in a PNPLA3 transcript, e.g., RNA transcript, produces produce an alternative amino acid codon. In some embodiments, provided oligonucleotides can direct a modification of an A in a target PNPLA3 transcript or a product thereof via ADAR-mediated deamination. In some embodiments, provided oligonucleotides can direct a modification of an A in a target PNPLA3 transcript or a product thereof via ADAR-mediated deamination by recruiting an endogenous ADAR (e.g., in a target cell) and facilitating the ADAR-mediated deamination. Regardless, however, the present disclosure is not limited to any particular mechanism. In some embodiments, the present disclosure provides oligonucleotides, compositions, methods, etc., capable of operating via double-stranded RNA interference, single-stranded RNA interference, RNase H-mediated knock-down, steric hindrance of translation, ADAR-mediated deamination or a combination of two or more such mechanisms.
[0177] In some embodiments, an oligonucleotide comprises a structural element or a portion thereof described herein, e.g., in a Table. In some embodiments, a oligonucleotide has a base sequence which comprises the base sequence (or a portion thereof) wherein each T can be independently substituted with U, pattern of chemical modifications (or a portion thereof), and / or a format of an oligonucleotide disclosed herein, e.g., in a Table or in the Figures, or otherwise disclosed herein.
[0178] Among other things, provided oligonucleotides may hybridize to their target PNPLA3 nucleic acids (e.g., pre-mRNA, mature mRNA, etc.). In some embodiments, oligonucleotide can hybridize to a target Page 65 of 743 12621738v1Attorney Docket No.: 2010581-1488 PNPLA3 RNA sequence nucleic acid in any stage of RNA processing, including but not limited to a pre- mRNA or a mature mRNA. In some embodiments, an oligonucleotide can hybridize to any element of a target PNPLA3 nucleic acid or its complement, including but not limited to: a promoter region, an enhancer region, a transcriptional stop region, a translational start signal, a translation stop signal, a coding region, a non-coding region, an exon, an intron, an intron / exon or exon / intron junction, the 5' UTR, or the 3' UTR.
[0179] In some embodiments, oligonucleotide hybridizes to two or more variants of transcripts derived from a sense strand of a target site (e.g., a target PNPLA3 sequence).
[0180] In some embodiments, provided oligonucleotides contain increased levels of one or more isotopes. In some embodiments, provided oligonucleotides are labeled, e.g., by one or more isotopes of one or more elements, e.g., hydrogen, carbon, nitrogen, etc. In some embodiments, provided oligonucleotides in provided compositions, e.g., oligonucleotides of a plurality of a composition, comprise base modifications, sugar modifications, and / or internucleotidic linkage modifications, wherein the oligonucleotides contain an enriched level of deuterium. In some embodiments, provided oligonucleotides are labeled with deuterium (replacing −1H with −2H) at one or more positions. In some embodiments, one or more1H of an oligonucleotide chain or any moiety conjugated to the oligonucleotide chain (e.g., a targeting moiety, etc.) is substituted with2H. Such oligonucleotides can be used in compositions and methods described herein.
[0181] In some embodiments, oligonucleotides comprise one or more modified nucleobases, one or more modified sugars, and / or one or more modified internucleotidic linkages as described herein. In some embodiments, oligonucleotides comprise a certain level of modified nucleobases, modified sugars, and / or modified internucleotidic linkages, e.g., about 5%-100%, about 10%-100%, 20-100%, 30%-100%, 40%- 100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%- 100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all nucleobases, sugars, and internucleotidic linkages, respectively, within an oligonucleotide.
[0182] In some embodiments, oligonucleotides comprise one or more modified sugars. In some embodiments, an oligonucleotide comprises about 1-50 (e.g., about 5, 6, 7, 8, 9, or 10 − about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, etc., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, etc.) modified sugars. In some embodiments, an oligonucleotide comprises about 1-50 (e.g., about 5, 6, 7, 8, 9, or 10 − about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, etc., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, etc.) modified sugars with 2’-F modification. In some embodiments, an oligonucleotide comprises about 2-50 (e.g., about 2, 3, 4, 5, 6, 7, 8, 9, or 10 − about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, Page 66 of 743 12621738v1Attorney Docket No.: 2010581-1488 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, etc., 2-40, 2-30, 2-25, 2-20, 2-15, 2-10, 3-40, 3-30, 3-25, 3- 20, 3-15, 3-10, 4-40, 4-30, 4-25, 4-20, 4-15, 4-10, 5-40, 5-30, 5-25, 5-20, 5-15, 5-10, 6-40, 6-30, 6-25, 6-20, 6-15, 6-10, 7-40, 7-30, 7-25, 7-20, 7-15, 7-10, 8-40, 8-30, 8-25, 8-20, 8-15, 8-10, 9-40, 9-30, 9-25, 9-20, 9-15, 9-10, 10-40, 10-30, 10-25, 10-20, 10-15, about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, etc.) consecutive modified sugars with 2’-F modification. In some embodiments, an oligonucleotide comprises 2 consecutive 2’-F modified sugars. In some embodiments, an oligonucleotide comprises 3 consecutive 2’-F modified sugars. In some embodiments, an oligonucleotide comprises 4 consecutive 2’-F modified sugars. In some embodiments, an oligonucleotide comprises 5 consecutive 2’-F modified sugars. In some embodiments, an oligonucleotide comprises 6 consecutive 2’-F modified sugars. In some embodiments, an oligonucleotide comprises 7 consecutive 2’-F modified sugars. In some embodiments, an oligonucleotide comprises 8 consecutive 2’-F modified sugars. In some embodiments, an oligonucleotide comprises 9 consecutive 2’-F modified sugars. In some embodiments, an oligonucleotide comprises 10 consecutive 2’-F modified sugars. In some embodiments, an oligonucleotide comprises two or more 2’-F modified sugar blocks, wherein each sugar in a 2’-F modified sugar block is independently a 2’-F modified sugar. In some embodiments, each 2’- F modified sugar block independently comprises or consists of 2, 3, 4, 5, 6, 7, 8, 9, or 10 consecutive 2’-F modified sugars as described herein. In some embodiments, two consecutive 2’-F modified sugar blocks are independently separated by a separating block which separating block comprises one or more sugars that are independently not 2’-F modified sugars. In some embodiments, an oligonucleotide comprises one or more (e.g., 1-20, 1-15, 1-14, 1-13, 1-12, 1-11, 1-10, 2-20, 3-15, 4-15, 5-15, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, etc.) 2’-F blocks and one or more (e.g., 1-20, 1-15, 1-14, 1-13, 1-12, 1-11, 1-10, 2-20, 3-15, 4-15, 5-15, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, etc.) separating blocks. In some embodiments, a first domain comprises one or more (e.g., 1-20, 1-15, 1-14, 1-13, 1-12, 1-11, 1-10, 2-20, 3-15, 4-15, 5-15, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, etc.) 2’-F blocks and one or more (e.g., 1-20, 1-15, 1-14, 1-13, 1-12, 1-11, 1-10, 2-20, 3-15, 4-15, 5-15, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, etc.) separating blocks. In some embodiments, each first domain block bonded to a first domain 2’-F block is a separating block. In some embodiments, each first domain block bonded to a first domain separating block is a first domain 2’-F block. In some embodiments, each sugar in a separating block is independently not 2’-F modified. In some embodiments, two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more) or all sugars in a separating block are independently not 2’-F modified. In some embodiments, a separating block comprises one or more bicyclic sugars (e.g., LNA sugar, cEt sugar, etc.) and / or one or more 2’-OR modified sugars, wherein R is optionally substituted C1-6aliphatic (e.g., 2’-OMe, 2’-MOE, etc.). In some embodiments, a separating block comprises one or more 2’-OR modified sugars, wherein R is optionally substituted C1-6aliphatic (e.g., 2’-OMe, 2’-MOE, etc.). In some embodiments, two or more non-2’-F modified sugars are consecutive. In some embodiments, two or more 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic (e.g., 2’-OMe, 2’-MOE, etc.) are consecutive. In some embodiments, a separating block comprises two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more) 2’-OR modified sugars wherein R is Page 67 of 743 12621738v1Attorney Docket No.: 2010581-1488 optionally substituted C1-6aliphatic (e.g., 2’-OMe, 2’-MOE, etc.). In some embodiments, a separating block comprises two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more) consecutive 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic (e.g., 2’-OMe, 2’-MOE, etc.). In some embodiments, each 2’-OR modified sugar is independently a 2’-OMe or 2’-MOE sugar. In some embodiments, each 2’-OR modified sugar is independently a 2’-OMe sugar. In some embodiments, each 2’-OR modified sugar is independently a 2’-MOE sugar. In some embodiments, a separating block comprises one or more 2’-F modified sugars. In some embodiments, none of 2’-F modified sugars in a separating block are next to each other. In some embodiments, a separating block contain no 2’-F modified sugars. In some embodiments, each sugar in a separating block is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic or a bicyclic sugar. In some embodiments, each sugar in each separating block is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic or a bicyclic sugar. In some embodiments, each sugar in a separating block is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic. In some embodiments, each sugar in each separating block is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic. In some embodiments, each sugar in a separating block is independently a 2’-OMe or 2’-MOE modified sugar. In some embodiments, each sugar in each separating block is independently a 2’-OMe or 2’-MOE modified sugar. In some embodiments, each sugar in a separating block is independently a 2’-OMe modified sugar. In some embodiments, each sugar in a separating block is independently a 2’-MOE modified sugar. In some embodiments, a separating block comprises a 2’-OMe sugar and 2’-MOE modified sugar. In some embodiments, each 2’-F block and each separating block independently contains 1, 2, 3, 4, or 5 nucleosides. In some embodiments, each 2’-F block and each separating block independently contains 1, 2, or 3 nucleosides.
[0183] In some embodiments, one or more sugars of N21, N20, N18, N16, N15, N14, N13, N12, N10, N9, N8, N7, N6, N5, N4, N3, N2, and N-3are independently a 2’-F modified sugar. In some embodiments, one or more sugars of N21and N20are independently a 2’-F modified sugar. In some embodiments, one or more sugars of N18, N16, N15, N14, N13, and N12are independently a 2’-F modified sugar. In some embodiments, one or more sugars of N10, N9, N8, N7, N6, N5, N4, N3, and N2are independently a 2’-F modified sugar.
[0184] In some embodiments, a sugar of N16is a 2’-F modified sugar. In some embodiments, a sugar of a 9thnucleoside from the 5’-end of an oligonucleotide is a 2’-F modified sugar. In some embodiments, a sugar of N15is a 2’-F modified sugar. In some embodiments, a sugar of a 10thnucleoside from the 5’-end of an oligonucleotide is a 2’-F modified sugar.
[0185] In some embodiments, about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%- 85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%- 85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars are modified sugars. In some embodiments, about 10%-100%, 20-100%, 30%- Page 68 of 743 12621738v1Attorney Docket No.: 2010581-1488 100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%- 95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars are modified sugars independently selected from 2’-F modified sugars, 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic, and bicyclic sugars (e.g., LNA sugars, cEt sugars, etc.). In some embodiments, a percentage is about or at least about 30%. In some embodiments, a percentage is about or at least about 40%. In some embodiments, a percentage is about or at least about 50%. In some embodiments, a percentage is about or at least about 60%. In some embodiments, a percentage is about or at least about 70%. In some embodiments, a percentage is about or at least about 80%. In some embodiments, a percentage is about or at least about 90%. In some embodiments, a percentage is about or at least about 95%.
[0186] In some embodiments, about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%- 85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%- 85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars are modified sugars independently selected from 2’-F modified sugars and 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic. In some embodiments, about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%- 90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%- 90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars are modified sugars independently selected from 2’-F modified sugars, 2’-OMe modified sugars and 2’-MOE modified sugars. In some embodiments, a percentage is about or at least about 30%. In some embodiments, a percentage is about or at least about 40%. In some embodiments, a percentage is about or at least about 50%. In some embodiments, a percentage is about or at least about 60%. In some embodiments, a percentage is about or at least about 70%. In some embodiments, a percentage is about or at least about 80%. In some embodiments, a percentage is about or at least about 90%. In some embodiments, a percentage is about or at least about 95%.
[0187] In some embodiments, about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%- 85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%- 85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars are modified sugars independently selected from 2’-F modified sugars and 2’-OMe Page 69 of 743 12621738v1Attorney Docket No.: 2010581-1488 modified sugars. In some embodiments, a percentage is about or at least about 30%. In some embodiments, a percentage is about or at least about 40%. In some embodiments, a percentage is about or at least about 50%. In some embodiments, a percentage is about or at least about 60%. In some embodiments, a percentage is about or at least about 70%. In some embodiments, a percentage is about or at least about 80%. In some embodiments, a percentage is about or at least about 90%. In some embodiments, a percentage is about or at least about 95%.
[0188] In some embodiments, about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%- 85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%- 85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars are 2’-F modified sugars. In some embodiments, a percentage is about or at least about 30%. In some embodiments, a percentage is about or at least about 40%. In some embodiments, a percentage is about or at least about 50%. In some embodiments, a percentage is about or at least about 60%. In some embodiments, a percentage is about or at least about 70%. In some embodiments, a percentage is about or at least about 80%. In some embodiments, a percentage is about or at least about 90%. In some embodiments, a percentage is about or at least about 95%. In some embodiments, 10 or more (e.g., about or at least about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 or more, 10-50, 10-40, 10-30, 10-25, 15-50, 15-40, 15-30, 15-25, 20-50, 20-40, 20-30, 20-25, etc.) sugars are 2’-F modified sugars. In some embodiments, an oligonucleotide comprises two or more (e.g., 2-30, 2-25, 2-20, 2-15, 3-10, 3-30, 3-25, 3-20, 3-15, 3-10, 4-30, 4-25, 4-20, 4-15, 4-10, 5-30, 5-25, 5-20, 5-15, 5-10, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) consecutive 2’-F modified sugars. In some embodiments, an oligonucleotide comprises one or more 2’-F blocks each independently comprising two or more (e.g., 2-30, 2- 25, 2-20, 2-15, 3-10, 3-30, 3-25, 3-20, 3-15, 3-10, 4-30, 4-25, 4-20, 4-15, 4-10, 5-30, 5-25, 5-20, 5-15, 5-10, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) consecutive 2’-F modified sugars. In some embodiments, an oligonucleotide comprises two or more 2’-F blocks as described herein separated by one or more separating blocks as described herein. In some embodiments, a 2’-F block has 2, 3, 4, 5, 6, 7, 8, 9, or 10 2’-F modified sugars. In some embodiments, a 2’-F block has no more than 2, 3, 4, 5, 6, 7, 8, 9, or 102’-F modified sugars. In some embodiments, each sugar in each 2’-F blocks is a 2’-F modified sugar, and each 2’- F block independently has 2, 3, 4, 5, 6, 7, 8, 9, or 102’-F modified sugars. In some embodiments, each sugar in each 2’-F blocks is a 2’-F modified sugar, and each 2’-F block independently has no more than 2, 3, 4, 5, 6, 7, 8, 9, or 102’-F modified sugars. In some embodiments, each sugar in each 2’-F blocks is a 2’-F modified sugar, and each 2’-F block independently has no more than 102’-F modified sugars. In some embodiments, each sugar in each 2’-F blocks is a 2’-F modified sugar, and each 2’-F block independently has no more than 92’-F modified sugars. In some embodiments, each sugar in each 2’-F blocks is a 2’-F modified sugar, and each 2’-F block independently has no more than 82’-F modified sugars. In some embodiments, each sugar in Page 70 of 743 12621738v1Attorney Docket No.: 2010581-1488 each 2’-F blocks is a 2’-F modified sugar, and each 2’-F block independently has no more than 72’-F modified sugars. In some embodiments, each sugar in each 2’-F blocks is a 2’-F modified sugar, and each 2’-F block independently has no more than 62’-F modified sugars. In some embodiments, each sugar in each 2’-F blocks is a 2’-F modified sugar, and each 2’-F block independently has no more than 52’-F modified sugars. In some embodiments, each sugar in each 2’-F blocks is a 2’-F modified sugar, and each 2’-F block independently has no more than 4 2’-F modified sugars. In some embodiments, each block bonded to a 2’-F block is independently a block that comprises no 2’-F modified sugar. In some embodiments, each block bonded to a 2’-F block is independently a block that comprises a natural DNA or RNA sugar, a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic or a bicyclic sugar. In some embodiments, each block bonded to a 2’-F block is independently a block that comprises a natural DNA or RNA sugar, a 2’-OMe modified sugar, 2’-MOE modified sugar or a bicyclic sugar. In some embodiments, each block bonded to a 2’-F block is independently a block that comprises a natural DNA or RNA sugar, a 2’-OMe modified sugar or 2’-MOE modified sugar. In some embodiments, each nucleoside in a first domain bonded to a 2’-F block in a first domain is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic or a bicyclic sugar. In some embodiments, each nucleoside in a first domain bonded to a 2’-F block in a first domain is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic. In some embodiments, each nucleoside in a first domain bonded to a 2’-F block in a first domain is independently a 2’- OMe or 2’-MOE modified sugar. In some embodiments, each nucleoside in a second domain bonded to a 2’- F block in a second domain is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic or a bicyclic sugar. In some embodiments, each nucleoside in a second domain bonded to a 2’-F block in a second domain is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic. In some embodiments, each nucleoside in a second domain bonded to a 2’-F block in a second domain is independently a 2’-OMe or 2’-MOE modified sugar.
[0189] In some embodiments, about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%- 85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%- 85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars are 2’-OR modified sugars, wherein R is optionally substituted C1-6aliphatic. In some embodiments, about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%- 95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%- 95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars are 2’-OMe or 2’-MOE modified sugars. In some embodiments, a percentage is about or at least about 30%. In some embodiments, a percentage is about or at least about 40%. In some embodiments, a Page 71 of 743 12621738v1Attorney Docket No.: 2010581-1488 percentage is about or at least about 50%. In some embodiments, a percentage is about or at least about 60%. In some embodiments, a percentage is about or at least about 70%. In some embodiments, a percentage is about or at least about 80%. In some embodiments, a percentage is about or at least about 90%. In some embodiments, a percentage is about or at least about 95%.
[0190] In some embodiments, about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%- 85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%- 85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars are 2’-OMe modified sugars. In some embodiments, a percentage is about or at least about 30%. In some embodiments, a percentage is about or at least about 40%. In some embodiments, a percentage is about or at least about 50%. In some embodiments, a percentage is about or at least about 60%. In some embodiments, a percentage is about or at least about 70%. In some embodiments, a percentage is about or at least about 80%. In some embodiments, a percentage is about or at least about 90%. In some embodiments, a percentage is about or at least about 95%.
[0191] In some embodiments, about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%- 85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%- 85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars are 2’-OR modified sugars, wherein R is optionally substituted C1-6aliphatic. In some embodiments, about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%- 95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%- 95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars are 2’-MOE modified sugars.
[0192] In some embodiments, sugars of the first (5’-end) one or several (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, 2-4, 2-3, 3-10, 3-9, 3-8, 3-7, 3-6, 3-5, 3- 4, etc.) and / or the last (3’-end) one or several (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, 2-4, 2-3, 3-10, 3-9, 3-8, 3-7, 3-6, 3-5, 3-4, etc.) nucleosides are independently modified sugars. In some embodiments, the first one or several sugars are independently modified sugars. In some embodiments, the last one or several sugars are independently modified sugars. In some embodiments, both the first and last one or several sugars are independently modified sugars. In some embodiments, modified sugars are independently non-2’-F modified sugars, e.g., bicyclic sugars, 2’-OR modified sugars wherein R is as described herein and is not −H (e.g., optionally substituted C1-6aliphatic). In Page 72 of 743 12621738v1Attorney Docket No.: 2010581-1488 some embodiments, they are independently selected from bicyclic sugars and 2’-OR modified sugars wherein R is optionally substituted C1-6 aliphatic. In some embodiments, they are independently 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic. In some embodiments, they are independently 2’-OMe modified sugars and 2’-MOE modified sugars. In some embodiments, the first several sugars comprises one or more 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic or bicyclic sugars (e.g., LNA, cEt, etc.) as described herein. In some embodiments, the first several sugars comprises one or more 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic. In some embodiments, the first several sugars comprises one or more 2’-OMe modified sugars. In some embodiments, the first several sugars comprises one or more 2’-MOE modified sugars. In some embodiments, the first several sugars comprises one or more 2’-OMe modified sugars and one or more 2’-MOE modified sugars. In some embodiments, the last several sugars comprises one or more 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic or bicyclic sugars (e.g., LNA, cEt, etc.) as described herein. In some embodiments, the last several sugars comprises one or more 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic. In some embodiments, the last several sugars comprises one or more 2’-OMe modified sugars. In some embodiments, the last several sugars comprises one or more 2’-MOE modified sugars. In some embodiments, the last several sugars comprises one or more 2’-OMe modified sugars and one or more 2’-MOE modified sugars. In some embodiments, the last several sugars are independently 2’-OMe modified sugars. In some embodiments, the first several sugars comprise two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) consecutive bicyclic sugars or 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic. In some embodiments, the first several sugars comprise two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) consecutive 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic. In some embodiments, the first several sugars comprise two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) consecutive modified sugars wherein each modified sugar is independently a 2’-OMe modified sugar or a 2’-MOE modified sugar. In some embodiments, the first several sugars comprise two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) consecutive 2’-OMe modified sugars. In some embodiments, the first several sugars comprise two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) consecutive 2’-MOE modified sugars. In some embodiments, the last several sugars comprise two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) consecutive 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic. In some embodiments, the last several sugars comprise two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) consecutive modified sugars wherein each modified sugar is independently a 2’-OMe modified sugar or a 2’-MOE modified sugar. In some embodiments, the last several sugars comprise two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) consecutive 2’-OMe modified sugars. In some embodiments, the last several sugars comprise three or more consecutive 2’-OMe modified sugars. In some embodiments, the last several sugars comprise four or more consecutive 2’-OMe modified sugars. In some embodiments, the last several sugars comprise five or more consecutive 2’-OMe modified sugars. In some embodiments, the last several sugars comprise six or more consecutive 2’-OMe modified sugars. In some embodiments, the last several sugars comprise two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10, etc.) consecutive 2’-MOE modified Page 73 of 743 12621738v1Attorney Docket No.: 2010581-1488 sugars.
[0193] In some embodiments, one or more (1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) of the first several (1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) sugars are modified sugars. In some embodiments, one or more (1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) of the first several (1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar (e.g., a sugar comprising 2’−O−CH2−4’, wherein the −CH2− is optionally substituted (e.g., a LNA sugar, a cET sugar (e.g., (S)-cEt))). In some embodiments, two or more of the first several sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar. In some embodiments, three or more of the first several sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar. In some embodiments, four or more of the first several sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar. In some embodiments, the one or more sugars are consecutive. In some embodiments, the first one, two, three or four sugars are modified sugars. In some embodiments, the first two sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar. In some embodiments, the first three sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar. In some embodiments, the first four sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar. In some embodiments, each 2’-OR modified sugar is independently a 2’-OMe or 2’-MOE modified sugar. In some embodiments, each bicyclic sugar is independently a LNA sugar or a cEt sugar. In some embodiments, each of the one or more (e.g., 1, 2, 3, 4, or 5) sugars of the first several sugars, or the first several (e.g., 1, 2, 3, 4, or 5) sugar(s), is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic. In some embodiments, each of the one or more (e.g., 1, 2, 3, 4, or 5) sugars of the first several sugars, or the first several (e.g., 1, 2, 3, 4, or 5) sugar(s), is independently a 2’-OMe or 2’-MOE modified sugar. In some embodiments, each of the one or more (e.g., 1, 2, 3, 4, or 5) sugars of the first several sugars, or the first several (e.g., 1, 2, 3, 4, or 5) sugar(s), is independently a 2’-OMe modified sugar. In some embodiments, each of the one or more (e.g., 1, 2, 3, 4, or 5) sugars of the first several sugars, or the first several (e.g., 1, 2, 3, 4, or 5) sugar(s), is independently a 2’-MOE modified sugar. In some embodiments, the first one, two, three, four or more sugars are independently 2’-OMe modified sugars. In some embodiments, the first sugar is a 2’-OMe modified sugar. In some embodiments, the first two sugars are independently 2’-OMe modified sugars. In some embodiments, the first three sugars are independently 2’-OMe modified sugars. In some embodiments, the first four sugars are independently 2’-OMe modified sugars. In some embodiments, the first one, two, three, four or more sugars are independently 2’-MOE modified sugars. In some embodiments, the first sugar is a 2’-MOE modified sugar. In some embodiments, the first two sugars are independently 2’-MOE modified sugars. In some embodiments, the first three sugars are independently 2’-MOE modified sugars. In some Page 74 of 743 12621738v1Attorney Docket No.: 2010581-1488 embodiments, the first four sugars are independently 2’-MOE modified sugars. In some embodiments, each of such modified sugars is independently the sugar of a nucleoside whose nucleobase is optionally substituted or protected A, T, C, G, or U, or an optionally substituted or protected tautomer of A, T, C, G, or U. In some embodiments, one or more such sugars are independently bonded to a non-negatively charged internucleotidic linkage. In some embodiments, one or more such sugars are independently bonded to a neutral internucleotidic linkage such as n001. In some embodiments, a non-negatively charged internucleotidic linkage or neutral internucleotidic linkage, e.g., n001, is chirally controlled. In some embodiments, it is Rp. In some embodiments, one or more such sugars are independently bonded to a phosphorothioate internucleotidic linkage. In some embodiments, a phosphorothioate internucleotidic linkage is chirally controlled. In some embodiments, it is Sp. In some embodiments, as described herein, the internucleotidic linkage between the first and second nucleosides is a non-negatively charged internucleotidic linkage. In some embodiments, it is a neutral internucleotidic linkage. In some embodiments, it is a phosphoryl guanidine internucleotidic linkage. In some embodiments, it is n001. In some embodiments, it is n025. In some embodiments, it is methylphosphonate. In some embodiments, it is MsPA. In some embodiments, it is chirally controlled. In some embodiments, it is Rp. In some embodiments, except the internucleotidic linkage between the first and second nucleosides, each internucleotidic linkages bonded to nucleosides comprising the one or more of the first several, or the first several modified sugars are independently phosphorothioate internucleotidic linkages. In some embodiments, each is chirally controlled. In some embodiments, each is Sp. In some embodiments, a first nucleoside is connected to an additional moiety, e.g., Mod001, optionally through a linker, e.g., L001, through its 5’-end carbon (in some embodiments, via a phosphate group).
[0194] In some embodiments, one or more (1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) of the last several (1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) sugars are modified sugars. In some embodiments, one or more (1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) of the last several (1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar (e.g., a sugar comprising 2’−O−CH2−4’, wherein the −CH2− is optionally substituted (e.g., a LNA sugar, a cET sugar (e.g., (S)-cEt))). In some embodiments, two or more of the last several sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar. In some embodiments, three or more of the last several sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar. In some embodiments, four or more of the last several sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar. In some embodiments, the one or more sugars are consecutive. In some embodiments, the last one, two, three or four sugars are modified sugars. In some embodiments, the last two sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a bicyclic sugar. In some embodiments, the last three sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic and a Page 75 of 743 12621738v1Attorney Docket No.: 2010581-1488 bicyclic sugar. In some embodiments, the last four sugars are modified sugars each independently selected from a 2’-OR modified sugar wherein R is optionally substituted C1-6 aliphatic and a bicyclic sugar. In some embodiments, each 2’-OR modified sugar is independently a 2’-OMe or 2’-MOE modified sugar. In some embodiments, each bicyclic sugar is independently a LNA sugar or a cEt sugar. In some embodiments, each of the one or more (e.g., 1, 2, 3, 4, or 5) sugars of the last several sugars, or the last several (e.g., 1, 2, 3, 4, or 5) sugar(s), is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic. In some embodiments, each of the one or more (e.g., 1, 2, 3, 4, or 5) sugars of the last several sugars, or the last several (e.g., 1, 2, 3, 4, or 5) sugar(s), is independently a 2’-OMe or 2’-MOE modified sugar. In some embodiments, each of the one or more (e.g., 1, 2, 3, 4, or 5) sugars of the last several sugars, or the last several (e.g., 1, 2, 3, 4, or 5) sugar(s), is independently a 2’-OMe modified sugar. In some embodiments, each of the one or more (e.g., 1, 2, 3, 4, or 5) sugars of the last several sugars, or the last several (e.g., 1, 2, 3, 4, or 5) sugar(s), is independently a 2’-MOE modified sugar. In some embodiments, the last one, two, three, four or more sugars are independently 2’-OMe modified sugars. In some embodiments, the last sugar is a 2’-OMe modified sugar. In some embodiments, the last two sugars are independently 2’-OMe modified sugars. In some embodiments, the last three sugars are independently 2’-OMe modified sugars. In some embodiments, the last four sugars are independently 2’-OMe modified sugars. In some embodiments, the last one, two, three, four or more sugars are independently 2’-MOE modified sugars. In some embodiments, the last sugar is a 2’- MOE modified sugar. In some embodiments, the last two sugars are independently 2’-MOE modified sugars. In some embodiments, the last three sugars are independently 2’-MOE modified sugars. In some embodiments, the last four sugars are independently 2’-MOE modified sugars. In some embodiments, each of such modified sugars is independently the sugar of a nucleoside whose nucleobase is optionally substituted or protected A, T, C, G, or U, or an optionally substituted or protected tautomer of A, T, C, G, or U. In some embodiments, one or more such sugars are independently bonded to a non-negatively charged internucleotidic linkage. In some embodiments, one or more such sugars are independently bonded to a neutral internucleotidic linkage such as n001. In some embodiments, a non-negatively charged internucleotidic linkage or neutral internucleotidic linkage, e.g., n001, is chirally controlled. In some embodiments, it is Rp. In some embodiments, one or more such sugars are independently bonded to a phosphorothioate internucleotidic linkage. In some embodiments, a phosphorothioate internucleotidic linkage is chirally controlled. In some embodiments, it is Sp. In some embodiments, as described herein, the internucleotidic linkage between the last and second last nucleosides is a non-negatively charged internucleotidic linkage. In some embodiments, it is a neutral internucleotidic linkage. In some embodiments, it is a phosphoryl guanidine internucleotidic linkage. In some embodiments, it is n001. In some embodiments, it is n025. In some embodiments, In some embodiments, it is chirally controlled. In some embodiments, it is Rp. In some embodiments, except the internucleotidic linkage between the last and second last nucleosides, each internucleotidic linkages bonded to nucleosides comprising the one or more of the last several, or the last several modified sugars are independently phosphorothioate internucleotidic linkages. In some embodiments, each is chirally controlled. In some Page 76 of 743 12621738v1Attorney Docket No.: 2010581-1488 embodiments, each is Sp.
[0195] In some embodiments, a sugar at position +1 is a 2’-F modified sugar. In some embodiments, a sugar at position +1 is a natural DNA sugar. In some embodiments, a sugar at position 0 is a natural DNA sugar (nucleoside at position 0 is opposite to a target adenosine when aligned). In some embodiments, a sugar at position -1 is a DNA sugar. In some embodiments, a sugar at position -2 is a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic or a bicyclic sugar (e.g., a sugar comprising 2’−O−CH2−4’, wherein the −CH2− is optionally substituted (e.g., a LNA sugar, a cET sugar (e.g., (S)-cEt))). In some embodiments, it is a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic. In some embodiments, it is a 2’- OMe modified sugar. In some embodiments, it is a 2’-MOE modified sugar. In some embodiments, it is a bicyclic sugar. In some embodiments, it is a LNA sugar. In some embodiments, it is a cEt sugar. In some embodiments, a sugar at position -3 is a 2’-F modified sugar. In some embodiments, each sugar after position -3 (e.g., position -4, -5, -6, etc.) is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic or a bicyclic sugar (e.g., a sugar comprising 2’−O−CH2−4’, wherein the −CH2− is optionally substituted (e.g., a LNA sugar, a cET sugar (e.g., (S)-cEt))). In some embodiments, each is independently a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic or a bicyclic sugar. In some embodiments, each is independently a 2’-OMe or 2’-MOE modified sugar. In some embodiments, each is a 2’-OMe modified sugar. In some embodiments, each is a 2’-MOE modified sugar. In some embodiments, one or more are independently 2’-OMe modified sugars, and one or more are independently 2’-MOE modified sugars. In some embodiments, as described herein, the internucleotidic linkage between nucleosides at positions -1 and-2 is a non-negatively charged internucleotidic linkage. In some embodiments, it is a neutral internucleotidic linkage. In some embodiments, it is a phosphoryl guanidine internucleotidic linkage. In some embodiments, it is n001. In some embodiments, it is chirally controlled. In some embodiments, it is Sp. In some embodiments, it is Rp. In some embodiments, the internucleotidic linkage between nucleosides at positions -2 and -3 is a natural phosphate linkage. In some embodiments, as described herein, the internucleotidic linkage between the last and second last nucleosides is a non-negatively charged internucleotidic linkage. In some embodiments, it is a neutral internucleotidic linkage. In some embodiments, it is a phosphoryl guanidine internucleotidic linkage. In some embodiments, it is n001. In some embodiments, it is chirally controlled. In some embodiments, it is Rp. In some embodiments, each internucleotidic linkages between nucleosides to the 3’-side of a nucleoside opposite to a target adenosine, except those between nucleosides at positions -1 and -2, and between nucleosides at positions -2 and -3, and between the last and the second last nucleosides, is independently a phosphorothioate internucleotidic linkages. In some embodiments, each phosphorothioate internucleotidic linkage is chirally controlled. In some embodiments, each is Sp.
[0196] In some embodiments, the first and / or last one or several sugars are modified sugars, e.g., bicyclic sugars and / or 2’-OR modified sugars wherein R is optionally substituted C1-6aliphatic (e.g., 2’-OMe modified sugars, 2’-MOE modified sugars, etc.). In some embodiments, such sugars may increase stability, affinity and / or activity of an oligonucleotide. In some embodiments, when conjugated to one or more additional Page 77 of 743 12621738v1Attorney Docket No.: 2010581-1488 chemical moieties, sugars at 5’- and / or 3’-ends of oligonucleotides are not bicyclic sugars or 2’-OR modified sugars wherein R is optionally substituted C1-6 aliphatic. In some embodiments, a 5’-end sugar is a bicyclic sugar or a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic. In some embodiments, such a 5’-end sugar is not connected to an additional chemical moiety. In some embodiments, a 5’-end sugar is a 2’-F modified sugar. In some embodiments, a 5’-end sugar is a 2’-F modified sugar conjugated to an additional chemical moiety. In some embodiments, a 3’-end sugar is a bicyclic sugar or a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic. In some embodiments, such a 3’-end sugar is not connected to an additional chemical moiety. In some embodiments, a 3’-end sugar is a 2’-F modified sugar. In some embodiments, a 3’-end sugar is a 2’-F modified sugar conjugated to an additional chemical moiety. In some embodiments, the last several sugars are 3’-side sugars relative to a nucleoside opposite to a target adenosine (e.g., sugars of 3’-side nucleosides such as N-1, N-2, etc.). In some embodiments, the last several sugars or the 3’-side sugars comprises one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more) 2’-F modified sugars. In some embodiments, the last several sugars or the 3’-side sugars comprises two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more) consecutive 2’-F modified sugars. In some embodiments, the last several sugars or the 3’-side sugars comprises one or more, or two or more consecutive, 2’-F modified sugars, and sugar of the last nucleoside of an oligonucleotide is a bicyclic sugar or a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic. In some embodiments, as described herein a 2’-OR modified sugar is a 2’-OMe modified sugar or a 2’-MOE modified sugar; in some embodiments, it is a 2’-OMe modified sugar; in some embodiments, it is a 2’-MOE modified sugar. In some embodiments, the last several sugars or the 3’-side sugars comprises one or more, or two or more consecutive, 2’-F modified sugars, and sugar of the last nucleoside of an oligonucleotide is a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic. In some embodiments, the last several sugars or the 3’-side sugars comprises one or more, or two or more consecutive, 2’-F modified sugars, and sugar of the last nucleoside of an oligonucleotide is a 2’-OMe modified sugar or a 2’-MOE modified sugar. In some embodiments, the last several sugars or the 3’-side sugars comprises one or more, or two or more consecutive, 2’-F modified sugars, and sugar of the last nucleoside of an oligonucleotide is a 2’-OMe modified sugar. In some embodiments, the last several sugars or the 3’-side sugars comprises one or more, or two or more consecutive, 2’-F modified sugars, and sugar of the last nucleoside of an oligonucleotide is a 2’-MOE modified sugar. In some embodiments, two and no more than two nucleosides at the 3’-side of a nucleoside opposite to an adenosine independently have a 2’-F modified sugar. In some embodiments, they are at positions -4 and -5. In some embodiments, they are the second and third last nucleosides of an oligonucleotide. In some embodiments, one and no more than one nucleoside at the 3’-side of a nucleoside opposite to an adenosine has a 2’-F modified sugar. In some embodiments, it is at position -3. In some embodiments, it is 4thlast nucleoside of an oligonucleotide.
[0197] In some embodiments, a bicyclic sugar or a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic is present in a region which comprises one or more (e.g., 1-30, 1-25, 1-20, 1-15, 1- 10, 2-30, 2-25, 2-20, 2-25, 2-10, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more) Page 78 of 743 12621738v1Attorney Docket No.: 2010581-1488 sugars are 2’-F modified. In some embodiments, a majority of sugars as described herein in such a region are 2’-F modified sugars. In some embodiments, two or more 2’-F modified sugars are consecutive. In some embodiments, a region is a first domain. In some embodiments, a bicyclic sugar is present in such a region. In some embodiments, a 2’-OR modified sugar wherein R is optionally substituted C1-6aliphatic is present in such a region. In some embodiments, a 2’-OMe modified sugar is present in such a region. In some embodiments, a 2’-MOE modified sugar is present in such a region.
[0198] In some embodiments, one or more sugars at positions -5, -4, -3, +1, +2, +4, +5, +6, +7, and +8 (position 0 being the position of a nucleoside opposite to a target adenosine; “+” is going from a nucleoside opposite to a target adenosine toward 5’-end of an oligonucleotide, and “-” is going from a nucleoside opposite to a target adenosine toward 3’-end of an oligonucleotide; for example, in 5’-N1N0N-1-3’, if N0is a nucleoside opposite to a target adenosine, it is at position 0, and N1is at position +1 and N-1is at position -1) are independently 2’-F modified sugars. In some embodiments, a sugar at position +1, and one or more sugars at positions -5, -4, -3, +2, +4, +5, +6, +7, and +8, are independently 2’-F modified sugars. In some embodiments, a sugar at position +1, and one sugar at position -5, -4, -3, +2, +4, +5, +6, +7, and +8, are independently 2’-F modified sugars.
[0199] In some embodiments, an oligonucleotide comprises one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more, 2-10, 3-10, 2-5, 2-4, 2-3, 3-5, 3-4, etc.) natural DNA sugars. In some embodiments, one or more natural DNA sugars are at an editing region, e.g., positions +1, 0, and / or -1. In some embodiments, a natural DNA sugar is within the first several nucleosides of an oligonucleotides (e.g., the first 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleosides). In some embodiments, the first, second, and / or third nucleosides of an oligonucleotides independently have a natural DNA sugar. In some embodiments, a natural DNA sugar is bonded to a modified internucleotidic linkage such as a non-negatively charged internucleotidic linkage, a neutral internucleotidic linkage, a phosphoryl guanidine internucleotidic linkage, n001, or a phosphorothioate internucleotidic linkage (in various embodiments, Sp).
[0200] Oligonucleotides may contain various types of internucleotidic linkages. In some embodiments, oligonucleotides comprises one or more modified internucleotidic linkages. In some embodiments, a modified internucleotidic linkage is a chiral internucleotidic linkages. In some embodiments, a modified internucleotidic linkage is a phosphorothioate internucleotidic linkage. In some embodiments, a modified internucleotidic linkage is a non-negatively charged internucleotidic linkage. In some embodiments, a modified internucleotidic linkage is a neutral internucleotidic linkage. In some embodiments, a modified internucleotidic linkage is a phosphoryl guanidine internucleotidic linkage. In some embodiments, a modified internucleotidic linkage is n001. In some embodiments, oligonucleotides comprises one or more natural phosphate linkages. In some embodiments, a natural phosphate linkage bonds to a nucleoside comprising a modified sugar that can improve stability (e.g., resistance toward nuclease). In some embodiments, a natural phosphate linkage bonds to a bicyclic sugar. In some embodiments, a natural phosphate linkage bonds to a 2’- modified sugar. In some embodiments, a natural phosphate linkage bonds to a 2’-OR modified sugar, wherein Page 79 of 743 12621738v1Attorney Docket No.: 2010581-1488 R is optionally substituted C1-6aliphatic. In some embodiments, a natural phosphate linkage bonds to a 2’- OMe modified sugar. In some embodiments, a natural phosphate linkage bonds to a 2’-MOE modified sugar. In some embodiments, an oligonucleotide comprises a phosphorothioate internucleotidic linkage, a non- negatively charged internucleotidic linkage, and a natural phosphate linkage. In some embodiments, an oligonucleotide comprises a phosphorothioate internucleotidic linkage, a neutral internucleotidic linkage, and a natural phosphate linkage. In some embodiments, an oligonucleotide comprises a phosphorothioate internucleotidic linkage, a phosphoryl guanidine internucleotidic linkage, and a natural phosphate linkage. In some embodiments, an oligonucleotide comprises a phosphorothioate internucleotidic linkage, n001, and a natural phosphate linkage. In some embodiments, each chiral internucleotidic linkage is independently chirally controlled. In some embodiments, one or more chiral internucleotidic linkage is not chirally controlled. In some embodiments, each phosphorothioate internucleotidic linkage is independently chirally controlled. In some embodiments, each chiral internucleotidic linkage is independently chirally controlled. In some embodiments, a majority or each phosphorothioate internucleotidic linkage is Sp as described herein. In some embodiments, a majority or each non-negatively charged internucleotidic linkage, e.g., n001, is Rp. In some embodiments, a majority or each non-negatively charged internucleotidic linkage, e.g., n001, is Sp.
[0201] In some embodiments, an oligonucleotide comprises a phosphorothioate internucleotidic linkage and a non-negatively charged internucleotidic linkage. In some embodiments, an oligonucleotide comprises a phosphorothioate internucleotidic linkage and a neutral internucleotidic linkage. In some embodiments, an oligonucleotide comprises a phosphorothioate internucleotidic linkage and a phosphoryl guanidine internucleotidic linkage. In some embodiments, an oligonucleotide comprises a phosphorothioate internucleotidic linkage and n001. In some embodiments, each chiral internucleotidic linkage is independently chirally controlled. In some embodiments, one or more chiral internucleotidic linkage is not chirally controlled. In some embodiments, each phosphorothioate internucleotidic linkage is independently chirally controlled. In some embodiments, each chiral internucleotidic linkage is independently chirally controlled. In some embodiments, a majority or each phosphorothioate internucleotidic linkage is Sp as described herein. In some embodiments, one or more (e.g., 1, 2, 3, 4, or 5) phosphorothioate internucleotidic linkages are Rp. In some embodiments, a majority or each non-negatively charged internucleotidic linkage, e.g., n001, is Rp. In some embodiments, a majority or each non-negatively charged internucleotidic linkage, e.g., n001, is Sp. In some embodiments, an oligonucleotide comprises no natural phosphate linkages. In some embodiments, each internucleotidic linkage is independently a phosphorothioate or a non-negatively charged internucleotidic linkage. In some embodiments, each internucleotidic linkage is independently a phosphorothioate or a neutral charged internucleotidic linkage. In some embodiments, each internucleotidic linkage is independently a phosphorothioate or phosphoryl guanidine internucleotidic linkages. In some embodiments, each internucleotidic linkage is independently a phosphorothioate or n001 internucleotidic linkage. In some embodiments, the last internucleotidic linkage of an oligonucleotide is a non-negatively charged internucleotidic linkage, or is a neutral internucleotidic linkage, or is a phosphoryl guanidine internucleotidic Page 80 of 743 12621738v1Attorney Docket No.: 2010581-1488 linkage, or is n001.
[0202] In some embodiments, oligonucleotides of the present disclosure comprise one or more modified nucleobases. Various modifications can be introduced to a sugar and / or nucleobase in accordance with the present disclosure. For example, in some embodiments, a modification is a modification described in US 9006198. In some embodiments, a modification is a modification described in US 9394333, US 9744183, US 9605019, US 9982257, US 20170037399, US 20180216108, US 20180216107, US 9598458, WO 2017 / 062862, WO 2018 / 067973, WO 2017 / 160741, WO 2017 / 192679, WO 2017 / 210647, WO 2018 / 098264, WO 2018 / 022473, WO 2018 / 223056, WO 2018 / 223073, WO 2018 / 223081, WO 2018 / 237194, WO 2019 / 032607, WO 2019 / 032612, WO 2019 / 055951, WO 2019 / 075357, WO 2019 / 200185, WO 2019 / 217784, WO 2019 / 032612, WO 2020 / 191252, WO 2021 / 071858, and / or WO 2022 / 099159, the sugars, bases, and internucleotidic linkages of each of which are independently incorporated herein by reference.
[0203] In some embodiments, a nucleobase in a nucleoside is or comprises Ring BA which has the structure of BA-I, BA-I-a, BA-I-b, BA-I-c, BA-I-d, BA-II, BA-II-a, BA-II-b, BA-II-c, BA-II-d, BA-III, BA- III-a, BA-III-b, BA-III-c, BA-III-d, BA-III-e, BA-IV, BA-IV-a, BA-IV-b, BA-V, BA-V-a, BA-V-b, or BA- VI, or a tautomer of Ring BA, wherein the nucleobase is optionally substituted or protected.
[0204] In some embodiments, a sugar is a modified sugar comprising a 2’-modificatin, e.g., 2’-F, 2’-OR wherein R is optionally substituted aliphatic, or a bicyclic sugar (e.g., a LNA sugar), or a acyclic sugar (e.g., a UNA sugar).
[0205] In some embodiments, as described herein, provided oligonucleotides comprise one or more domains, each of which independently has certain lengths, modifications, linkage phosphorus stereochemistry, etc., as described herein. In some embodiments, the present disclosure provides an oligonucleotide comprising one or more modified sugars and / or one or more modified internucleotidic linkages, wherein the oligonucleotide comprises a first domain and a second domain each independently comprising one or more nucleobases. In some embodiments, the present disclosure provides oligonucleotide comprising one or more domains and / or subdomains as described herein. In some embodiments, the present disclosure provides oligonucleotides comprising a first domain as described herein. In some embodiments, the present disclosure provides oligonucleotides comprising a second domain as described herein. In some embodiments, the present disclosure provides oligonucleotides comprising a first subdomain as described herein. In some embodiments, the present disclosure provides oligonucleotides comprising a second subdomain as described herein. In some embodiments, the present disclosure provides oligonucleotides comprising a third subdomain as described herein. In some embodiments, the present disclosure provides oligonucleotides comprising one or more regions each independently selected from a first domain, a second domain, a first subdomain, a second subdomain and a third subdomain, each of which is independently as described herein. In some embodiments, the present disclosure provides an oligonucleotide comprising: a first domain; and a second domain, Page 81 of 743 12621738v1Attorney Docket No.: 2010581-1488 wherein: the first domain comprises one or more 2’-F modifications; the second domain comprises one or more sugars that do not have a 2’-F modification.
[0206] In some embodiments, an oligonucleotide or a portion thereof (e.g., a first domain, a second domain, a first subdomain, a second subdomain, a third subdomain, etc.) comprises a certain level of modified sugars. In some embodiments, a modified sugar comprises a 2’-modification. In some embodiments, a modified sugar is a bicyclic sugar. In some embodiments, a modified sugar is an acyclic sugar (e.g., by breaking a C2-C3 bond of a corresponding cyclic sugar). In some embodiments, a modified sugar comprises a 5’-modification. Typically, oligonucleotides of the present disclosure have a free 5’-OH at its 5’-end and a free 3’-OH at its 3’-end unless indicated otherwise, e.g., by context. In some embodiments, a 5’-end sugar of an oligonucleotide may comprise a modified 5’-OH.
[0207] In some embodiments, a level is about e.g., about 5%-100%, about 10%-100%, 20-100%, 30%- 100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%-90%, 70%- 95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all sugars in an oligonucleotide or a portion thereof, respectively. In some embodiments, a percentage is at least about 50%. In some embodiments, a percentage is at least about 55%. In some embodiments, a percentage is at least about 60%. In some embodiments, a percentage is at least about 65%. In some embodiments, a percentage is at least about 70%. In some embodiments, a percentage is at least about 75%. In some embodiments, a percentage is at least about 80%. In some embodiments, a percentage is at least about 85%. In some embodiments, a percentage is at least about 90%. In some embodiments, a percentage is at least about 95%. In some embodiments, a percentage is about 100%.
[0208] In some embodiments, a majority is at least 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more. In some embodiments, a majority is about 50%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%- 100%, 70%-80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%- 100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%. In some embodiments, a majority is about or at least about 50%. In some embodiments, a majority is about or at least about 55%. In some embodiments, a majority is about or at least about 60%. In some embodiments, a majority is about or at least about 65%. In some embodiments, a majority is about or at least about 70%. In some embodiments, a majority is about or at least about 75%. In some embodiments, a majority is about or at least about 80%. In some embodiments, a majority is about or at least about 85%. In some embodiments, a majority is about or at least about 90%. In some embodiments, a majority is about or at least about 95%. Page 82 of 743 12621738v1Attorney Docket No.: 2010581-1488
[0209] In some embodiments, an oligonucleotide or a portion thereof (e.g., a first domain, a second domain, a first subdomain, a second subdomain, a third subdomain, etc.) comprises a certain level of modified internucleotidic linkages. In some embodiments, an oligonucleotide or a portion thereof (e.g., a first domain, a second domain, a first subdomain, a second subdomain, a third subdomain, etc.) comprises a certain level of chiral internucleotidic linkages. In some embodiments, a level is about e.g., about 5%-100%, about 10%- 100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%- 85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all internucleotidic linkages in an oligonucleotide or a portion thereof, respectively. In some embodiments, a percentage is at least about 50%. In some embodiments, a percentage is at least about 55%. In some embodiments, a percentage is at least about 60%. In some embodiments, a percentage is at least about 65%. In some embodiments, a percentage is at least about 70%. In some embodiments, a percentage is at least about 75%. In some embodiments, a percentage is at least about 80%. In some embodiments, a percentage is at least about 85%. In some embodiments, a percentage is at least about 90%. In some embodiments, a percentage is at least about 95%. In some embodiments, a percentage is about 100%.
[0210] In some embodiments, an oligonucleotide or a portion thereof (e.g., a first domain, a second domain, a first subdomain, a second subdomain, a third subdomain, etc.) comprises a certain level of chirally controlled internucleotidic linkages. In some embodiments, an oligonucleotide or a portion thereof (e.g., a first domain, a second domain, a first subdomain, a second subdomain, a third subdomain, etc.) comprises a certain level of Sp internucleotidic linkages. In some embodiments, a level is about e.g., about 5%-100%, about 10%- 100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%- 85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all internucleotidic linkages in an oligonucleotide or a portion thereof, respectively. In some embodiments, a level is about e.g., about 5%-100%, about 10%-100%, 20-100%, 30%-100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%- 80%, 70%-85%, 70%-90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all chiral internucleotidic linkages in an oligonucleotide or a portion thereof, respectively. In some embodiments, a percentage is at least about 50%. In some embodiments, a percentage is at least about 55%. In some embodiments, a percentage is at least about 60%. In some embodiments, a percentage is at least about 65%. In some embodiments, a Page 83 of 743 12621738v1Attorney Docket No.: 2010581-1488 percentage is at least about 70%. In some embodiments, a percentage is at least about 75%. In some embodiments, a percentage is at least about 80%. In some embodiments, a percentage is at least about 85%. In some embodiments, a percentage is at least about 90%. In some embodiments, a percentage is at least about 95%. In some embodiments, a percentage is about 100%.
[0211] In some embodiments, an oligonucleotide or a portion thereof (e.g., a first domain, a second domain, a first subdomain, a second subdomain, a third subdomain, etc.) comprises a certain level of Sp internucleotidic linkages. In some embodiments, a level is about e.g., about 5%-100%, about 10%-100%, 20- 100%, 30%-100%, 40%-100%, 50%-80%, 50%-85%, 50%-90%, 50%-95%, 60%-80%, 60%-85%, 60%-90%, 60%-95%, 60%-100%, 65%-80%, 65%-85%, 65%-90%, 65%-95%, 65%-100%, 70%-80%, 70%-85%, 70%- 90%, 70%-95%, 70%-100%, 75%-80%, 75%-85%, 75%-90%, 75%-95%, 75%-100%, 80%-85%, 80%-90%, 80%-95%, 80%-100%, 85%-90%, 85%-95%, 85%-100%, 90%-95%, 90%-100%, 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, etc. of all internuc...
Claims
Attorney Docket No.: 2010581-1488 CLAIMS 1. An oligonucleotide, wherein the oligonucleotide is an oligonucleotide selected from: RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[ Ssp].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].[fl2r](C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r]( U)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp ].[fl2r](C)[Ssp].d(A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[ nC6o]}|CHEM2{[GalNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[ Ssp].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r](U)[ Ssp].[fl2r](G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp ].d(A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHE M2{[GalNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[ Ssp].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].[fl2r](C)[n001R].m(U)[n001R].m(G)p.[fl2r](U)[ Ssp].[fl2r](G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp ].d(A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHE M2{[GalNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[ Ssp].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r](U)[ Ssp].[fl2r](G)[n001R].m(G)p.[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r]( C)[Ssp].d(A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]} |CHEM2{[GalNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[ Ssp].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].m(U)[n001R].m(G)p.[fl2r](U)[Ssp].[f l2r](G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[ Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHEM2{[Ga lNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].d(A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp] .[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl 2r](G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[ Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHEM2{[Ga lNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](U)[Ssp].m(A)[Ssp].[fl2r](G)[ Ssp].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].m(U)[n001R].m(G)p.[fl2r](U)[Ssp].[f l2r](A)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[ Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHEM2{[Ga Page 719 of 743 12621738v1Attorney Docket No.: 2010581-1488 lNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0; and RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].d(T)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp] .[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl 2r](A)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[ Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHEM2{[Ga lNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0, RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ss p].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].[fl2r](C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r](U) [Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[ fl2r](C)[Ssp].d(A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ss p].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ss p].[fl2r](G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d (A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ss p].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].[fl2r](C)[n001R].m(U)[n001R].m(G)p.[fl2r](U)[Ss p].[fl2r](G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d (A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ss p].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ss p].[fl2r](G)[n001R].m(G)p.[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C) [Ssp].d(A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ss p].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].m(U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r ](G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ss p].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].d(A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[ moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r ](G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ss p].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](U)[Ssp].m(A)[Ssp].[fl2r](G)[Ss p].[moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].m(U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r ](A)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ss p].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].d(T)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[ moe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r Page 720 of 743 12621738v1Attorney Docket No.: 2010581-1488 ](A)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ss p].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 or a salt thereof, wherein: [GalNAc3C12oyl] represents ; e end −CH2−is bonded to an oxygen atom that is bonded to the linkage phosphorus of a phosphate linkage; d represents a natural DNA sugar in a nucleoside; m represents a 2’-OMe modified sugar in a nucleoside; [fl2r] represents a 2’-F modified sugar in a nucleoside; [3nU] represents a nucleoside whose base ;p represents a phosphate linkage; [Ssp] represents a phosphorothioate linkage in the Sp configuration; and [n001R] represent wherein the phosphorus is of the Rp configuration.
2. The oligonucleoti, herein the oligonucleotide is RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[m oe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].[fl2r](C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp]. [fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r]( C)[Ssp].d(A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]} |CHEM2{[GalNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 or a salt thereof.
3. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[m Page 721 of 743 12621738v1Attorney Docket No.: 2010581-1488 oe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl 2r](G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[ Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHEM2{[Ga lNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 or a salt thereof.
4. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[m oe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].[fl2r](C)[n001R].m(U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl 2r](G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[ Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHEM2{[Ga lNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 or a salt thereof.
5. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[m oe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl 2r](G)[n001R].m(G)p.[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp ].d(A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHE M2{[GalNAc3C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 or a salt thereof.
6. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[m oe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].m(U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r](G)[ n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ssp].m( [3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHEM2{[GalNAc3 C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 or a salt thereof.
7. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].d(A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[moe]( G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r](G)[ n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ssp].m( [3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHEM2{[GalNAc3 C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 or a salt thereof.
8. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](U)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[m oe](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].m(U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r](A)[ n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ssp].m( [3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHEM2{[GalNAc3 C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 or a salt thereof.
9. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{p.[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].d(T)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[moe]( Page 722 of 743 12621738v1Attorney Docket No.: 2010581-1488 G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r](A)[ n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ssp].m( [3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}|CHEM1{[nC6o]}|CHEM2{[GalNAc3 C12oyl]}$CHEM1,RNA1,1:R1-1:R1|CHEM1,CHEM2,1:R2-1:R1$$$V2.0 or a salt thereof.
10. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[moe ](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].[fl2r](C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl 2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[ Ssp].d(A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 or a salt thereof.
11. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[moe ](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r] (G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ssp ].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 or a salt thereof.
12. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[moe ](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].[fl2r](C)[n001R].m(U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r] (G)[n001R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ssp ].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 or a salt thereof.
13. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[moe ](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[n001R].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r] (G)[n001R].m(G)p.[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d( A)[Ssp].m([3nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 or a salt thereof.
14. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[moe ](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].m(U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r](G)[n0 01R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ssp].m([3 nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 or a salt thereof.
15. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].d(A)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[moe](G) p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r](G)[n0 01R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ssp].m([3 nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 or a salt thereof.
16. The oligonucleotide of claim 1, wherein the oligonucleotide is Page 723 of 743 12621738v1Attorney Docket No.: 2010581-1488 RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].[fl2r](U)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[moe ](G)p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].m(U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r](A)[n0 01R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ssp].m([3 nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 or a salt thereof.
17. The oligonucleotide of claim 1, wherein the oligonucleotide is RNA1{[moe](G)[n001R].[moe](G)p.[moe](A)p.[fl2r](U)[Ssp].d(T)[Ssp].m(A)[Ssp].[fl2r](G)[Ssp].[moe](G) p.[fl2r](C)[Ssp].[fl2r](C)[Ssp].[fl2r](A)[Ssp].m(C)[Ssp].[fl2r](U)[n001R].m(G)p.[fl2r](U)[Ssp].[fl2r](A)[n0 01R].m(G)p.[fl2r](A)[Ssp].m(A)p.[fl2r](A)[Ssp].[fl2r](G)[Ssp].[fl2r](G)[Ssp].[fl2r](C)[Ssp].d(A)[Ssp].m([3 nU])[Ssp].d(G)[n001R].m(A)p.[fl2r](A)[Ssp].m(G)[n001R].m(C)}$$$V2.0 or a salt thereof.
18. An oligonucleotide, wherein the oligonucleotide is the compound below or a salt thereof. Page 724 of 743 12621738v1Attorney Docket No.: 2010581-1488 19.Page 725 of 743 12621738v1Attorney Docket No.: 2010581-1488 20.Page 726 of 743 12621738v1Attorney Docket No.: 2010581-1488 21.Page 727 of 743 12621738v1Attorney Docket No.: 2010581-1488 22.Page 728 of 743 12621738v1Attorney Docket No.: 2010581-1488 23.Page 729 of 743 12621738v1Attorney Docket No.: 2010581-1488 24.Page 730 of 743 12621738v1Attorney Docket No.: 2010581-1488 25.Page 731 of 743 12621738v1Attorney Docket No.: 2010581-1488 26.GCUUCAUSCCUUUCUAC, wherein S is either G or C; or an oligonucleotide capable of editing a target adenosine in a nucleic acid encoding a PNPLA3 polypeptide to produce a PNPLA3 polypeptide variant that differs by at least one amino acid residue; or an oligonucleotide, wherein the base sequence of the oligonucleotide comprises at least 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 contiguous bases of a base sequence that is identical with or complementary to a base sequence of a PNPLA3 gene or a transcript thereof, wherein the oligonucleotide comprises one or more modified sugars, one or more modified nucleobases, and / or one or more modified internucleotidic Page 732 of 743 12621738v1Attorney Docket No.: 2010581-1488 linkages; or an oligonucleotide comprising 5’-N1N0N-1−3’, wherein N1, N0, and N-1 are each independently a nucleoside and are linked by internucleotidic linkages, wherein the oligonucleotide is capable of binding to a target nucleic acid with N0opposite to a target adenosine; or an oligonucleotide comprising: a first domain; and a second domain, wherein: the first domain comprises one or more 2’-F modifications; the second domain comprises one or more sugars that do not have a 2’-F modification; or an oligonucleotide comprising a modified nucleobase, nucleoside, sugar or internucleotidic linkage as described in the present disclosure; or an oligonucleotide, wherein about or at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% of all sugars are 2’-F modified sugars; or an oligonucleotide comprising a second subdomain as described in the present disclosure; or an oligonucleotide comprising one or more modified sugars and / or one or more modified internucleotidic linkages, wherein the oligonucleotide comprises a first domain and a second domain each independently comprising one or more nucleobases.
27. The oligonucleotide of any one of the preceding claims, wherein: 1) the base sequence of the oligonucleotide comprises at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 contiguous bases of GGAUAAGGCCACUGUAGAAGGGGAUGAAGC, GGGACACGGUGAUGGAGAAGGGCAUGAAGC, AUAAGGCCACUGUAGAAGGGGAUGAAGCAG, GGGAUAAGGCCACUGAGAAGGGGAUGAAGC, AGGGAUAAGGCCACUAGAAGGGGAUGAAGC, AGGAGGGAUAAGGCCAGAAGGGGAUGAAGC, GGAUAAGGCCACUGUAGAAGGGCAUGAAGC, GAUAAGGCCACUGUAGAAGGGCAUGAAGCA, AUAAGGCCACUGUAGAAGGGCAUGAAGCAG, GGGAUAAGGCCACUGAGAAGGGCAUGAAGC, AGGGAUAAGGCCACUAGAAGGGCAUGAAGC, AGGAGGGAUAAGGCCAGAAGGGCAUGAAGC, GGAUAAGGCCACUGUAGAAAGGCAUGAAGC, GAUAAGGCCACUGUAGAAAGGCAUGAAGCA, GAUAACGCCACUGUAGAAAGCCAUGAAGCA, GAUAACGCCTCUGUAGAAAGCCAUGAAGCA, GAUAACGCCACUGUAGAAAGCCAUGAAGCA, GAUAACGCCTCUGUAGAAAGCCAUGAAGCA, AUAAGGCCACUGUAGAAAGGCAUGAAGCAG, UAAGGCCACUGUAGAAAGGCAUGAAGCAGG, AAGGCCACUGUAGAAAGGCAUGAAGCAGGA, GGAUAAGGCCACUGUAGAAAGCCAUGAAGC, GGAUAAGGCCACUGUAGAAACGCAUGAAGC, GGAUAAGGCCACUGUAGAAUGGCAUGAAGC, GGAUAAGGCCACUGUAGAUAGGCAUGAAGC, GGAUAAGGCCACUGUAGUAAGGCAUGAAGC, GGAUAAGGCCACUGUACAAAGGCAUGAAGC, GGAUAAGGCCACUGUUGAAAGGCAUGAAGC, GGAUAAGGCCACUGUAGAAAGGCGUGAAGC, GGAUAAGGCCACUGUAGAGAGGCAUGAAGC, Page 733 of 743 12621738v1Attorney Docket No.: 2010581-1488 GGAUAAGGCCACUGUAGGAAGGCAUGAAGC, GGAUAAGGCCACUGUGGAAAGGCAUGAAGC, GGAUAAGGCCACUGUAGGGAGGCAUGAAGC, GGAUAAGGCCACUGUGGGGAGGCAUGAAGC, GGAUAAGGCCACUGUAGAAAGGUAUGAAGC, GGAUAAGGCCACUGUAGAAGGGUAUGAAGC, GGAUAAGGCCACUGUGGAAAGGUAUGAAGC, GGGAUAAGGCCACUGUAGAAAGGCAUGAAGCA, or GGAUAAGGCCACUGUAGAAAGGCAUGAAGCAG, wherein each T can be independently replaced with U and vice versa. 2) when the oligonucleotide is contacted with a target PNPLA3 transcript comprising a target adenosine in a system, a target adenosine in the target PNPLA3 transcript is modified; 3) when the oligonucleotide is contacted with a target PNPLA3 transcript comprising a target adenosine in a system, level of the target PNPLA3 transcript is reduced compared to absence of the product or presence of a reference oligonucleotide; 4) when the oligonucleotide is contacted with a target PNPLA3 transcript comprising a target adenosine in a system, level of a product of the target PNPLA3 transcript is altered compared to absence of the product or presence of a reference oligonucleotide; 5) level of a product is increased, wherein the product is or is encoded by a PNPLA3 transcript which is otherwise identical to the target PNPLA3 transcript but the target adenosine is modified; 6) level of a product is increased, wherein the product is or is encoded by a PNPLA3 transcript which is otherwise identical to the target PNPLA3 transcript but the target adenosine is replaced with inosine; and / or 7) level of a product is increased, wherein the product is or is encoded by a PNPLA3 transcript which is otherwise identical to the target PNPLA3 transcript but the adenine of the target adenosine is replaced with guanine.
28. The oligonucleotide of any one of claims 26-27, wherein the target adenosine is more associated with a condition, disorder or disease than a guanine at the same position.
29. The oligonucleotide of any one of the preceding claims from claim 26, wherein the oligonucleotide has a length of about 10-200 (e.g., about 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10- 120, 10-150, 20-30, 20-40, 20-50, 20-60, 20-70, 20-80, 20-90, 20-100, 20-120, 20-150, 20-200, 25-30, 25- 40, 25-50, 25-60, 25-70, 25-80, 25-90, 25-100, 25-120, 25-150, 25-200, 30-40, 30-50, 30-60, 30-70, 30-80, 30-90, 30-100, 30-120, 30-150, 30-200, 10, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, etc.) nucleobases, preferably wherein the oligonucleotide has a length of about 26-35 nucleobases.
30. The oligonucleotide of any one of the preceding claims from claim 26, wherein the oligonucleotide can hybridize to a PNPLA3 transcript, wherein the portion the oligonucleotide hybridizes to is, comprises, or overlaps with gcuucauccccuucuacaguggccuuaucc or gcuucaugccuuucuacaguggccuuaucc.
31. The oligonucleotide of any one of the preceding claims from claim 26, wherein the first 3, 4, 5, 6, 7, 8, 9, 10 or more sugars from the 5’-end of the oligonucleotide independently comprise a 2’-OR modification, Page 734 of 743 12621738v1Attorney Docket No.: 2010581-1488 wherein R is optionally substituted C1-6aliphatic.
32. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N23and N22is a natural phosphate linkage, and / or wherein the 2ndinternucleotidic linkage from the 5’-end of the oligonucleotide is a natural phosphate linkage.
33. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N22and N21is a natural phosphate linkage, and / or wherein the 3rdinternucleotidic linkage from the 5’-end of the oligonucleotide is a natural phosphate linkage.
34. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N17and N16is a natural phosphate linkage, and / or wherein the 8thinternucleotidic linkage from the 5’-end of the oligonucleotide is a natural phosphate linkage.
35. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N11and N10is a natural phosphate linkage, and / or wherein the 14thinternucleotidic linkage from the 5’-end of the oligonucleotide is a natural phosphate linkage.
36. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N8and N7is a natural phosphate linkage or a PS internucleotidic linkage, and / or wherein the 17thinternucleotidic linkage from the 5’-end of the oligonucleotide is a natural phosphate linkage or a PS internucleotidic linkage.
37. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N8and N7is a natural phosphate linkage, and / or wherein the 17thinternucleotidic linkage from the 5’-end of the oligonucleotide is a natural phosphate linkage.
38. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N6and N5is a natural phosphate linkage or a PS internucleotidic linkage, and / or wherein the 19thinternucleotidic linkage from the 5’-end of the oligonucleotide is a natural phosphate linkage or a PS internucleotidic linkage.
39. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N6and N5is a natural phosphate linkage, and / or wherein the 19thinternucleotidic linkage from the 5’-end of the oligonucleotide is a natural phosphate linkage.
40. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N-2and N-3is a natural phosphate linkage, and / or wherein the 27thinternucleotidic linkage from the 5’-end of the oligonucleotide is a natural phosphate linkage.
41. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N24and N23is a PN linkage, and / or wherein the 1stinternucleotidic linkage from the 5’-end of the oligonucleotide is a PN linkage.
42. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N13and N12is a PN or a PS linkage, and / or wherein the 12thinternucleotidic linkage from the 5’-end of the oligonucleotide is a PN or PS linkage. Page 735 of 743 12621738v1Attorney Docket No.: 2010581-1488 43. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N13 and N12 is a PS linkage, and / or wherein the 12thinternucleotidic linkage from the 5’-end of the oligonucleotide is a PS linkage.
44. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N12and N11is a PN linkage, and / or wherein the 13thinternucleotidic linkage from the 5’-end of the oligonucleotide is a PN linkage.
45. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N9and N8is a PN or a PS linkage, and / or wherein the 16thinternucleotidic linkage from the 5’-end of the oligonucleotide is a PN or PS linkage.
46. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N9and N8is a PN linkage, and / or wherein the 16thinternucleotidic linkage from the 5’-end of the oligonucleotide is a PN linkage.
47. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N-1and N-2is a PN or a methylphosphonate linkage, and / or wherein the 26thinternucleotidic linkage from the 5’-end of the oligonucleotide is a PN or a methylphosphonate linkage.
48. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N-1and N-2is a PN linkage, and / or wherein the 26thinternucleotidic linkage from the 5’-end of the oligonucleotide is a PN linkage.
49. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N-4and N-5is a PN linkage, and / or wherein the 29thinternucleotidic linkage from the 5’-end of the oligonucleotide is a PN linkage, and / or wherein the first internucleotidic linkage from the 3’-end of the oligonucleotide is a PN internucleotidic linkage.
50. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N1and N0is a PS linkage, and / or wherein the 24thinternucleotidic linkage from the 5’-end of the oligonucleotide is a PS linkage.
51. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N0and N-1is a PS linkage, and / or wherein the 25thinternucleotidic linkage from the 5’-end of the oligonucleotide is a PS linkage.
52. The oligonucleotide of any one of the preceding claims from claim 26, wherein the internucleotidic linkage between N-3and N-4is a PS linkage, and / or wherein the 28thinternucleotidic linkage from the 5’-end of the oligonucleotide is a PS linkage.
53. The oligonucleotide of any one of the preceding claims from claim 26, wherein the first internucleotidic linkage of the 5’-end of oligonucleotide is a PN internucleotidic linkage.
54. The oligonucleotide of any one of the preceding claims from claim 26, wherein the first internucleotidic linkage of the 3’-end of oligonucleotide is a PN internucleotidic linkage.
55. The oligonucleotide of any one of the preceding claims from claim 26, wherein the PN Page 736 of 743 12621738v1Attorney Docket No.: 2010581-1488 internucleotidic linkage is a phosphoramidate internucleotidic linkage.
56. The oligonucleotide of any one of the preceding claims from claim 26, wherein the PN internucleotidic linkage is a phosphoryl guanidine internucleotidic linkage.
57. The oligonucleotide of any one of claims 26-54, wherein the PN internucleotidic linkage is n001.
58. The oligonucleotide of any one of claims 26-54, wherein the PN internucleotidic linkage is n006.
59. The oligonucleotide of any one of claims 26-54, wherein the PN internucleotidic linkage is MsPA.
60. The oligonucleotide of any one of the preceding claims from claim 26, wherein the linkage phosphorus of the PN internucleotidic linkage is Rp.
61. The oligonucleotide of any one of the preceding claims from claim 26, wherein each internucleotidic linkage is independently a natural phosphate linkage, a PS internucleotidic linkage, or a PN internucleotidic linkage.
62. The oligonucleotide of any one of the preceding claims from claim 26, wherein each PS internucleotidic linkage is independently a phosphorothioate internucleotidic linkage.
63. The oligonucleotide of any one of the preceding claims from claim 26, wherein each phosphorothioate internucleotidic linkage is independently Sp.
64. The oligonucleotide of any one of the preceding claims from claim 26, wherein each PN internucleotidic linkage is independently a phosphoramidate internucleotidic linkage.
65. The oligonucleotide of any one of the preceding claims from claim 26, wherein the nucleobase of N9or the nucleobase of the 16thnucleoside from the 5’-end of the oligonucleotide is G or A.
66. The oligonucleotide of any one of claims 26-65, wherein the nucleobase of N20or the 5thnucleoside from the 5’-end of the oligonucleotide is T, U or A.
67. The oligonucleotide of any one of the preceding claims from claim 26, wherein N24is the first nucleoside.
68. The oligonucleotide of any one of claims 0-30, wherein the oligonucleotide consists of a first domain and a second domain, wherein the first domain has a length of about 2-50 (e.g., about 5, 6, 7, 8, 9, or 10 - about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, etc.) nucleobases, and the second domain has a length of about 2-50 (e.g., about 5, 6, 7, 8, 9, or 10 - about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, or about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40 or 50, etc.) nucleobases.
69. The oligonucleotide of any one of the preceding claims, wherein the nucleobase of N0is .. e oligonucleotide of any one of the preceding claims from claim 26, wherein the sugar of N0is a Page 737 of 743 12621738v1Attorney Docket No.: 2010581-1488 2’-OMe modified sugar.
71. The oligonucleotide of any one of the preceding claims from claim 26, wherein the sugar of N1 is a natural DNA sugar, or a 2’-modified sugar.
72. The oligonucleotide of any one of the preceding claims, wherein the sugar of N-1is a natural DNA sugar.
73. The oligonucleotide of any one of the preceding claims from claim 26, wherein sugar of N-2is a 2’- OMe modified sugar.
74. The oligonucleotide of any one of the preceding claims from claim 26, wherein sugar of N-3is a 2’-F modified sugar.
75. The oligonucleotide of any one of the preceding claims from claim 26, wherein sugar of each of N24, N23, and / or N22is independently a 2’-OR modified sugar, and / or wherein each of the 1st, 2ndand / or 3rdsugars from the 5’-end of the oligonucleotide is independently a 2’-OR modified sugar.
76. The oligonucleotide of any one of the preceding claims from claim 26, wherein sugar of N27is a 2’- OR modified sugar, and / or wherein the 8thsugar from the 5’-end of the oligonucleotide is a 2’-OR modified sugar.
77. The oligonucleotide of any one of claims 75-76, wherein the 2’-OR modified sugar is a 2’-MOE modified sugar.
78. The oligonucleotide of any one of the preceding claims from claim 26, wherein sugar of each of N29, N11, and / or N8is independently a 2’-OR modified sugar, and / or wherein each of the 6th, 14thand 17thsugars from the 5’-end of the oligonucleotide is independently a 2’-OR modified sugar.
79. The oligonucleotide of any one of the preceding claims from claim 26, wherein sugar of each of N-4, and / or N-5is independently a 2’-OR modified sugar, and / or wherein each of the last sugar and the second last sugar from the 5’-end of the oligonucleotide is independently a 2’-OR modified sugar.
80. The oligonucleotide of any one of claims 78-79, wherein the 2’-OR modified sugar is a 2’-OMe modified sugar.
81. The oligonucleotide of any one of the preceding claims from claim 26, wherein sugar of each of N21, N18, N16, N15, N14, N10, N9, N7, N5, N4, N3and / or N2is independently a 2’-F modified sugar, and / or wherein each of the 4th, 7th, 9th, 10th, 11th, 15th, 16th, 18th, 20th, 21st, 22ndand / or 23rdsugars from the 5’-end of the oligonucleotide is independently a 2’-F modified sugar.
82. The oligonucleotide of any one of the preceding claims from claim 26, wherein the oligonucleotide comprises an asialoglycoprotein receptor ligand.
83. An oligonucleotide comprising a duplexing region and a targeting region, wherein a targeting region is or comprises a second region of any one of the preceding claims, or 5’-N1N0N-1-3’ of any one of the preceding claims.
84. An oligonucleotide, which is a diastereomer of an oligonucleotide of any one of the preceding claims. Page 738 of 743 12621738v1Attorney Docket No.: 2010581-1488 85. The oligonucleotide of any one of the preceding claims, wherein the oligonucleotide is in a salt form.
86. The oligonucleotide of any one of the preceding claims, wherein each chiral linkage phosphorus independently has a diastereomeric purity of about or at least about 85%, 90%, 91%.92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, and / or wherein the diastereopurity of the oligonucleotide is about or at least about (DS)nc, wherein DS is about 85%-100% (e.g., about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5% or more) and nc is the number of chiral linkage phosphorus.
87. The oligonucleotide of any one of the preceding claims, wherein the target adenosine is at a position within the PNPLA3 transcript encoding for I148M of a PNPLA3 polypeptide, and N0is opposite to the target adenosine.
88. A pharmaceutical composition comprising an oligonucleotide of any one of the preceding claims and a pharmaceutically acceptable carrier.
89. A chirally controlled composition comprising an oligonucleotide of any one of the preceding claims.
90. The composition of any one of claims 88-89, wherein each chiral linkage phosphorus of the oligonucleotide independently has a diastereomeric purity of about or at least about 85%, 90%, 91%.92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, or wherein the diastereomeric purity of the oligonucleotide in the composition is about or at least about (DS)nc, wherein DS is about 85%-100% (e.g., about or at least about 85%, 90%, 91%.92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%), and nc is the number of chiral linkage phosphorus in the oligonucleotide.
91. A composition comprising a plurality of oligonucleotides, wherein each oligonucleotides of the plurality is independently a particular oligonucleotide or a salt thereof, wherein the particular oligonucleotide is an oligonucleotide of any one of the preceding claims; or an oligonucleotide composition comprising a plurality of oligonucleotides, wherein oligonucleotides of the plurality share: 1) a common base sequence, and 2) the same linkage phosphorus stereochemistry independently at one or more (e.g., about 1-50, 1- 40, 1-30, 1-25, 1-20, 1-15, 1-10, 5-50, 5-40, 5-30, 5-25, 5-20, 5-15, 5-10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more) chiral internucleotidic linkages (“chirally controlled internucleotidic linkages”); wherein each oligonucleotide of the plurality is independently an oligonucleotide of any one of the preceding claims (e.g., in an acid, base, or salt form); or an oligonucleotide composition comprising a plurality of oligonucleotides, wherein oligonucleotides of the plurality share: 1) a common base sequence, and 2) the same linkage phosphorus stereochemistry independently at one or more (e.g., about 1-50, 1- 40, 1-30, 1-25, 1-20, 1-15, 1-10, 5-50, 5-40, 5-30, 5-25, 5-20, 5-15, 5-10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more) chiral internucleotidic linkages (“chirally Page 739 of 743 12621738v1Attorney Docket No.: 2010581-1488 controlled internucleotidic linkages”); wherein the common base sequence is complementary to a base sequence of a portion of PNPLA3 transcript which portion comprises a target adenosine.
92. The composition of claim 91, wherein the level of oligonucleotides of a plurality in oligonucleotides in the composition that share the common constitution of the plurality is about or at least about (DS)nc, wherein DS is about 85%-100% (e.g., about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5% or more) and nc is the number of chiral linkage phosphorus, or wherein the level of oligonucleotides of a plurality in oligonucleotides in the composition that share the common constitution of the plurality is about or at least about 20%-100%, or is about or at least about 20%-95%, 30%-90%, 40%-85%, 40%-80%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, or 90%.
93. A method for increasing lipase activity of a PNPLA3 polypeptide or characteristic portion thereof in a subject, comprising administering or delivering to the subject an effective amount of an oligonucleotide or composition of any one of the preceding claims; or a method for increasing lipase activity of a PNPLA3 polypeptide or characteristic portion thereof in a subject, comprising converting the amino acid at position 148 of the PNPLA3 polypeptide into a valine; or a method for producing a RNA encoding a PNPLA3 polypeptide that comprises I148V in a subject, comprising editing a target adenosine in PNPLA3 in the genome of the subject, wherein the target adenosine is in the codon encoding an amino acid at position 148 in the PNPLA3 polypeptide; or a method for producing a RNA encoding a PNPLA3 polypeptide that comprises I148V in a subject, comprising editing a target adenosine in a transcript encoding the PNPLA3 polypeptide, wherein the target adenosine is in the codon encoding an amino acid at position 148 in the PNPLA3 polypeptide; or a method for producing a RNA encoding a PNPLA3 polypeptide that comprises I148V in a subject, comprising administering or delivering to the subject an effective amount of an oligonucleotide or composition of any one of the preceding claims; or a method for producing a PNPLA3 polypeptide comprising I148V in a subject, comprising editing a target adenosine in PNPLA3 in the genome of the subject, wherein the target adenosine is in the codon encoding an amino acid at position 148 in the PNPLA3 polypeptide; or a method for producing a PNPLA3 polypeptide comprising I148V in a subject, comprising editing a target adenosine in a transcript encoding the PNPLA3 polypeptide, wherein the target adenosine is in the codon encoding an amino acid at position 148 in the PNPLA3 polypeptide; or a method for producing a PNPLA3 polypeptide comprising I148V in a subject, comprising administering or delivering to the subject an effective amount of an oligonucleotide or composition of any one of the preceding claims.
94. A method for preventing or treating a condition, disorder or disease, comprising editing a target adenosine in PNPLA3 in the genome of a subject susceptible thereto or suffering therefrom, wherein the target adenosine is in the codon encoding an amino acid at position 148 of a PNPLA3 polypeptide; or Page 740 of 743 12621738v1Attorney Docket No.: 2010581-1488 a method for preventing or treating a condition, disorder or disease, comprising editing a target adenosine in a PNPLA3 transcript in a subject susceptible thereto or suffering therefrom, wherein the target adenosine is in the codon encoding an amino acid at position 148 of a PNPLA3 polypeptide.
95. A method for preventing or treating a condition, disorder or disease, comprising administering or delivering to a subject susceptible thereto or suffering therefrom an effective amount of an oligonucleotide or composition of any one of the preceding claims.
96. The method of any one of claims 94-95, wherein the subject comprises an I148M mutation in PNPLA3, optionally wherein the subject is homozygous for the mutation.
97. The method of any one of claims 94-96, wherein: the condition, disorder or disease is amenable to an A to G or A to I modification; the condition, disease or disorder is associated with a PNPLA3 I148M mutation; and / or the condition, disease or disorder is amenable to or can benefit from changing I148M to I148V in PNPLA3; and / or wherein: the condition, disorder or disease is a liver condition, disorder or disease; the condition, disorder or disease is a metabolic liver condition, disorder or disease; the condition, disorder or disease is hepatitis; the condition, disorder or disease is fibrosis; the condition, disorder or disease is cirrhosis; the condition, disorder or disease is hepatocellular the condition, disorder or disease is steatosis; the condition, disorder or disease is liver failure; the condition, disorder or disease is metabolic dysfunction-associated steatohepatitis (MASH); the condition, disorder or disease is nonalcoholic steatohepatitis (NASH); or the condition, disorder or disease is non-alcoholic fatty liver disease (NAFLD).
98. The method of any one of the preceding claims, comprising assessment of liver fat and / or liver stiffness, and / or comprising liver biopsy, and / or comprising liver biopsy histology.
99. A method for modulating a protein interaction with an agent in a system wherein a protein is translated from its encoding RNA, comprising administering to the system an oligonucleotide or composition of any one of the preceding claims, wherein an adenosine in the encoding RNA is edited, wherein a protein is translated from the edited mRNA (“the edited protein”), wherein the edited protein differs from the unedited protein at an amino acid residue involving in the protein-agent interaction.
100. A method for delivering to a system an oligonucleotide, comprising administering to the system a conjugate of the oligonucleotide with an additional chemical moiety or a salt thereof.
101. A nucleic acid comprising a sequence of GCUUCIUSCCUUUCUAC, wherein: S is either G or C; and each U can be optionally and independently replaced with T; or Page 741 of 743 12621738v1Attorney Docket No.: 2010581-1488 a nucleic acid comprising a sequence with about or at least about 50% sequence identity to GCUUCGUGCCUUUCUACAGUGGCCUUAUCC or GCUUCGUCCCCUUCUACAGUGGCCUUAUCC, wherein each U can be optionally and independently replaced with T; or a polypeptide comprising an amino acid sequence with about or at least about 50% sequence identity to VDALVCSCFVPF or VDALVCSCFVPF, or a polypeptide comprising SEQ ID NO: 2 or a characteristic portion thereof; or a cell comprising a nucleic acid above, and / or comprising or expressing the polypeptide above; or a method for increasing lipase activity of a PNPLA3 polypeptide or characteristic portion thereof, comprising modifying an amino acid residue at a position that is or corresponds to position 148 of SEQ ID NO:
2.
102. A method for preparing an oligonucleotide or composition of any one of the preceding claims, comprising utilizing a phosphoramidite (e.g., a phosphoramidite comprising a chiral auxiliary).
103. Use of an oligonucleotide or composition of any one of the preceding claims for editing a target adenosine in a codon, for preventing or treating a condition, disease or disorder, for manufacturing a medicament for preventing or treating a condition, disease or disorder, for a method of any one of the preceding claims, or for manufacturing a medicament for a method of any one of the preceding claims.
104. An oligonucleotide or composition of any one of the preceding claims, for preventing or treating a condition, disease or disorder, for manufacturing a medicament for preventing or treating a condition, disease or disorder, for use in a method of any one of the preceding claims, or for use in manufacturing a medicament for a method of any one of the preceding claims.
105. A nucleic acid, polypeptide, oligonucleotide, composition, use or method of any one of Embodiments 1-958. Page 742 of 743 12621738v1
Citation Information
Cited By
Oligonucleotide compositions and methods of use thereof
US12674168B2
Inhibin subunit beta e-related double stranded oligonucleotide compositions and methods relating thereto
WO2026055502A3