WO2022026719A2 - Nrl antisense oligonucleotides, compositions containing the same, and methods of their use - Google Patents

Nrl antisense oligonucleotides, compositions containing the same, and methods of their use Download PDF

Info

Publication number
WO2022026719A2
WO2022026719A2 PCT/US2021/043716 US2021043716W WO2022026719A2 WO 2022026719 A2 WO2022026719 A2 WO 2022026719A2 US 2021043716 W US2021043716 W US 2021043716W WO 2022026719 A2 WO2022026719 A2 WO 2022026719A2
Authority
WO
WIPO (PCT)
Prior art keywords
oligonucleotide
seq
internucleoside
internucleoside linkages
nucleotide sequence
Prior art date
Application number
PCT/US2021/043716
Other languages
French (fr)
Other versions
WO2022026719A3 (en
Inventor
Gerald SEWACK
Paul NAKAMURA
Original Assignee
Nayan Therapeutics, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Nayan Therapeutics, Inc. filed Critical Nayan Therapeutics, Inc.
Publication of WO2022026719A2 publication Critical patent/WO2022026719A2/en
Publication of WO2022026719A3 publication Critical patent/WO2022026719A3/en

Links

Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/11DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/10Type of nucleic acid
    • C12N2310/11Antisense
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/30Chemical structure
    • C12N2310/32Chemical structure of the sugar
    • C12N2310/323Chemical structure of the sugar modified ring structure
    • C12N2310/3231Chemical structure of the sugar modified ring structure having an additional ring, e.g. LNA, ENA
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/30Chemical structure
    • C12N2310/33Chemical structure of the base
    • C12N2310/334Modified C
    • C12N2310/33415-Methylcytosine
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/30Chemical structure
    • C12N2310/34Spatial arrangement of the modifications
    • C12N2310/341Gapmers, i.e. of the type ===---===

Definitions

  • the invention provides oligonucleotides, compositions containing the same, and methods of their use.
  • Retinitis pigmentosa is a group of inherited, progressive diseases causing retinal degeneration. Patients having retinitis pigmentosa experience a gradual decline in their vision because photoreceptor cells in the retina degenerate.
  • rod cells are affected first. Because rods are concentrated in outer portions of the retina and are triggered by dim light, their degeneration affects peripheral and night vision. When the disease progresses and cones become affected, visual acuity, color perception, and central vision are diminished. Night blindness is one of the earliest and most frequent symptoms of retinitis pigmentosa. On the other hand, patients with cone degeneration first experience decreased central vision and reduced ability to discriminate colors and perceive details.
  • Retinitis pigmentosa is typically diagnosed in adolescents and young adults. The rate of progression and degree of visual loss varies from person to person. Most people with retinitis pigmentosa are legally blind by age 40 with a central visual field of less than 20 degrees in diameter.
  • retinitis pigmentosa There is currently no cure for retinitis pigmentosa. Applicability of various supplements, such as vitamin A, docosahexaenoic acid, and lutein, to slow the progression of retinitis pigmentosa remain largely unresolved.
  • the main marketed treatment for retinitis pigmentosa is an electronic retinal implant. This treatment approach, however, requires intraocular, surgical implantation and is prosthetic by design. Therefore, it does not prevent the loss of rod and cone cells underlying the symptoms of retinitis pigmentosa.
  • the invention provides oligonucleotides including a nucleobase sequence including at least 6 contiguous nucleobases complementary to an equal-length portion within a NRL target nucleic acid.
  • the invention also provides compositions containing oligonucleotides of the invention and methods of using the same.
  • the invention provides a single-stranded oligonucleotide including a total of 12 to 50 interlinked nucleotides and having a nucleobase sequence including at least 6 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
  • the invention provides a single-stranded oligonucleotide comprising a total of 12 to 50 interlinked nucleotides and having a nucleobase sequence comprising at least 6 contiguous nucleobases complementary to the target sequence of any one of SEQ ID NOs: 6-17.
  • the oligonucleotide includes at least one modified nucleobase.
  • at least one modified nucleobase is 5-methylcytosine.
  • at least one modified nucleobase is 7-deazaguanine.
  • at least one modified nucleobase is 6- thioguanine.
  • the oligonucleotide includes at least one modified internucleoside linkage.
  • the modified internucleoside linkage is a phosphorothioate linkage.
  • the phosphorothioate linkage is a stereochemically enriched phosphorothioate linkage.
  • at least 50% of internucleoside linkages in the oligonucleotide are each independently the modified internucleoside linkage.
  • at least 70% of internucleoside linkages in the oligonucleotide are each independently the modified internucleoside linkage.
  • 100% of the internucleoside linkages in the oligonucleotide are the modified internucleoside linkage.
  • the oligonucleotide includes at least one modified sugar nucleoside. In some embodiments, at least one modified sugar nucleoside is a bridged nucleic acid. In some embodiments, the bridged nucleic acid is a locked nucleic acid (LNA), ethylene-bridged nucleic acid (ENA), or cEt nucleic acid. In some embodiments, the oligonucleotide is a gapmer. In some embodiments, at least one modified sugar nucleoside is a 2’-modified sugar nucleoside.
  • At least one 2’-modified sugar nucleoside includes a 2’-modification selected from the group consisting of 2’-fluoro, 2’-methoxy, and 2’-methoxyethoxy.
  • the oligonucleotide includes deoxyribonucleotides. In some embodiments, the oligonucleotide includes ribonucleotides.
  • the oligonucleotide is a morpholino oligomer.
  • the oligonucleotide includes a hydrophobic moiety covalently attached at a 5’-terminus, 3’-terminus, or internucleoside linkage of the oligonucleotide.
  • the oligonucleotide includes a total of at least 7 interlinked nucleotides.
  • the single-stranded oligonucleotide includes at least 7 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
  • the oligonucleotide includes a total of at least 8 interlinked nucleotides.
  • the single-stranded oligonucleotide includes at least 8 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
  • the oligonucleotide includes a total of at least 9 interlinked nucleotides.
  • the single-stranded oligonucleotide includes at least 9 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
  • the oligonucleotide includes a total of at least 10 interlinked nucleotides.
  • the single-stranded oligonucleotide includes at least 10 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof. In some embodiments, the oligonucleotide includes a total of 10 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of at least 11 interlinked nucleotides.
  • the single-stranded oligonucleotide includes at least 11 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
  • the oligonucleotide includes a total of at least 12 interlinked nucleotides.
  • the single-stranded oligonucleotide includes at least 12 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
  • the oligonucleotide includes a total of at least 13 interlinked nucleotides.
  • the single-stranded oligonucleotide includes at least 13 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
  • the oligonucleotide includes a total of at least 14 interlinked nucleotides.
  • the single-stranded oligonucleotide includes at least 14 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
  • the oligonucleotide includes a total of at least 15 interlinked nucleotides.
  • the single-stranded oligonucleotide includes at least 15 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
  • the oligonucleotide includes a total of at least 16 interlinked nucleotides.
  • the single-stranded oligonucleotide includes at least 16 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
  • the oligonucleotide includes a total of 25 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 20 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 19 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 18 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 17 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 16 interlinked nucleotides or fewer.
  • the oligonucleotide includes a total of 15 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 14 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 13 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 12 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 11 interlinked nucleotides or fewer.
  • the nucleotide sequence is set forth in SEQ ID NO: 6. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 7. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 8. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 9. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 10. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 11. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 12. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 13.
  • the nucleotide sequence is set forth in SEQ ID NO: 14. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 15. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 16. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 17. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 18. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 19. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 20. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 21 .
  • the nucleotide sequence is set forth in SEQ ID NO: 22. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 23. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 24. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 25. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 26. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 27. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 28. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 29.
  • sequence of the oligonucleotide comprises or consists of the nucleotide sequence referenced in the claim.
  • the invention provides an oligonucleotide having a nucleotide sequence that comprises the sequence of any one of SEQ ID NOs: 6-29 or a chemically modified version thereof (e.g., SEQ ID NOs: 18-29).
  • the oligonucleotide has a nucleotide sequence that consists of the sequence of any one of SEQ ID NOs: 6-29 or a chemically modified version thereof (e.g., SEQ ID NOs: 18-29).
  • the oligonucleotide comprises a feature or modification as set forth above and elsewhere herein.
  • the “chemically modified version thereof comprises a 5-methyl-dC nucleotide in place of C.
  • a “chemically modified version thereof of any one of SEQ ID NOs: 6-17 is SEQ ID NO: 18-29, respectively.
  • the invention provides a pharmaceutically acceptable salt of an oligonucleotide as set forth above and elsewhere herein.
  • the invention provides a double-stranded oligonucleotide including an oligonucleotide of the invention hybridized to a complementary oligonucleotide.
  • the complementary oligonucleotide has the same length as the oligonucleotide of the invention.
  • the complementary oligonucleotide has a length that is at least, e.g., ⁇ 1 , ⁇ 2, ⁇ 3, ⁇ 4, or ⁇ 5 nucleotides relative to the number of nucleotides in the oligonucleotide of the invention.
  • the invention provides a pharmaceutical composition including the oligonucleotide of the invention and a pharmaceutically acceptable excipient.
  • the invention provides methods of use of the oligonucleotides of the invention.
  • the method is a method of inhibiting or reducing the production of an NRL protein in a cell including (e.g., expressing) an NRL gene by contacting the cell with the oligonucleotide of the invention.
  • the cell is in a subject. In particular embodiments, the cell is in the subject’s eye.
  • the method is a method of treating a subject in need thereof by administering to the subject a therapeutically effective amount of the oligonucleotide of the invention or the pharmaceutical composition of the invention.
  • the oligonucleotide or pharmaceutical composition is administered intraocularly or topically to the eye of the subject.
  • the subject is in need of a treatment for an ocular disease, disorder, or condition associated with a dysfunction of ABCA4, AIPL1 , BBS1 , BEST1 , CEP290, CDH3, CHM, CNGA3, CNGB3, CRB1 , GUCY2D, MERTK, MRFP, MY07A,
  • the subject is in need of a treatment for retinitis pigmentosa, Stargardt disease, cone-rod dystrophy, Leber congenital amaurosis, Bardet Biedl syndrome, macular dystrophy, dry macular degeneration, geographic atrophy, atrophic age-related macular degeneration (AMD), advanced dry AMD, retinal dystrophy, choroideremia, Usher syndrome type 1 , retinoschisis, Leber hereditary optic neuropathy, and achromatopsia.
  • retinitis pigmentosa Stargardt disease, cone-rod dystrophy, Leber congenital amaurosis, Bardet Biedl syndrome, macular dystrophy, dry macular degeneration, geographic atrophy, atrophic age-related macular degeneration (AMD), advanced dry AMD, retinal dystrophy, choroideremia, Usher syndrome type 1 , retinoschisis, Leber hereditary optic neuropathy, and achromatopsia.
  • retinitis pigmentosa is Rho P23H-associated retinitis pigmentosa, PDE6-associated retinitis pigmentosa, MERTK-associated retinitis pigmentosa, BBS1- associated retinitis pigmentosa, Rho-associated retinitis pigmentosa, MRFP-associated retinitis pigmentosa, RLBP1 -associated retinitis pigmentosa, RP1 -associated retinitis pigmentosa, RPGR-X- linked retinitis pigmentosa, NR2E3-associated retinitis pigmentosa, or SPATA7-associated retinitis pigmentosa.
  • the invention also provides the oligonucleotides described herein, and corresponding salts and/or compositions, for use in treating the diseases and conditions described herein, as well as for inhibiting or reducing production of an NRL protein in a cell as described herein.
  • acyl represents a chemical substituent of formula -C(0)-R, where R is alkyl, aryl, arylalkyl, cycloalkyl, heterocyclyl, heterocyclyl alkyl, heteroaryl, or heteroaryl alkyl.
  • R is alkyl, aryl, arylalkyl, cycloalkyl, heterocyclyl, heterocyclyl alkyl, heteroaryl, or heteroaryl alkyl.
  • An optionally substituted acyl is an acyl that is optionally substituted as described herein for each group R.
  • acyloxy represents a chemical substituent of formula -OR, where R is acyl.
  • An optionally substituted acyloxy is an acyloxy that is optionally substituted as described herein for acyl.
  • aliphatic refers to an acyclic, branched or acyclic, linear hydrocarbon chain, or a monocyclic, bicyclic, tricyclic, or tetracyclic hydrocarbon. Unless specified otherwise, an aliphatic group includes a total of 1 to 60 carbon atoms.
  • An optionally substituted aliphatic is an optionally substituted acyclic aliphatic or an optionally substituted cyclic aliphatic.
  • An optionally substituted acyclic aliphatic is optionally substituted as described herein for alkyl.
  • An optionally substituted cyclic aliphatic is an optionally substituted aromatic aliphatic or an optionally substituted non-aromatic aliphatic.
  • an optionally substituted aromatic aliphatic is optionally substituted as described herein for alkyl.
  • An optionally substituted non-aromatic aliphatic is optionally substituted as described herein for cycloalkyl.
  • an acyclic aliphatic is alkyl.
  • a cyclic aliphatic is aryl.
  • a cyclic aliphatic is cycloalkyl.
  • alkanoyl represents a chemical substituent of formula -C(0)-R, where R is alkyl.
  • An optionally substituted alkanoyl is an alkanoyl that is optionally substituted as described herein for alkyl.
  • alkoxy represents a chemical substituent of formula -OR, where R is a Ci-6 alkyl group, unless otherwise specified.
  • An optionally substituted alkoxy is an alkoxy group that is optionally substituted as defined herein for alkyl.
  • alkyl refers to an acyclic straight or branched chain saturated hydrocarbon group, which, when unsubstituted, has from 1 to 12 carbons, unless otherwise specified. In certain preferred embodiments, unsubstituted alkyl has from 1 to 6 carbons.
  • two substituents combine to form a group -L-CO-R, where L is a bond or optionally substituted Ci-n alkylene, and R is hydroxyl or alkoxy.
  • L is a bond or optionally substituted Ci-n alkylene
  • R is hydroxyl or alkoxy.
  • Each of the substituents may itself be unsubstituted or, valency permitting, substituted with unsubstituted substituent(s) defined herein for each respective group.
  • alkylene represents a divalent substituent that is an alkyl having one hydrogen atom replaced with a valency.
  • An optionally substituted alkylene is an alkylene that is optionally substituted as described herein for alkyl.
  • altmer refers to an oligonucleotide having a pattern of structural features characterized by internucleoside linkages, in which no two consecutive internucleoside linkages have the same structural feature.
  • an altmer is designed such that it includes a repeating pattern.
  • an altmer is designed such that it does not include a repeating pattern.
  • the altmer is a “stereoaltmer.”
  • aryl represents a mono-, bicyclic, or multicyclic carbocyclic ring system having one or two aromatic rings.
  • Aryl group may include from 6 to 10 carbon atoms. All atoms within an unsubstituted carbocyclic aryl group are carbon atoms.
  • Non-limiting examples of carbocyclic aryl groups include phenyl, naphthyl, 1 ,2-dihydronaphthyl, 1 ,2,3,4-tetrahydronaphthyl, fluorenyl, indanyl, indenyl, etc.
  • the aryl group may be unsubstituted or substituted with one, two, three, four, or five substituents independently selected from the group consisting of: alkyl; alkoxy; acyloxy; amino; aryl; aryloxy; azido; cycloalkyl; cycloalkoxy; halo; heterocyclyl; heteroaryl; heterocyclylalkyl; heteroarylalkyl; heterocyclyloxy; heteroaryloxy; hydroxy; nitro; thiol; silyl; and cyano.
  • Each of the substituents may itself be unsubstituted or substituted with unsubstituted substituent(s) defined herein for each respective group.
  • aryl alkyl represents an alkyl group substituted with an aryl group.
  • aryl and alkyl portions may be optionally substituted as the individual groups as described herein.
  • arylene represents a divalent substituent that is an aryl having one hydrogen atom replaced with a valency.
  • An optionally substituted arylene is an arylene that is optionally substituted as described herein for aryl.
  • aryloxy represents a group -OR, where R is aryl.
  • Aryloxy may be an optionally substituted aryloxy.
  • An optionally substituted aryloxy is aryloxy that is optionally substituted as described herein for aryl.
  • bicyclic sugar moiety represents a modified sugar moiety including two fused rings.
  • the bicyclic sugar moiety includes a furanosyl ring.
  • blockmer refers to an oligonucleotide strand having a pattern of structural features characterized by the presence of at least two consecutive internucleoside linkages with the same structural feature.
  • same structural feature is meant the same stereochemistry at the internucleoside linkage phosphorus or the same modification at the linkage phosphorus.
  • the two or more consecutive internucleoside linkages with the same structure feature are referred to as a “block.”
  • the blockmer is a “stereoblockmer.”
  • C x-y indicates that the group, the name of which immediately follows the expression, when unsubstituted, contains a total of from x to y carbon atoms. If the group is a composite group (e.g., aryl alkyl), C x-y indicates that the portion, the name of which immediately follows the expression, when unsubstituted, contains a total of from x to y carbon atoms.
  • (Ce-io- aryl)-Ci-6-alkyl is a group, in which the aryl portion, when unsubstituted, contains a total of from 6 to 10 carbon atoms, and the alkyl portion, when unsubstituted, contains a total of from 1 to 6 carbon atoms.
  • nucleobase sequence refers to the nucleobase sequence having a pattern of contiguous nucleobases that permits an oligonucleotide having the nucleobase sequence to hybridize to another oligonucleotide or nucleic acid to form a duplex structure under physiological conditions.
  • Complementary sequences include Watson-Crick base pairs formed from natural and/or modified nucleobases.
  • Complementary sequences can also include non- Watson-Crick base pairs, such as wobble base pairs (guanosine-uracil, hypoxanthine-uracil, hypoxanthine-adenine, and hypoxanthine-cytosine) and Hoogsteen base pairs.
  • oligonucleotide refers to nucleosides, nucleobases, sugar moieties, or internucleoside linkages that are immediately adjacent to each other.
  • contiguous nucleobases means nucleobases that are immediately adjacent to each other in a sequence.
  • cycloalkyl refers to a cyclic alkyl group having from three to ten carbons (e.g., a C3-C10 cycloalkyl), unless otherwise specified. Cycloalkyl groups may be monocyclic or bicyclic. Bicyclic cycloalkyl groups may be of bicyclo[p.q.0]alkyl type, in which each of p and q is, independently, 1 , 2, 3, 4, 5, 6, or 7, provided that the sum of p and q is 2, 3, 4, 5, 6, 7, or 8.
  • bicyclic cycloalkyl groups may include bridged cycloalkyl structures, e.g., bicyclo[p.q.r]alkyl, in which r is 1 , 2, or 3, each of p and q is, independently, 1 , 2, 3, 4, 5, or 6, provided that the sum of p, q, and r is 3, 4, 5, 6, 7, or 8.
  • the cycloalkyl group may be a spirocyclic group, e.g., spiro[p.q]alkyl, in which each of p and q is, independently, 2, 3, 4, 5, 6, or 7, provided that the sum of p and q is 4, 5, 6, 7, 8, or 9.
  • Non-limiting examples of cycloalkyl include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, 1- bicyclo[2.2.1 .jheptyl, 2-bicyclo[2.2.1 .jheptyl, 5-bicyclo[2.2.1 .jheptyl, 7-bicyclo[2.2.1 .jheptyl, and decalinyl.
  • Each of the substituents may itself be unsubstituted or substituted with unsubstituted substituent(s) defined herein for each respective group.
  • cycloalkylene represents a divalent substituent that is a cycloalkyl having one hydrogen atom replaced with a valency.
  • An optionally substituted cycloalkylene is a cycloalkylene that is optionally substituted as described herein for cycloalkyl.
  • cycloalkoxy represents a group -OR, where R is cycloalkyl. Cycloalkoxy may be an optionally substituted cycloalkoxy. An optionally substituted cycloalkoxy is cycloalkoxy that is optionally substituted as described herein for cycloalkyl.
  • duplex represents two oligonucleotides that are paired through hybridization of complementary nucleobases.
  • gapmer refers to an oligonucleotide having an RNase H recruiting region (gap) flanked by a 5' wing and 3' wing, each of the wings including at least one affinity enhancing nucleoside (e.g., 1 , 2, 3, or 4 affinity enhancing nucleosides).
  • halo represents a halogen selected from bromine, chlorine, iodine, and fluorine.
  • headmer refers to an oligonucleotide having an RNase H recruiting region (gap) flanked by a 5’ wing including at least one affinity enhancing nucleoside (e.g., 1 , 2, 3, or 4 affinity enhancing nucleosides).
  • heteroalkyl refers to an alkyl group interrupted one or more times by one or two heteroatoms each time. Each heteroatom is, independently, O, N, or S. None of the heteroalkyl groups includes two contiguous oxygen atoms.
  • the heteroalkyl group may be unsubstituted or substituted (e.g., optionally substituted heteroalkyl). When heteroalkyl is substituted and the substituent is bonded to the heteroatom, the substituent is selected according to the nature and valency of the heteratom.
  • substituents may itself be unsubstituted or substituted with unsubstituted substituent(s) defined herein for each respective group.
  • substituent When heteroalkyl is substituted and the substituent is bonded to carbon, the substituent is selected from those described for alkyl, provided that the substituent on the carbon atom bonded to the heteroatom is not Cl, Br, or I. It is understood that carbon atoms are found at the termini of a heteroalkyl group.
  • heteroalkyl is PEG
  • heteroalkylene represents a divalent substituent that is a heteroalkyl having one hydrogen atom replaced with a valency.
  • An optionally substituted heteroalkylene is a heteroalkylene that is optionally substituted as described herein for heteroalkyl.
  • heteroaryl represents a monocyclic 5-, 6-, 7-, or 8-membered ring system, or a fused or bridging bicyclic, tricyclic, or tetracyclic ring system; the ring system contains one, two, three, or four heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur; and at least one of the rings is an aromatic ring.
  • heteroaryl groups include benzimidazolyl, benzofuryl, benzothiazolyl, benzothienyl, benzoxazolyl, furyl, imidazolyl, indolyl, isoindazolyl, isoquinolinyl, isothiazolyl, isothiazolyl, isoxazolyl, oxadiazolyl, oxazolyl, purinyl, pyrrolyl, pyridinyl, pyrazinyl, pyrimidinyl, qunazolinyl, quinolinyl, thiadiazolyl (e.g., 1 ,3,4-thiadiazole), thiazolyl, thienyl, triazolyl, tetrazolyl, dihydroindolyl, tetrahydroquinolyl, tetrahydroisoquinolyl, etc.
  • bicyclic, tricyclic, and tetracyclic heteroaryls include at least one ring having at least one heteroatom as described above and at least one aromatic ring.
  • a ring having at least one heteroatom may be fused to one, two, or three carbocyclic rings, e.g., an aryl ring, a cyclohexane ring, a cyclohexene ring, a cyclopentane ring, a cyclopentene ring, or another monocyclic heterocyclic ring.
  • fused heteroaryls examples include 1 ,2,3,5,8,8a-hexahydroindolizine; 2,3-dihydrobenzofuran; 2,3-dihydroindole; and 2,3- dihydrobenzothiophene.
  • heteroaryloxy refers to a structure -OR, in which R is heteroaryl. Heteroaryloxy can be optionally substituted as defined for heteroaryl.
  • heterocyclyl represents a monocyclic, bicyclic, tricyclic, or tetracyclic ring system having fused or bridging 4-, 5-, 6-, 7-, or 8-membered rings, unless otherwise specified, the ring system containing one, two, three, or four heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur.
  • Heterocyclyl may be aromatic or non-aromatic.
  • An aromatic heterocyclyl is heteroaryl as described herein.
  • Non-aromatic 5-membered heterocyclyl has zero or one double bonds
  • non-aromatic 6- and 7-membered heterocyclyl groups have zero to two double bonds
  • non-aromatic 8-membered heterocyclyl groups have zero to two double bonds and/or zero or one carbon- carbon triple bond.
  • Heterocyclyl groups have a carbon count of 1 to 16 carbon atoms unless otherwise specified. Certain heterocyclyl groups may have a carbon count up to 9 carbon atoms.
  • Non-aromatic heterocyclyl groups include pyrrolinyl, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, homopiperidinyl, piperazinyl, pyridazinyl, oxazolidinyl, isoxazolidiniyl, morpholinyl, thiomorpholinyl, thiazolidinyl, isothiazolidinyl, thiazolidinyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, dihydrothienyl, pyranyl, dihydropyranyl, dithiazolyl, etc.
  • heterocyclyl also represents a heterocyclic compound having a bridged multicyclic structure in which one or more carbons and/or heteroatoms bridges two non-adjacent members of a monocyclic ring, e.g., quinuclidine, tropanes, or diaza-bicyclo[2.2.2]octane.
  • heterocyclyl includes bicyclic, tricyclic, and tetracyclic groups in which any of the above heterocyclic rings is fused to one, two, or three carbocyclic rings, e.g., a cyclohexane ring, a cyclohexene ring, a cyclopentane ring, a cyclopentene ring, or another heterocyclic ring.
  • fused heterocyclyls include 1 ,2,3,5,8,8a-hexahydroindolizine; 2,3-dihydrobenzofuran; 2,3-dihydroindole; and 2,3-dihydrobenzothiophene.
  • heterocyclyl alkyl represents an alkyl group substituted with a heterocyclyl group.
  • the heterocyclyl and alkyl portions of an optionally substituted heterocyclyl alkyl are optionally substituted as described for heterocyclyl and alkyl, respectively.
  • heterocyclylene represents a divalent substituent that is a heterocyclyl having one hydrogen atom replaced with a valency.
  • An optionally substituted heterocyclylene is a heterocyclylene that is optionally substituted as described herein for heterocyclyl.
  • heterocyclyloxy refers to a structure -OR, in which R is heterocyclyl. Heterocyclyloxy can be optionally substituted as described for heterocyclyl.
  • hydroxyl and “hydroxy,” as used interchangeably herein, represent -OH.
  • hydrophobic moiety represents a monovalent group covalently linked to an oligonucleotide backbone, where the monovalent group is a bile acid (e.g., cholic acid, taurocholic acid, deoxycholic acid, oleyl lithocholic acid, or oleoyl cholenic acid), glycolipid, phospholipid, sphingolipid, isoprenoid, vitamin, saturated fatty acid, unsaturated fatty acid, fatty acid ester, triglyceride, pyrene, porphyrine, texaphyrine, adamantine, acridine, biotin, coumarin, fluorescein, rhodamine, Texas- Red, digoxygenin, dimethoxytrityl, f-butydimethylsilyl, f-butyldiphenylsilyl, cyanine dye (e.g., Cy3 or Cy5), Hoechst 33258 dye
  • a bile acid
  • Non-limiting examples of the monovalent group include ergosterol, stigmasterol, b-sitosterol, campesterol, fucosterol, saringosterol, avenasterol, coprostanol, cholesterol, vitamin A, vitamin D, vitamin E, cardiolipin, and carotenoids.
  • the linker connecting the monovalent group to the oligonucleotide may be an optionally substituted Ci-eo aliphatic (e.g., optionally substituted Ci-eo alkylene) or an optionally substituted C2-60 heteroaliphatic (e.g., optionally substituted C2-60 heteroalkylene), where the linker may be optionally interrupted with one, two, or three instances independently selected from the group consisting of an optionally substituted arylene, optionally substituted heterocyclylene, and optionally substituted cycloalkylene.
  • the linker may be bonded to an oligonucleotide through, e.g., an oxygen atom attached to a 5’-terminal carbon atom, a 3’-terminal carbon atom, a 5’-terminal phosphate or phosphorothioate, a 3’-terminal phosphate or phosphorothioate, or an internucleoside linkage.
  • internucleoside linkage represents a group or bond that forms a covalent linkage between adjacent nucleosides in an oligonucleotide.
  • An internucleoside linkage is an unmodified internucleoside linkage or a modified internucleoside linkage.
  • An “unmodified internucleoside linkage” is a phosphate (-0-P(0)(0H)-0-) internucleoside linkage (“phosphate phosphodiester”).
  • a “modified internucleoside linkage” is an internucleoside linkage other than a phosphate phosphodiester.
  • the two main classes of modified internucleoside linkages are defined by the presence or absence of a phosphorus atom.
  • Non-limiting examples of phosphorus-containing internucleoside linkages include phosphodiester linkages, phosphotriester linkages, phosphorothioate diester linkages, phosphorothioate triester linkages, morpholino internucleoside linkages, methylphosphonates, and phosphoramidate.
  • Nonlimiting examples of non-phosphorus internucleoside linkages include methylenemethylimino ( — CH2 — N(CH 3 )— O— CM2— ), thiodiester (— O— C(O)— S— ), thionocarbamate (— O— C(0)(NH)— S— ), siloxane ( — O — Si(H)2 — O — ), and N,N'-dimethylhydrazine ( — CH2 — N(CH 3 ) — N(CH 3 ) — ).
  • Phosphorothioate linkages are phosphodiester linkages and phosphotriester linkages in which one of the non-bridging oxygen atoms is replaced with a sulfur atom.
  • an internucleoside linkage is a group of the following structure: where
  • Z is O, S, or Se
  • Y is -X-L-R 1 ; each X is independently -O-, -S-, -N(-L-R 1 )-, or L; each L is independently a covalent bond or a linker (e.g., optionally substituted Ci-eo aliphatic linker or optionally substituted C2-60 heteroaliphatic linker); each R 1 is independently hydrogen, -S-S-R 2 , -O-CO-R 2 , -S-CO-R 2 , optionally substituted C1-9 heterocyclyl, or a hydrophobic moiety; and each R 2 is independently optionally substituted C1-10 alkyl, optionally substituted C2-10 heteroalkyl, optionally substituted Ce-io aryl, optionally substituted Ce-io aryl Ci-e alkyl, optionally substituted C1-9 heterocyclyl, or optionally substituted C1-9 heterocyclyl Ci-e alkyl.
  • a linker e.g., optional
  • L When L is a covalent bond, R 1 is hydrogen, Z is oxygen, and all X groups are -O-, the internucleoside group is known as a phosphate phosphodiester.
  • R 1 When L is a covalent bond, R 1 is hydrogen, Z is sulfur, and all X groups are -O-, the internucleoside group is known as a phosphorothioate diester.
  • Z When Z is oxygen, all X groups are -O-, and either (1) L is a linker or (2) R 1 is not a hydrogen, the internucleoside group is known as a phosphotriester.
  • morpholino represents an oligomer of at least 10 morpholino monomer units interconnected by morpholino internucleoside linkages.
  • a morpholino includes a 5’ group and a 3’ group.
  • a morpholino may be of the following structure: where n is an integer of at least 10 (e.g., 12 to 30) indicating the number of morpholino units; each B is independently a nucleobase;
  • R 1 is a 5’ group
  • R 2 is a 3’ group
  • L is (i) a morpholino internucleoside linkage or, (ii) if L is attached to R 2 , a covalent bond.
  • a 5’ group in morpholino may be, e.g., hydroxyl, a hydrophobic moiety, phosphate, diphosphate, triphosphate, phosphorothioate, diphosphorothioate, triphosphorothioate, phosphorodithioate, disphorodithioate, triphosphorodithioate, phosphonate, phosphoramidate, a cell penetrating peptide, an endosomal escape moiety, or a neutral organic polymer.
  • a 3’ group in morpholino may be, e.g., hydrogen, a hydrophobic moiety, phosphate, diphosphate, triphosphate, phosphorothioate, diphosphorothioate, triphosphorothioate, phosphorodithioate, disphorodithioate, triphosphorodithioate, phosphonate, phosphoramidate, a cell penetrating peptide, an endosomal escape moiety, or a neutral organic polymer.
  • morpholino internucleoside linkage represents a divalent group of the following structure:
  • Z is O or S
  • X 1 is a bond, -CH2-, or -O-;
  • X 2 is a bond, -CH2-O-, or -O-;
  • Y is -NR2, where each R is independently C1-6 alkyl (e.g., methyl), or both R combine together with the nitrogen atom to which they are attached to form a C2-9 heterocyclyl (e.g., N-piperazinyl); provided that both X 1 and X 2 are not simultaneously a bond.
  • R is independently C1-6 alkyl (e.g., methyl), or both R combine together with the nitrogen atom to which they are attached to form a C2-9 heterocyclyl (e.g., N-piperazinyl); provided that both X 1 and X 2 are not simultaneously a bond.
  • NRL refers to a ribonucleic acid (e.g., pre-mRNA or mRNA) that encodes the protein Neural Retina Leucine Zipper in humans.
  • An exemplary genomic DNA sequence of a human NRL gene is given by SEQ ID NO. 1 (NCBI Reference Sequence: NG_011697.2).
  • pre-mRNA is produced from the genomic DNA in accordance with the central dogma; pre-mRNA is then spliced to produce transcripts, e.g., NRL transcript 1 , NRL transcript 2, NRL transcript 3, or NRL transcript 4.
  • Exemplary mRNA sequences of a human NRL gene are given by SEQ ID NOs.
  • SEQ ID NO. 2 corresponds to NRL transcript 1 .
  • SEQ ID NO. 3 corresponds to NRL transcript 2.
  • SEQ ID NO. 4 corresponds to NRL transcript 3.
  • SEQ ID NO. 5 corresponds to NRL transcript 4.
  • SEQ ID NOs. 2, 3, 4, and 5 are based on NCBI Reference Sequences for NRL transcripts 1 , 2, 3, and 4, which are provided as RNA sequences with thymidines in the NCBI Reference Sequences.
  • an RNA sequence typically includes uridines instead of thymidines.
  • target RNA sequences may include one or more uridines instead of thymidines without affecting the sequence of an oligonucleotide of the invention.
  • SEQ ID NO: 1 has the following nucleobase sequence (5’-3’)
  • cagcagtaga tccaggcagt cacacagaga agcttgaatg gtgacgatgg tttctgctcc
  • 34801 caaaatatgg tggtcaagtc ctggagatcc cctgtgggaa aagttgctttt cctttctgat
  • SEQ ID NO: 2 has the following nucleobase sequence (5’-3’)
  • SEQ ID NO: 3 has the following nucleobase sequence (5’-3’)
  • SEQ ID NO: 4 has the following nucleobase sequence (5’-3’)
  • SEQ ID NO: 5 has the following nucleobase sequence (5’-3’)

Abstract

Disclosed are oligonucleotides having a nucleobase sequence with at least 6 contiguous nucleobases complementary to an equal-length portion within an NRL target nucleic acid. Also disclosed are pharmaceutical compositions containing the oligonucleotides and methods of their use.

Description

NRL ANTISENSE OLIGONUCLEOTIDES,
COMPOSITIONS CONTAINING THE SAME, AND METHODS OF THEIR USE
FIELD OF THE INVENTION
The invention provides oligonucleotides, compositions containing the same, and methods of their use.
BACKGROUND
Retinitis pigmentosa is a group of inherited, progressive diseases causing retinal degeneration. Patients having retinitis pigmentosa experience a gradual decline in their vision because photoreceptor cells in the retina degenerate.
In most forms of retinitis pigmentosa, rod cells are affected first. Because rods are concentrated in outer portions of the retina and are triggered by dim light, their degeneration affects peripheral and night vision. When the disease progresses and cones become affected, visual acuity, color perception, and central vision are diminished. Night blindness is one of the earliest and most frequent symptoms of retinitis pigmentosa. On the other hand, patients with cone degeneration first experience decreased central vision and reduced ability to discriminate colors and perceive details.
Retinitis pigmentosa is typically diagnosed in adolescents and young adults. The rate of progression and degree of visual loss varies from person to person. Most people with retinitis pigmentosa are legally blind by age 40 with a central visual field of less than 20 degrees in diameter.
There is currently no cure for retinitis pigmentosa. Applicability of various supplements, such as vitamin A, docosahexaenoic acid, and lutein, to slow the progression of retinitis pigmentosa remain largely unresolved. Currently, the main marketed treatment for retinitis pigmentosa is an electronic retinal implant. This treatment approach, however, requires intraocular, surgical implantation and is prosthetic by design. Therefore, it does not prevent the loss of rod and cone cells underlying the symptoms of retinitis pigmentosa.
There is a need for new therapeutic approaches to the treatment of retinitis pigmentosa.
SUMMARY OF THE INVENTION
In general, the invention provides oligonucleotides including a nucleobase sequence including at least 6 contiguous nucleobases complementary to an equal-length portion within a NRL target nucleic acid. The invention also provides compositions containing oligonucleotides of the invention and methods of using the same.
In one aspect, the invention provides a single-stranded oligonucleotide including a total of 12 to 50 interlinked nucleotides and having a nucleobase sequence including at least 6 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
In another aspect, the invention provides a single-stranded oligonucleotide comprising a total of 12 to 50 interlinked nucleotides and having a nucleobase sequence comprising at least 6 contiguous nucleobases complementary to the target sequence of any one of SEQ ID NOs: 6-17. In some embodiments, the oligonucleotide includes at least one modified nucleobase. In some embodiments, at least one modified nucleobase is 5-methylcytosine. In some embodiments, at least one modified nucleobase is 7-deazaguanine. In some embodiments, at least one modified nucleobase is 6- thioguanine.
In some embodiments, the oligonucleotide includes at least one modified internucleoside linkage. In some embodiments, the modified internucleoside linkage is a phosphorothioate linkage. In some embodiments, the phosphorothioate linkage is a stereochemically enriched phosphorothioate linkage. In some embodiments, at least 50% of internucleoside linkages in the oligonucleotide are each independently the modified internucleoside linkage. In some embodiments, at least 70% of internucleoside linkages in the oligonucleotide are each independently the modified internucleoside linkage. In some embodiments, 100% of the internucleoside linkages in the oligonucleotide are the modified internucleoside linkage.
In some embodiments, the oligonucleotide includes at least one modified sugar nucleoside. In some embodiments, at least one modified sugar nucleoside is a bridged nucleic acid. In some embodiments, the bridged nucleic acid is a locked nucleic acid (LNA), ethylene-bridged nucleic acid (ENA), or cEt nucleic acid. In some embodiments, the oligonucleotide is a gapmer. In some embodiments, at least one modified sugar nucleoside is a 2’-modified sugar nucleoside. In some embodiments, at least one 2’-modified sugar nucleoside includes a 2’-modification selected from the group consisting of 2’-fluoro, 2’-methoxy, and 2’-methoxyethoxy. In some embodiments, the oligonucleotide includes deoxyribonucleotides. In some embodiments, the oligonucleotide includes ribonucleotides.
In some embodiments, the oligonucleotide is a morpholino oligomer.
In some embodiments, the oligonucleotide includes a hydrophobic moiety covalently attached at a 5’-terminus, 3’-terminus, or internucleoside linkage of the oligonucleotide.
In some embodiments, the oligonucleotide includes a total of at least 7 interlinked nucleotides. In some embodiments, the single-stranded oligonucleotide includes at least 7 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
In some embodiments, the oligonucleotide includes a total of at least 8 interlinked nucleotides. In some embodiments, the single-stranded oligonucleotide includes at least 8 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
In some embodiments, the oligonucleotide includes a total of at least 9 interlinked nucleotides. In some embodiments, the single-stranded oligonucleotide includes at least 9 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
In some embodiments, the oligonucleotide includes a total of at least 10 interlinked nucleotides.
In some embodiments, the single-stranded oligonucleotide includes at least 10 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof. In some embodiments, the oligonucleotide includes a total of 10 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of at least 11 interlinked nucleotides.
In some embodiments, the single-stranded oligonucleotide includes at least 11 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
In some embodiments, the oligonucleotide includes a total of at least 12 interlinked nucleotides.
In some embodiments, the single-stranded oligonucleotide includes at least 12 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
In some embodiments, the oligonucleotide includes a total of at least 13 interlinked nucleotides.
In some embodiments, the single-stranded oligonucleotide includes at least 13 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
In some embodiments, the oligonucleotide includes a total of at least 14 interlinked nucleotides.
In some embodiments, the single-stranded oligonucleotide includes at least 14 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
In some embodiments, the oligonucleotide includes a total of at least 15 interlinked nucleotides.
In some embodiments, the single-stranded oligonucleotide includes at least 15 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
In some embodiments, the oligonucleotide includes a total of at least 16 interlinked nucleotides.
In some embodiments, the single-stranded oligonucleotide includes at least 16 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof (e.g., SEQ ID NOs: 18-29).
In some embodiments, the oligonucleotide includes a total of 25 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 20 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 19 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 18 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 17 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 16 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 15 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 14 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 13 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 12 interlinked nucleotides or fewer. In some embodiments, the oligonucleotide includes a total of 11 interlinked nucleotides or fewer.
In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 6. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 7. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 8. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 9. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 10. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 11. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 12. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 13. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 14. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 15. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 16. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 17. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 18. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 19. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 20. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 21 . In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 22. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 23. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 24. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 25. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 26. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 27. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 28. In some embodiments, the nucleotide sequence is set forth in SEQ ID NO: 29.
In some embodiments, the sequence of the oligonucleotide comprises or consists of the nucleotide sequence referenced in the claim.
In another aspect, the invention provides an oligonucleotide having a nucleotide sequence that comprises the sequence of any one of SEQ ID NOs: 6-29 or a chemically modified version thereof (e.g., SEQ ID NOs: 18-29).
In some embodiments, the oligonucleotide has a nucleotide sequence that consists of the sequence of any one of SEQ ID NOs: 6-29 or a chemically modified version thereof (e.g., SEQ ID NOs: 18-29).
In some embodiments, the oligonucleotide comprises a feature or modification as set forth above and elsewhere herein.
In some embodiments, the “chemically modified version thereof comprises a 5-methyl-dC nucleotide in place of C.
In some embodiments, a “chemically modified version thereof of any one of SEQ ID NOs: 6-17 is SEQ ID NO: 18-29, respectively.
In another aspect, the invention provides a pharmaceutically acceptable salt of an oligonucleotide as set forth above and elsewhere herein.
In another aspect, the invention provides a double-stranded oligonucleotide including an oligonucleotide of the invention hybridized to a complementary oligonucleotide. In some embodiments, the complementary oligonucleotide has the same length as the oligonucleotide of the invention. In further embodiments, the complementary oligonucleotide has a length that is at least, e.g., ±1 , ±2, ±3, ±4, or ±5 nucleotides relative to the number of nucleotides in the oligonucleotide of the invention.
In another aspect, the invention provides a pharmaceutical composition including the oligonucleotide of the invention and a pharmaceutically acceptable excipient.
In a yet another aspect, the invention provides methods of use of the oligonucleotides of the invention.
In some embodiments, the method is a method of inhibiting or reducing the production of an NRL protein in a cell including (e.g., expressing) an NRL gene by contacting the cell with the oligonucleotide of the invention. In certain embodiments, the cell is in a subject. In particular embodiments, the cell is in the subject’s eye.
In further embodiments, the method is a method of treating a subject in need thereof by administering to the subject a therapeutically effective amount of the oligonucleotide of the invention or the pharmaceutical composition of the invention.
In yet further embodiments, the oligonucleotide or pharmaceutical composition is administered intraocularly or topically to the eye of the subject. In still further embodiments, the subject is in need of a treatment for an ocular disease, disorder, or condition associated with a dysfunction of ABCA4, AIPL1 , BBS1 , BEST1 , CEP290, CDH3, CHM, CNGA3, CNGB3, CRB1 , GUCY2D, MERTK, MRFP, MY07A,
ND4, NR2E3, PDE6, PRPH2, RD3, RHO, RLBP1 , RP1 , RPE65, RPGR, RPGRIP1 , RS1 , or SPATA7 gene. In some embodiments, the subject is in need of a treatment for retinitis pigmentosa, Stargardt disease, cone-rod dystrophy, Leber congenital amaurosis, Bardet Biedl syndrome, macular dystrophy, dry macular degeneration, geographic atrophy, atrophic age-related macular degeneration (AMD), advanced dry AMD, retinal dystrophy, choroideremia, Usher syndrome type 1 , retinoschisis, Leber hereditary optic neuropathy, and achromatopsia. In preferred embodiments, the subject is in need of a treatment for retinitis pigmentosa. In certain embodiments, retinitis pigmentosa is Rho P23H-associated retinitis pigmentosa, PDE6-associated retinitis pigmentosa, MERTK-associated retinitis pigmentosa, BBS1- associated retinitis pigmentosa, Rho-associated retinitis pigmentosa, MRFP-associated retinitis pigmentosa, RLBP1 -associated retinitis pigmentosa, RP1 -associated retinitis pigmentosa, RPGR-X- linked retinitis pigmentosa, NR2E3-associated retinitis pigmentosa, or SPATA7-associated retinitis pigmentosa.
The invention also provides the oligonucleotides described herein, and corresponding salts and/or compositions, for use in treating the diseases and conditions described herein, as well as for inhibiting or reducing production of an NRL protein in a cell as described herein.
Definitions
The term “acyl,” as used herein, represents a chemical substituent of formula -C(0)-R, where R is alkyl, aryl, arylalkyl, cycloalkyl, heterocyclyl, heterocyclyl alkyl, heteroaryl, or heteroaryl alkyl. An optionally substituted acyl is an acyl that is optionally substituted as described herein for each group R.
The term “acyloxy,” as used herein, represents a chemical substituent of formula -OR, where R is acyl. An optionally substituted acyloxy is an acyloxy that is optionally substituted as described herein for acyl.
The term “aliphatic,” as used herein, refers to an acyclic, branched or acyclic, linear hydrocarbon chain, or a monocyclic, bicyclic, tricyclic, or tetracyclic hydrocarbon. Unless specified otherwise, an aliphatic group includes a total of 1 to 60 carbon atoms. An optionally substituted aliphatic is an optionally substituted acyclic aliphatic or an optionally substituted cyclic aliphatic. An optionally substituted acyclic aliphatic is optionally substituted as described herein for alkyl. An optionally substituted cyclic aliphatic is an optionally substituted aromatic aliphatic or an optionally substituted non-aromatic aliphatic. An optionally substituted aromatic aliphatic is optionally substituted as described herein for alkyl. An optionally substituted non-aromatic aliphatic is optionally substituted as described herein for cycloalkyl. In some embodiments, an acyclic aliphatic is alkyl. In certain embodiments, a cyclic aliphatic is aryl. In particular embodiments, a cyclic aliphatic is cycloalkyl. The term “alkanoyl,” as used herein, represents a chemical substituent of formula -C(0)-R, where R is alkyl. An optionally substituted alkanoyl is an alkanoyl that is optionally substituted as described herein for alkyl.
The term “alkoxy,” as used herein, represents a chemical substituent of formula -OR, where R is a Ci-6 alkyl group, unless otherwise specified. An optionally substituted alkoxy is an alkoxy group that is optionally substituted as defined herein for alkyl.
The term “alkyl,” as used herein, refers to an acyclic straight or branched chain saturated hydrocarbon group, which, when unsubstituted, has from 1 to 12 carbons, unless otherwise specified. In certain preferred embodiments, unsubstituted alkyl has from 1 to 6 carbons. Alkyl groups are exemplified by methyl; ethyl; n- and iso-propyl; n-, sec-, iso- and tert-butyl; neopentyl, and the like, and may be optionally substituted, valency permitting, with one, two, three, or, in the case of alkyl groups of two carbons or more, four or more substituents independently selected from the group consisting of: alkoxy; acyloxy; amino; aryl; aryloxy; azido; cycloalkyl; cycloalkoxy; halo; heterocyclyl; heteroaryl; heterocyclylalkyl; heteroarylalkyl; heterocyclyloxy; heteroaryloxy; hydroxy; nitro; thiol; silyl; cyano; =0; =S; and =NR’, where R’ is H, alkyl, aryl, or heterocyclyl. In some embodiments, two substituents combine to form a group -L-CO-R, where L is a bond or optionally substituted Ci-n alkylene, and R is hydroxyl or alkoxy. Each of the substituents may itself be unsubstituted or, valency permitting, substituted with unsubstituted substituent(s) defined herein for each respective group.
The term “alkylene,” as used herein, represents a divalent substituent that is an alkyl having one hydrogen atom replaced with a valency. An optionally substituted alkylene is an alkylene that is optionally substituted as described herein for alkyl.
The term “altmer,” as used herein, refers to an oligonucleotide having a pattern of structural features characterized by internucleoside linkages, in which no two consecutive internucleoside linkages have the same structural feature. In some embodiments, an altmer is designed such that it includes a repeating pattern. In some embodiments, an altmer is designed such that it does not include a repeating pattern. In instances, where the “same structural feature” refers to the stereochemical configuration of the internucleoside linkages, the altmer is a “stereoaltmer.”
The term “aryl,” as used herein, represents a mono-, bicyclic, or multicyclic carbocyclic ring system having one or two aromatic rings. Aryl group may include from 6 to 10 carbon atoms. All atoms within an unsubstituted carbocyclic aryl group are carbon atoms. Non-limiting examples of carbocyclic aryl groups include phenyl, naphthyl, 1 ,2-dihydronaphthyl, 1 ,2,3,4-tetrahydronaphthyl, fluorenyl, indanyl, indenyl, etc. The aryl group may be unsubstituted or substituted with one, two, three, four, or five substituents independently selected from the group consisting of: alkyl; alkoxy; acyloxy; amino; aryl; aryloxy; azido; cycloalkyl; cycloalkoxy; halo; heterocyclyl; heteroaryl; heterocyclylalkyl; heteroarylalkyl; heterocyclyloxy; heteroaryloxy; hydroxy; nitro; thiol; silyl; and cyano. Each of the substituents may itself be unsubstituted or substituted with unsubstituted substituent(s) defined herein for each respective group.
The term “aryl alkyl,” as used herein, represents an alkyl group substituted with an aryl group.
The aryl and alkyl portions may be optionally substituted as the individual groups as described herein.
The term “arylene,” as used herein, represents a divalent substituent that is an aryl having one hydrogen atom replaced with a valency. An optionally substituted arylene is an arylene that is optionally substituted as described herein for aryl. The term “aryloxy,” as used herein, represents a group -OR, where R is aryl. Aryloxy may be an optionally substituted aryloxy. An optionally substituted aryloxy is aryloxy that is optionally substituted as described herein for aryl.
The term “bicyclic sugar moiety,” as used herein, represents a modified sugar moiety including two fused rings. In certain embodiments, the bicyclic sugar moiety includes a furanosyl ring.
The term “blockmer,” as used herein, refers to an oligonucleotide strand having a pattern of structural features characterized by the presence of at least two consecutive internucleoside linkages with the same structural feature. By same structural feature is meant the same stereochemistry at the internucleoside linkage phosphorus or the same modification at the linkage phosphorus. The two or more consecutive internucleoside linkages with the same structure feature are referred to as a “block.” In instances, where the “same structural feature” refers to the stereochemical configuration of the internucleoside linkages, the blockmer is a “stereoblockmer.”
The expression “Cx-y,” as used herein, indicates that the group, the name of which immediately follows the expression, when unsubstituted, contains a total of from x to y carbon atoms. If the group is a composite group (e.g., aryl alkyl), Cx-y indicates that the portion, the name of which immediately follows the expression, when unsubstituted, contains a total of from x to y carbon atoms. For example, (Ce-io- aryl)-Ci-6-alkyl is a group, in which the aryl portion, when unsubstituted, contains a total of from 6 to 10 carbon atoms, and the alkyl portion, when unsubstituted, contains a total of from 1 to 6 carbon atoms.
The term "complementary," as used herein in reference to a nucleobase sequence, refers to the nucleobase sequence having a pattern of contiguous nucleobases that permits an oligonucleotide having the nucleobase sequence to hybridize to another oligonucleotide or nucleic acid to form a duplex structure under physiological conditions. Complementary sequences include Watson-Crick base pairs formed from natural and/or modified nucleobases. Complementary sequences can also include non- Watson-Crick base pairs, such as wobble base pairs (guanosine-uracil, hypoxanthine-uracil, hypoxanthine-adenine, and hypoxanthine-cytosine) and Hoogsteen base pairs.
The term “contiguous,” as used herein in the context of an oligonucleotide, refers to nucleosides, nucleobases, sugar moieties, or internucleoside linkages that are immediately adjacent to each other.
For example, “contiguous nucleobases” means nucleobases that are immediately adjacent to each other in a sequence.
The term “cycloalkyl,” as used herein, refers to a cyclic alkyl group having from three to ten carbons (e.g., a C3-C10 cycloalkyl), unless otherwise specified. Cycloalkyl groups may be monocyclic or bicyclic. Bicyclic cycloalkyl groups may be of bicyclo[p.q.0]alkyl type, in which each of p and q is, independently, 1 , 2, 3, 4, 5, 6, or 7, provided that the sum of p and q is 2, 3, 4, 5, 6, 7, or 8. Alternatively, bicyclic cycloalkyl groups may include bridged cycloalkyl structures, e.g., bicyclo[p.q.r]alkyl, in which r is 1 , 2, or 3, each of p and q is, independently, 1 , 2, 3, 4, 5, or 6, provided that the sum of p, q, and r is 3, 4, 5, 6, 7, or 8. The cycloalkyl group may be a spirocyclic group, e.g., spiro[p.q]alkyl, in which each of p and q is, independently, 2, 3, 4, 5, 6, or 7, provided that the sum of p and q is 4, 5, 6, 7, 8, or 9. Non-limiting examples of cycloalkyl include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, 1- bicyclo[2.2.1 .jheptyl, 2-bicyclo[2.2.1 .jheptyl, 5-bicyclo[2.2.1 .jheptyl, 7-bicyclo[2.2.1 .jheptyl, and decalinyl. The cycloalkyl group may be unsubstituted or substituted (e.g., optionally substituted cycloalkyl) with one, two, three, four, or five substituents independently selected from the group consisting of: alkyl; alkoxy; acyloxy; amino; aryl; aryloxy; azido; cycloalkyl; cycloalkoxy; halo; heterocyclyl; heteroaryl; heterocyclylalkyl; heteroarylalkyl; heterocyclyloxy; heteroaryloxy; hydroxy; nitro; thiol; silyl; cyano; =0; =S; =NR’, where R’ is H, alkyl, aryl, or heterocyclyl. Each of the substituents may itself be unsubstituted or substituted with unsubstituted substituent(s) defined herein for each respective group.
The term “cycloalkylene,” as used herein, represents a divalent substituent that is a cycloalkyl having one hydrogen atom replaced with a valency. An optionally substituted cycloalkylene is a cycloalkylene that is optionally substituted as described herein for cycloalkyl.
The term “cycloalkoxy,” as used herein, represents a group -OR, where R is cycloalkyl. Cycloalkoxy may be an optionally substituted cycloalkoxy. An optionally substituted cycloalkoxy is cycloalkoxy that is optionally substituted as described herein for cycloalkyl.
The term “duplex,” as used herein, represents two oligonucleotides that are paired through hybridization of complementary nucleobases.
The term “gapmer,” as used herein, refers to an oligonucleotide having an RNase H recruiting region (gap) flanked by a 5' wing and 3' wing, each of the wings including at least one affinity enhancing nucleoside (e.g., 1 , 2, 3, or 4 affinity enhancing nucleosides).
The term “halo,” as used herein, represents a halogen selected from bromine, chlorine, iodine, and fluorine.
The term “headmer,” as used herein, refers to an oligonucleotide having an RNase H recruiting region (gap) flanked by a 5’ wing including at least one affinity enhancing nucleoside (e.g., 1 , 2, 3, or 4 affinity enhancing nucleosides).
The term “heteroalkyl,” as used herein refers to an alkyl group interrupted one or more times by one or two heteroatoms each time. Each heteroatom is, independently, O, N, or S. None of the heteroalkyl groups includes two contiguous oxygen atoms. The heteroalkyl group may be unsubstituted or substituted (e.g., optionally substituted heteroalkyl). When heteroalkyl is substituted and the substituent is bonded to the heteroatom, the substituent is selected according to the nature and valency of the heteratom. Thus, the substituent bonded to the heteroatom, valency permitting, is selected from the group consisting of =0, -N(RN2)2, -SC>20RN3, -SC>2RN2, -SORN3, -COORN3, an N protecting group, alkyl, aryl, cycloalkyl, heterocyclyl, or cyano, where each RN2 is independently H, alkyl, cycloalkyl, aryl, or heterocyclyl, and each RN3 is independently alkyl, cycloalkyl, aryl, or heterocyclyl. Each of these substituents may itself be unsubstituted or substituted with unsubstituted substituent(s) defined herein for each respective group. When heteroalkyl is substituted and the substituent is bonded to carbon, the substituent is selected from those described for alkyl, provided that the substituent on the carbon atom bonded to the heteroatom is not Cl, Br, or I. It is understood that carbon atoms are found at the termini of a heteroalkyl group. In some embodiments, heteroalkyl is PEG
The term “heteroalkylene,” as used herein, represents a divalent substituent that is a heteroalkyl having one hydrogen atom replaced with a valency. An optionally substituted heteroalkylene is a heteroalkylene that is optionally substituted as described herein for heteroalkyl.
The term “heteroaryl,” as used herein, represents a monocyclic 5-, 6-, 7-, or 8-membered ring system, or a fused or bridging bicyclic, tricyclic, or tetracyclic ring system; the ring system contains one, two, three, or four heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur; and at least one of the rings is an aromatic ring. Non-limiting examples of heteroaryl groups include benzimidazolyl, benzofuryl, benzothiazolyl, benzothienyl, benzoxazolyl, furyl, imidazolyl, indolyl, isoindazolyl, isoquinolinyl, isothiazolyl, isothiazolyl, isoxazolyl, oxadiazolyl, oxazolyl, purinyl, pyrrolyl, pyridinyl, pyrazinyl, pyrimidinyl, qunazolinyl, quinolinyl, thiadiazolyl (e.g., 1 ,3,4-thiadiazole), thiazolyl, thienyl, triazolyl, tetrazolyl, dihydroindolyl, tetrahydroquinolyl, tetrahydroisoquinolyl, etc. The term bicyclic, tricyclic, and tetracyclic heteroaryls include at least one ring having at least one heteroatom as described above and at least one aromatic ring. For example, a ring having at least one heteroatom may be fused to one, two, or three carbocyclic rings, e.g., an aryl ring, a cyclohexane ring, a cyclohexene ring, a cyclopentane ring, a cyclopentene ring, or another monocyclic heterocyclic ring. Examples of fused heteroaryls include 1 ,2,3,5,8,8a-hexahydroindolizine; 2,3-dihydrobenzofuran; 2,3-dihydroindole; and 2,3- dihydrobenzothiophene. Heteroaryl may be optionally substituted with one, two, three, four, or five substituents independently selected from the group consisting of: alkyl; alkoxy; acyloxy; aryloxy; amino; arylalkoxy; cycloalkyl; cycloalkoxy; halogen; heterocyclyl; heterocyclyl alkyl; heteroaryl; heteroaryl alkyl; heterocyclyloxy; heteroaryloxy; hydroxyl; nitro; thiol; cyano; =0; -NR2, where each R is independently hydrogen, alkyl, acyl, aryl, arylalkyl, cycloalkyl, heterocyclyl, or heteroaryl; -COORA, where RA is hydrogen, alkyl, aryl, arylalkyl, cycloalkyl, heterocyclyl, or heteroaryl; and -CON(RB)2, where each RB is independently hydrogen, alkyl, aryl, arylalkyl, cycloalkyl, heterocyclyl, or heteroaryl. Each of the substituents may itself be unsubstituted or substituted with unsubstituted substituent(s) defined herein for each respective group.
The term “heteroaryloxy,” as used herein, refers to a structure -OR, in which R is heteroaryl. Heteroaryloxy can be optionally substituted as defined for heteroaryl.
The term “heterocyclyl,” as used herein, represents a monocyclic, bicyclic, tricyclic, or tetracyclic ring system having fused or bridging 4-, 5-, 6-, 7-, or 8-membered rings, unless otherwise specified, the ring system containing one, two, three, or four heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur. Heterocyclyl may be aromatic or non-aromatic. An aromatic heterocyclyl is heteroaryl as described herein. Non-aromatic 5-membered heterocyclyl has zero or one double bonds, non-aromatic 6- and 7-membered heterocyclyl groups have zero to two double bonds, and non-aromatic 8-membered heterocyclyl groups have zero to two double bonds and/or zero or one carbon- carbon triple bond. Heterocyclyl groups have a carbon count of 1 to 16 carbon atoms unless otherwise specified. Certain heterocyclyl groups may have a carbon count up to 9 carbon atoms. Non-aromatic heterocyclyl groups include pyrrolinyl, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, homopiperidinyl, piperazinyl, pyridazinyl, oxazolidinyl, isoxazolidiniyl, morpholinyl, thiomorpholinyl, thiazolidinyl, isothiazolidinyl, thiazolidinyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, dihydrothienyl, pyranyl, dihydropyranyl, dithiazolyl, etc. The term “heterocyclyl” also represents a heterocyclic compound having a bridged multicyclic structure in which one or more carbons and/or heteroatoms bridges two non-adjacent members of a monocyclic ring, e.g., quinuclidine, tropanes, or diaza-bicyclo[2.2.2]octane. The term “heterocyclyl” includes bicyclic, tricyclic, and tetracyclic groups in which any of the above heterocyclic rings is fused to one, two, or three carbocyclic rings, e.g., a cyclohexane ring, a cyclohexene ring, a cyclopentane ring, a cyclopentene ring, or another heterocyclic ring. Examples of fused heterocyclyls include 1 ,2,3,5,8,8a-hexahydroindolizine; 2,3-dihydrobenzofuran; 2,3-dihydroindole; and 2,3-dihydrobenzothiophene. The heterocyclyl group may be unsubstituted or substituted with one, two, three, four or five substituents independently selected from the group consisting of: alkyl; alkoxy; acyloxy; aryloxy; amino; arylalkoxy; cycloalkyl; cycloalkoxy; halogen; heterocyclyl; heterocyclyl alkyl; heteroaryl; heteroaryl alkyl; heterocyclyloxy; heteroaryloxy; hydroxyl; nitro; thiol; cyano; =0; =S; -NR2, where each R is independently hydrogen, alkyl, acyl, aryl, arylalkyl, cycloalkyl, heterocyclyl, or heteroaryl; -COORA, where RA is hydrogen, alkyl, aryl, arylalkyl, cycloalkyl, heterocyclyl, or heteroaryl; and -CON(RB)2, where each RB is independently hydrogen, alkyl, aryl, arylalkyl, cycloalkyl, heterocyclyl, or heteroaryl.
The term “heterocyclyl alkyl,” as used herein, represents an alkyl group substituted with a heterocyclyl group. The heterocyclyl and alkyl portions of an optionally substituted heterocyclyl alkyl are optionally substituted as described for heterocyclyl and alkyl, respectively.
The term “heterocyclylene,” as used herein, represents a divalent substituent that is a heterocyclyl having one hydrogen atom replaced with a valency. An optionally substituted heterocyclylene is a heterocyclylene that is optionally substituted as described herein for heterocyclyl.
The term “heterocyclyloxy,” as used herein, refers to a structure -OR, in which R is heterocyclyl. Heterocyclyloxy can be optionally substituted as described for heterocyclyl.
The terms “hydroxyl” and “hydroxy,” as used interchangeably herein, represent -OH.
The term “hydrophobic moiety,” as used herein, represents a monovalent group covalently linked to an oligonucleotide backbone, where the monovalent group is a bile acid (e.g., cholic acid, taurocholic acid, deoxycholic acid, oleyl lithocholic acid, or oleoyl cholenic acid), glycolipid, phospholipid, sphingolipid, isoprenoid, vitamin, saturated fatty acid, unsaturated fatty acid, fatty acid ester, triglyceride, pyrene, porphyrine, texaphyrine, adamantine, acridine, biotin, coumarin, fluorescein, rhodamine, Texas- Red, digoxygenin, dimethoxytrityl, f-butydimethylsilyl, f-butyldiphenylsilyl, cyanine dye (e.g., Cy3 or Cy5), Hoechst 33258 dye, psoralen, or ibuprofen. Non-limiting examples of the monovalent group include ergosterol, stigmasterol, b-sitosterol, campesterol, fucosterol, saringosterol, avenasterol, coprostanol, cholesterol, vitamin A, vitamin D, vitamin E, cardiolipin, and carotenoids. The linker connecting the monovalent group to the oligonucleotide may be an optionally substituted Ci-eo aliphatic (e.g., optionally substituted Ci-eo alkylene) or an optionally substituted C2-60 heteroaliphatic (e.g., optionally substituted C2-60 heteroalkylene), where the linker may be optionally interrupted with one, two, or three instances independently selected from the group consisting of an optionally substituted arylene, optionally substituted heterocyclylene, and optionally substituted cycloalkylene. The linker may be bonded to an oligonucleotide through, e.g., an oxygen atom attached to a 5’-terminal carbon atom, a 3’-terminal carbon atom, a 5’-terminal phosphate or phosphorothioate, a 3’-terminal phosphate or phosphorothioate, or an internucleoside linkage.
The term “internucleoside linkage,” as used herein, represents a group or bond that forms a covalent linkage between adjacent nucleosides in an oligonucleotide. An internucleoside linkage is an unmodified internucleoside linkage or a modified internucleoside linkage. An “unmodified internucleoside linkage” is a phosphate (-0-P(0)(0H)-0-) internucleoside linkage (“phosphate phosphodiester”). A “modified internucleoside linkage” is an internucleoside linkage other than a phosphate phosphodiester. The two main classes of modified internucleoside linkages are defined by the presence or absence of a phosphorus atom. Non-limiting examples of phosphorus-containing internucleoside linkages include phosphodiester linkages, phosphotriester linkages, phosphorothioate diester linkages, phosphorothioate triester linkages, morpholino internucleoside linkages, methylphosphonates, and phosphoramidate. Nonlimiting examples of non-phosphorus internucleoside linkages include methylenemethylimino ( — CH2 — N(CH3)— O— CM2— ), thiodiester (— O— C(O)— S— ), thionocarbamate (— O— C(0)(NH)— S— ), siloxane ( — O — Si(H)2 — O — ), and N,N'-dimethylhydrazine ( — CH2 — N(CH3) — N(CH3) — ). Phosphorothioate linkages are phosphodiester linkages and phosphotriester linkages in which one of the non-bridging oxygen atoms is replaced with a sulfur atom. In some embodiments, an internucleoside linkage is a group of the following structure:
Figure imgf000012_0001
where
Z is O, S, or Se;
Y is -X-L-R1; each X is independently -O-, -S-, -N(-L-R1)-, or L; each L is independently a covalent bond or a linker (e.g., optionally substituted Ci-eo aliphatic linker or optionally substituted C2-60 heteroaliphatic linker); each R1 is independently hydrogen, -S-S-R2, -O-CO-R2, -S-CO-R2, optionally substituted C1-9 heterocyclyl, or a hydrophobic moiety; and each R2 is independently optionally substituted C1-10 alkyl, optionally substituted C2-10 heteroalkyl, optionally substituted Ce-io aryl, optionally substituted Ce-io aryl Ci-e alkyl, optionally substituted C1-9 heterocyclyl, or optionally substituted C1-9 heterocyclyl Ci-e alkyl.
When L is a covalent bond, R1 is hydrogen, Z is oxygen, and all X groups are -O-, the internucleoside group is known as a phosphate phosphodiester. When L is a covalent bond, R1 is hydrogen, Z is sulfur, and all X groups are -O-, the internucleoside group is known as a phosphorothioate diester. When Z is oxygen, all X groups are -O-, and either (1) L is a linker or (2) R1 is not a hydrogen, the internucleoside group is known as a phosphotriester. When Z is sulfur, all X groups are -O-, and either (1) L is a linker or (2) R1 is not a hydrogen, the internucleoside group is known as a phosphorothioate triester. Nonlimiting examples of phosphorothioate triester linkages and phosphotriester linkages are described in US 2017/0037399, the disclosure of which is incorporated herein by reference.
The term “morpholino,” as used herein in reference to a class of oligonucleotides, represents an oligomer of at least 10 morpholino monomer units interconnected by morpholino internucleoside linkages. A morpholino includes a 5’ group and a 3’ group. For example, a morpholino may be of the following structure:
Figure imgf000012_0002
where n is an integer of at least 10 (e.g., 12 to 30) indicating the number of morpholino units; each B is independently a nucleobase;
R1 is a 5’ group;
R2 is a 3’ group; and
L is (i) a morpholino internucleoside linkage or, (ii) if L is attached to R2, a covalent bond.
A 5’ group in morpholino may be, e.g., hydroxyl, a hydrophobic moiety, phosphate, diphosphate, triphosphate, phosphorothioate, diphosphorothioate, triphosphorothioate, phosphorodithioate, disphorodithioate, triphosphorodithioate, phosphonate, phosphoramidate, a cell penetrating peptide, an endosomal escape moiety, or a neutral organic polymer. A 3’ group in morpholino may be, e.g., hydrogen, a hydrophobic moiety, phosphate, diphosphate, triphosphate, phosphorothioate, diphosphorothioate, triphosphorothioate, phosphorodithioate, disphorodithioate, triphosphorodithioate, phosphonate, phosphoramidate, a cell penetrating peptide, an endosomal escape moiety, or a neutral organic polymer.
The term “morpholino internucleoside linkage,” as used herein, represents a divalent group of the following structure:
Z
-I_c1_ _c2_
5 J, where
Z is O or S;
X1 is a bond, -CH2-, or -O-;
X2 is a bond, -CH2-O-, or -O-; and
Y is -NR2, where each R is independently C1-6 alkyl (e.g., methyl), or both R combine together with the nitrogen atom to which they are attached to form a C2-9 heterocyclyl (e.g., N-piperazinyl); provided that both X1 and X2 are not simultaneously a bond.
The term “NRL,” as used herein, represents refers to a ribonucleic acid (e.g., pre-mRNA or mRNA) that encodes the protein Neural Retina Leucine Zipper in humans. An exemplary genomic DNA sequence of a human NRL gene is given by SEQ ID NO. 1 (NCBI Reference Sequence: NG_011697.2). One of skill in the art will recognize that a pre-mRNA is produced from the genomic DNA in accordance with the central dogma; pre-mRNA is then spliced to produce transcripts, e.g., NRL transcript 1 , NRL transcript 2, NRL transcript 3, or NRL transcript 4. Exemplary mRNA sequences of a human NRL gene are given by SEQ ID NOs. 2, 3, 4, and 5 (NCBI Reference Sequences: NM_006177.4, NM_001354768.1 , NM_001354769.1 , and NM_001354770.1). SEQ ID NO. 2 corresponds to NRL transcript 1 . SEQ ID NO. 3 corresponds to NRL transcript 2. SEQ ID NO. 4 corresponds to NRL transcript 3. SEQ ID NO. 5 corresponds to NRL transcript 4. SEQ ID NOs. 2, 3, 4, and 5 are based on NCBI Reference Sequences for NRL transcripts 1 , 2, 3, and 4, which are provided as RNA sequences with thymidines in the NCBI Reference Sequences. One of skill in the art will recognize that an RNA sequence typically includes uridines instead of thymidines. Accordingly, target RNA sequences may include one or more uridines instead of thymidines without affecting the sequence of an oligonucleotide of the invention.
SEQ ID NO: 1 has the following nucleobase sequence (5’-3’)
1 tcttacaaac cttggttaat aaggagcttg tcaaattccc acaccagtcc gctttcatgc 61 cctcctgggc aactagaacc ttagcggcct ggctgtacag tcctgacttc tggcccacct
121 tgctgtcaat gaaggtgatg ccatcctggt gtccagccag tgcacccaca ggcttggggt
181 catcctcccg catggtgcgt cgatcccaca ctttgcagat ggcatcatct cccccagaga
241 acaggatttg ggagcttata tcagcaaagg ccactgcatt cacatcatcc tcatgggact
301 caatctaggc gaaaaggagg ccaggatata agacctcttt ctaggtctta taaaaagcca
361 aaaaccagga ggcagaggct ctatctcagg agccatacct gaagggtgcg ccggttctgt
421 tctcggtcaa agacatacag gcagccatca ttggccctga aagggaaggg ataaaggagg
481 gtcctggagc catgatcgag aggaccaacg tggtatatgc tctagagagt tccactgaga
541 aatcctgctc tgggtcaagc cctttgctct ttttatacag gaagtggggg aagagttagc 601 tgtgtttcaa ggaggcttga cacctccaat ctcgtgctgg ggaaatggag agcaaggggt
661 gaagcaactt gtaaatcctg accttgggag aaggtctggt tgttctctgc agctgccagt
721 gccatctgtg taacagcaga actcatctct ggcagaaccc ccatcttgtt attgagggaa
781 acatacccca caagcactta ccctcctagt acttctcgtc catctgagga gacagcaatg
841 gagaagacag caaagcgacg ctcatctggc ctaaaagcaa gaaggagctg ggttaagtgg
901 acttccttca gcttttgtta atctacataa aatctgacaa cggttgtaag gcacatcccc
961 aggggaaaaa agaagtctgg ctaacatgca ccataatgca gatgctcagt gagaacccag
1021 aaatcatcct gcaaccatct attttaccca gtcctctggc tgacaagatg gtgcttccct
1081 cccaggaatg cacacagacc caccagtata ctttttcccc taaacagaac ttccaactca
1141 agaggtttgc tcccaaagag cttcccttga gaagtttctg atgagtctga ccagaaaggg
1201 aagccagtac ctgagatcca gggcagtgtg tgtatctccc tcaccataga tattgcagat
1261 atgaactaag agaagcaaga aaaacaagaa tctttcaggg atgggggaag aagagtggaa
1321 gtgaagctag ggaagagatc aaacagggga caagggtact ggagcacttt gggagtgatt
1381 ttcccaggac aaagtgaggg atcctggctc agaggggaca ggcacatgga aacctcaggt
1441 cccaggctgg agagtcagtg gaagcctggt gcatactcac tgtaatcaga ccagctagag
1501 tagaggaagt ggttcccatc aggggtgaag gccacatcca agacgctcca gcctacgtcg
1561 cgggccttga tgctcttgaa tttacggaaa cggccatatc ggcagtcata gagtcggatt
1621 gtctggtctg tgtaagtaaa gatcaggcag aattatggga cagtttcctt gtaacttttc
1681 tagattagac atctcccact cagtgtacct gtggagtctt ccctttatca tgggaaacat
1741 ggtctggcta agcatcctta agccaggtct gagctccccg tctgtggctt tctagcctca
1801 gtcaggggga atgtcccatg ttccaggaaa agatagttta taggaccagg gtctggtacc
1861 ttggcaagca gacatgaata tttgaccatc tttgctgtag atgccacaga aagccttctg
1921 agagtagcta tcagtgaagc ccagatcatt gggcaagaag ctagggaagg agagagaaag
1981 tgagggtgag gggtgctcag gataaggagt gtcccaatca gcagaatcct aacagagctg
2041 gaatatcaga acagtcattc ttcccttttg gctgtgagtg caatcccgtc tttcaaccat
2101 tccaccatcc tctaaatttc tacaattttc tacacttttc tactttgttt actctcaaag
2161 tttcaacccc atttaaccta acctttaata tctctgaggc tcctttaaca cctacccctt
2221 caaagtttag gagataagac ctatctggcc cttagagtct cttcaccaag ccccatactc
2281 actgagatat cactcgagac tgttctccaa gggagaagct tccccgatgg cagaggcccc
2341 gttctctcta aatggaaggg attggggaat attgctagca gaaatagagg gccacttcag
2401 ccatatcaag ccccctcctc caaagatatt gctcttgtta tagaaatgga cacacacatc
2461 atagtctgtc ccacagaact ccgatggagg ctggttaact ctccagcccc agcgcttgag
2521 gcttctactt tggaaagttg acttcctttt tctctggggc tggcagagct tctggctgct
2581 ttggcaggcc tgctgccagg ctgggaggtg gagaggccta cctggtgcaa cattcgagga
2641 aagctgtgct tctgggcggc ccgcctaagc cccagctgcc ctgtggccag ttccacttgt
2701 gtcttgatct cattgaattc cagctcccgg gtgtcagggg tagcatccac tgtgagtacc
2761 aaggagaagt ttcatcctag gtctgccagc ctcagaggac agttagcaga actgtaccca
2821 agcccacccc tgtggctgaa tatactgggg ctgtaaggac tccttattcc ttaaattatc
2881 gtaccttctt tcaatgtaac ctatcattca aaatatcact aaaaggtttt ctagtaaaag
2941 tcttccaaca ttaggggctt ttcctcttac caggtgggtt gtatcgatcc ccaagacgac
3001 catcccaagc tctgtcattc tcttcctctg agtccaagag ggcctgaatg aattgtaaat
3061 ttgctgcacc tcctccctgc accaacctca cttggcctct gtggagagac ccccattata
3121 aaggagggga cttcttcccc caaaccaacc aaattcagag tcaatggcta tctagctctt 3181 agaccacttg gtactcattt tgaggtttga ggctgactag accttggctg ttatttttgg
3241 tctcctataa aacacagtag gaaagagagt tttactctta cagcaagagc aagaccaaca
3301 tgctgtggac gtgacctact aagttgacct cccagcgagc taaacattct aacatcattt
3361 ccttagaaca agagcaagac caatacgctg tggacatgac ctactaagtt gacctcccaa
3421 caagctaaac atcctcacag catttccttc tgagcctctg cctgagaagt ccaccacaga
3481 agacaatatt ctaagctggg tgcggtggtg tgtgcaactg tagtcttagc tacctgggag
3541 gcaaggattg cttgagccca ggagttgcag gctgtggtgt gcacttgatc acacctgtga
3601 atagcccgtt ctccagactg gggaacacag tgagccctgt ctatgtctac taaaaacaac
3661 acaaaacaca aacaaaaaag aatacaatat tctgaaggga cccccaaacc catcttctcc
3721 tcaaagagcc ataagcaaag aaagaaagcc agctgcaccc ttttccagtc aattccaggt
3781 ggtctctccc ttcaaggcat tctttcctca agaacaggtt agagtcaggg caaattaaac
3841 ttgtttttca agtaaatcga agtggcctca tatcatgtgt caactgcctt actaaaaagt
3901 tcaacactcc cttcccatct cttcacccct tacatcactc ctttcccact aggacccccc
3961 cctttttttt ttcaagctta cttggaaaat agactatatt tgtgtagtca cagagacagg
4021 ctcccttgaa tagcccctca aacacatgag caggtcctct tggtgaccct ccctaggtaa
4081 gaaccactct tactgggtat ggagctgagt gccatgggtg cccagcaggg aaaggctgtt
4141 cagctcaaac agaacagctg tcctgagcga atcccatttc ctaacctctg taattttcct
4201 gcctggagtt gggatcaagg cactgtggta gcacctgctg ggggtcacac cagagggtaa
4261 gttacctgcg gaggagatag gccagtacct gggccagatc cacatcttca tcctcttctt
4321 cctcttcctc actccgacgc aggccagccc ctcttcgggg caagccctcg gaggggtctc
4381 cggacccgga tcctgcactg ctgctgttcc gcgatcccat cttctggtca cagcattctt
4441 aggtcctgtg cgggggctcc tcctgtcacc tccttgggtt tggtgaaagc aaagcgtgct
4501 ctagaaatac cagggtctcc tgagacgggg tagtagctat ctctaggagg gtgacccttc
4561 ctcggggctg agatcccttt tctttagcct atgccaacta ccaaggcgtc gggaacacaa
4621 accttctcca atcctgtgaa gcaaagaaag caagagtgaa ccgtagtgcg ctaccctagc
4681 tcaccaactg aagaaagatt tgttttctac accaaactca cctatcgaag tccccggact
4741 ggggagcggg aggggtgttg ggcggtgttg gatttccagg taacctctct gaccgaccaa
4801 tcgaaatccc tctcggaaga aagcgcttca ctagcttatc tcatctaacc aattagaagc
4861 cttaggactc aaagaccctc gacgccccca ccttatcgac caatcagagc gcccccttac
4921 aaaggccggc agcagtgaca gccaatgaaa atagaatttg gcctaacacc cctccttcct
4981 cgcctcacgc ccacgtggtg cgccgggggt gtgtacgcca tgagggggag gaagccgaga
5041 agcacctccc actgaagccg gcggtaaccg ccccacgcga gaccacccac cagccaggag
5101 cggtcgcagg acccgcagcg gcgcgaggcc ttgtttacac cgactgccgc cactgcgttg
5161 gccaaccgct cctccgtcac gcgcttcgct cgtcacgcat ctcgcggctt cctggccggc
5221 gggctgcaaa cgtcacacga cggccccgcc cccttggcca gccaactgga cagcggagca
5281 cgatgattga taggtaggcg ggagaatgcg cgaggtgcct gaggggagga gaaagtgcac
5341 acccaaggag ggctgttagc tcttgctggg gaggagtaag tgggaactgc cagcttcctg
5401 aatcagagac agccgaacta ggcgtaacgg ctgagaggcg gggcttaaaa aagaaacgtt
5461 tggtggttcg ctaccgagag gtattttagc aagggatata atttactgtc tgtccctaaa
5521 gatcatttgg catcgcactt ttcagacagt gcccaagggc ctcctttctc cccactgctt
5581 cccctgtcca gctggagccg ttcttctgtc gctggccgca gctccagtcg gttctgccct
5641 aaggggtgcc cagcgtccca gtagacctcc ataccgtcct tccgggctta gcttttggaa
5701 gccttgctct tgggacggtc cccttttaga cctcccttta tccggtctga caatttttta 5761 agacaatccc tggctttccg ccgcggtctt tgcagacgtt ccctaataca cgcgtctttc
5821 tgtcaaagct tttccggttc cgctgtcccc tttgacgctc ccttggccct ccgggatttg
5881 cagaccttcg ctagtccctc tgtcctcgcg gtgcctctcc gcccccggcc gcgggtccag
5941 ggtgcgcgct cgccgcctcc tgccccctcc tgccccctcc tgcgggttta tgagtaacaa
6001 gcctgagtcc aaggccggga gttgccacat ctctgatcct cgccctggct gggtggggac
6061 gtgtgggttg aatgaccttg ctgtctcggg ctcagaggct cagggtccga gctgaacttc
6121 attccctgca gcctgcactt ccttgggaaa gctgcgagct tccctccgcc cgctcctgag
6181 ggcagggatg ggagcgaggg ctcgtggcct tcttgggccc tcctggggcc tctcccagtg
6241 agggcgaggg tttggccagc tttcgggcga cgtctcctag tctctagatc cggagacctg
6301 agcttgtcac cagggctagc tttgatggcc tctgcgctta gaagggtcct gaatgtttgg
6361 tttaatgttc tagtgttaac ggtcttgaaa ttattagtaa ttttaaagca agtgcctggt
6421 attttcatct tgcactcggc tccactgatt atgtaggcgg tctgctgggc gcccatcctc
6481 tattgccaga ttacttacta tctgtgcttt aacgtttatt gagactttag gattccgtgg
6541 tttctgggtt atccagcctg gaaaatcggg atctttattt attgattgat tttacctgcg
6601 ttctcccaga atgtgacgga atcatttttt ttttttatta tactctaagt tttagggtac
6661 atgtgcacat tgtgcaggtt agttacatat gtatacatgt gccatgctgg tgcgctgcac
6721 cactaacgtg tcatctagca ttaggtatat ctcccaatgc tatccctccc ccctcccccg
6781 accccaccac agtccccaga gtgtgatatt ccccttcctg tgtccatgtg atctcattgt
6841 tcaattccca cctatgagtg agaatatgcg gtgtttggtt ttttgttctt gcgatagttt
6901 actgagaatg atggtttcca atttcatcca tgtccctaca aaggacatga actcatcatt
6961 ttttatggct gcatagtatt ccatggtgta tatgtgccac attttcttaa tccagtctat
7021 cattgttgga catttgggtt ggttccaagt ctttgctatt gtgaatagtg ccgcaataaa
7081 catacgtgtg catgtgtctt tatagcagca tgatttatag tcctttgggt atatacccag
7141 taatgggatg gctgggtcaa atggtatttc tagttctaga tccctgagga atcgccacac
7201 tgacttccac aatggttgaa ctagtttaca gtcccaccaa cagtgtaaaa gtgttcctat
7261 ttctccacat cctctccagc acctgttgtt tcctgacttt ttaatgattg ccattctaac
7321 tggtgtgaga tgatatctca tagtggtttt gatttgcatt tctctgatgg ccagtgatga
7381 tgagcatttc ttcatgtgtt ttttggctgc ataaatgtct gcttttgaga agtgtctgtt
7441 catgtccttc gcccactttt tgatggggtt gtttgttttt ttcttgtaaa tttgtttgag
7501 ttcattgtag attctggata ttagcccttt gtcagatgag taggttgcga aaattttctc
7561 ccatgttgta ggttgcctgt tcactctgat ggtagtttct tttgctgtgc agaagctctt
7621 tagtttaatt agatcccatt tgtcatcctc cctaactcat tttatgaggc cagcatcatt
7681 ctgataccaa agccgggcag agacacaacc aaaaaagaga attttagacc aatatccttg
7741 atgaacattg atgcaaaaat cctcaataaa atactggcaa accgaatcca gcagcacatc
7801 aaaaagctta tcgaccatga tcaagtgggc ttcatccctg ggatgcaagg ctggttcaat
7861 atacgcaaat caataaatgt aatccagcat ataaacagag ccaaagacaa aaaccacatg
7921 attatctcaa tagatgcaga aaaagccttt gacaaaattc aacaaccctt catgctaaaa
7981 actctcaata aattaggtat tgatgggacg tatttcaaaa taataagagc tatctatgac
8041 aaacccacag ccaatatcat actgaatggg caaaaactgg aagcattccc tttgaaaact
8101 ggcacaagac agggatgccc tctctcaccg ctcctattca acatagtgtt ggaagttctg
8161 gccagggcaa tcaggcagga gaaggaaata aagggtattc aattaggaaa agaggaagtc
8221 aaattgtccc tgtttgcaga cgacatgatt gtttatctag aaaaccccat cgtctcagcc
8281 caaaatctcc ttaagctgat aagcaacttc agcaaagtct caggacggaa tcatttttta 8341 aaaaaattgg ccgggcgcgg tggctcacgc ctgtaatccc agcactttgg gaggccaagg
8401 cgggtggatc acctgaggtc aggagttcga gaccagcctg gccaacatgg tgaaaccccg
8461 tcactaaaaa aaaaaaagcc gagtgtggtg gcatgcgctt gtaatcccag ccactcgaga
8521 ggctgaggca agagaatcgc ttgaacccgg gaggtggagg ttgcattgag ccgagatcac
8581 gccactgcac tccagcctgg gctacaaaag cgaaactccg tcacacacac acaaaaaaca
8641 atcaaccaac caaacaaaaa acacctatgc ctcttccggt agttgatctg ctgaagaatc
8701 ctcctctaac agcatttagt gcttaacgca caagtgagct gggcacggtg gcttacgact
8761 gtaattccag cactgtggga ggccgaggag gaggatcatt tgtggccagg agttcaaggc
8821 cagcctgggc aacatagtga gacccagtct acaaaaagaa aaaaaaaata gccggccatc
8881 gtggcgcgtg cctatggtcc caacttactt gggaaggatg aaggagggaa tcttgagcct
8941 atgaggtgga ggctgcagtg agccatgatt gctccactgt actccagcct ggggatagag
9001 ctaaagactg tctctaaaag aaaatcaaca aatggctcac tattgttcat tgtttcaaat
9061 acaaacttcc aaacctggat gtctattttt agtaacctca ttttttgata tttctgctaa
9121 gcaaatatgc caataaatag cttgtttatt tttacctctg caccttccca ggagaatttc
9181 ttattagagg gaagctgtct acaaaactcc cttcctcaca gccttgcact ttgacccagt
9241 aatactgctt ccagaaatct aggccggaca tgcataaaaa tttatgttct acatagcaat
9301 tattgataaa agtggaacac tggaaacaaa gatctaaata tcttgcaata tgggattgtt
9361 aaataaatta tggtccatgt agtatagaca cagaaatacc aggtagctat taaaatggtg
9421 ttgtagtctt caattttttt ttaaggtacc tattcctggt ataggtttgt tgtagccttc
9481 tatttttata ccataggaaa ttgtgcaaac tacattgtca agttaaaaaa ataaagataa
9541 tcatttcttc tggtgacatg taatagatgc aaaaacgatg tggtttcatt ttttcattag
9601 aaagtataat aggcgtggta gctcacacct gtaatcccag tactttgaga ggctgaggcg
9661 ggcagctcgc ttgaccacag gaatttgaga tcagcctggg caatgtgacg aaaccccatc
9721 tctacgaaaa atacaaaaac aaaattgagc tgggcctgta gtcttggcta cccaggatgc
9781 tgaggtggaa ggatcacctg agtctggtca aggctgcagt gagccatgat tgcgccactg
9841 cacttcatcc agcctgggcg agaatgagac cccgtctcaa agaaaaaaaa aaaaagtata
9901 ataataccca gctcattaca tcattaaaca aagtggggag ggcttgcatg aactggtgac
9961 aaaggtgtag cttctacaaa ggattatgat gaatacagct atagcacctg aggtccagaa
10021 aaacgaacaa aaaacttctg ttaaacttat ctccttaaca attcattttt tgattctctt
10081 ttctcttctt cttacaaatt agtttaaacc tgaataaaat cttttaattc aagcttttgt
10141 aatatggaac ttgtacatta ttgagtaaaa catttaaaag tcatggtaaa tgttaaaata
10201 actgaggttt tatgacaaaa ttgagtcctt cacatcacat gggaaagaat ataagattaa
10261 tcactggatt cattgattaa tttttttgcg tataaaagat tttttttttt tttttttgag
10321 atggagtctt gctctgtcac ccaggctgga gtgcagtgga ccgatctcgg ctcactgcaa
10381 gctccgcctc ccgggttcat gctattctcc tgcctcagcc tcccgagtac ctgggactac
10441 aggcgcccgc caccatgccc ggctaatttt ttgtattttt cttagtagag acggggtttc
10501 accatgttag ccaggatggt ctcgatctcc tgacctcatg atctgaccac ctaggcctcc
10561 caaagtgctg ggattacagg tgtgagccac cacgcctggc agcatataaa agatttttaa
10621 gcctatgaac ttgattatct cactatgacc tgtaatgttt ttcaaaatgt gtaagagcat
10681 ttatatctta gggtatacag tgtgtctatt gaaataaata aaatggcata tctttaaaaa
10741 taattatggt gaagtcattt tgatagacta aattttgcct atgctgtctt gattttgaaa
10801 tttggtacgt tgcgtggtta cagtttgtga agcacttttc atttgggtaa cctctactct
10861 ctccagttgc acttaaagtc acttaaagcc acagagaggt ttttctacct tcagcaccca 10921 ttttaggaca atttctggta attgctaagt aaatgtcagc tagttgactt cctgcctgac
10981 ctgtcttggc ctgtttcctg ctcattagca tctccactag agggcaggct gggctgctga
11041 ggagagaagg aaaggagtgt tttcattctc tagctaaccc tgtcctcctc tcctctactg
11101 cagctcccag cttggtgacc acacagagct cctgggacag ttccgtgttt ggagtgactg
11161 atgctcatac atgtgtttga acattgcctt atagtattct ctgtgtcgat ggaaatggag
11221 agtgtgctaa taatttacct agggacttaa aatgtgttga ctagaaagcc actaagtaac
11281 tatgggatgt tctaatactc tcatgtcttg tgtctgtaag aatcagattt ttctgtgtgt
11341 agggtaggag ctatagatgt aatataagta aatacccttt agtggcccgg ggtagtggct
11401 cacacctgta atcccagcac tttgagaggc tgaggcaggt ggattgcttg aaaccaggag
11461 ttcaagacca gcctgggcaa catagtgaga ccccatctct aaaaaaaaaa aaaaaattag
11521 ccaggtgtgg tggcttacac ctgtagctac tcgggaggct gaggcaagag gatcatttga
11581 gcccaggaat tcaaggctgc agtgagctgt gatcacgcta ctgcattaca gcctgggcaa
11641 caaagcaaga ccatgtttcc agaaaaccct ttagccctga ttttgaatag aacatgtcag
11701 tatgagttca tgaggtttta tcttctgtcg ctatccacca aaaagatcta gaaacaatga
11761 ccaatccagt atcaatgaac actcctagca tccagattgt ggtcttaaaa cgccatttcc
11821 ccctgaaaga agccagagct tcttagagaa aaagctgatt ccaggtttgg ggaaggaaat
11881 gaacacaatg agcatggagc aacttatacc agatagccgg gaagcaagga gtatgtatca
11941 tgtcaaaagg actcagctct ttttggccta gcttccatag ccaaatgtgg gacaatttga
12001 acatttaata aggtcaattt aataaacact aagtatgttt aaatccatga gttcataatg
12061 tttgtgtgta actaactggt taccttttca aaggataata ggaaatcaaa tcattttttt
12121 gaagatgata aataaagata aagaattaag cagttatcct gctgtttcta tataaacaat
12181 accatagggt aatgaaatag aagtgtccat tttataaaat tattgcaatg ttatgacaac
12241 tcaaatatgg ctgttttgca atccctagtg agttaatgca tttagacact gaacatctga
12301 gtctggattc gtcaatgggt aaattgaagg aaaagaaagg aatggagggg gaatctgtag
12361 actgatagag acttgaaaga catatgaaaa aaattttaaa tgggagcaaa gctaaactat
12421 agtgtctaag gatctacatt taggtgatca aactataaaa aaatgcaaag aagtaattat
12481 tactcaccat agtatccact atggcaggaa ggggtggcta tgatagagat gggcaacagg
12541 gtcggggcgg ggcggggctg ggttggtgtc tgcaaagttc tgtttctttc cctgggtagt
12601 gttccaaagg tgttcacttt atgatagttt attcagccat aactttgttt tagatggtct
12661 tctgtatctg tgttttattt taaaataaaa agattataat gtgttaacta tattttatca
12721 gttatctgga gctgaagggc atgcagcccc attttattct aattaataaa aataattttt
12781 aaggctaaca ctttcttgtc cctgtgcatt tagaagatac cagaaaggtg cctggaaccc
12841 cagttccctg cctcttagct ggagggattt atttttaaat ctattttctt tctctcctag
12901 attttattta cattgctcat gttcctttta aactgtagag tcagcaatat gtaatatacg
12961 cttacagggc ctactctaat cattataaag tggaaaggtg atgatagcta acatgtatta
13021 aatggttatt cggtgccagg catagttctg agtgctttat tccactgact cttttaatct
13081 tcccaacaag actgtaaagt gtaggcattt ccattttaca gatgaagcaa ctgagaggca
13141 cctctggctc aagtctacta tgtgtttaat acctgtgcta tgttgctttt gacggtattc
13201 agttatcata tgctatttat gaagctaagg atttggctgt gttttattat tatttttaaa
13261 tttttaaatt tatttattta tttatttttt ttttgagaca gagtctcact ctgtcgccta
13321 ggctggagtg cagtggtgtg atctcagctc actgcaacct cagcctccca gtttcaagtg
13381 attctcccgc ctcagcttcc tgagtagctg gaattacagg catgggccac catgcctggc
13441 taatttttgt atttttagta gagatggggt ttcaccatgt tggtctagct ggtctcaaac 13501 tgctgacctc aggtgatctg cccacctcgg cctcccaaag tgtgagccac cgcgcctggc
13561 tggctgtgtt ttaaagtaca atatactcca ctgctaactt tgttctaacc tctgttccac
13621 tctgaccttt agatttttac acattctggc tggtcactgg catttcctat gagaacactt
13681 ggtgtttcct cttctagttt tttcctttga gggagttccc aataattcca ttttatttgt
13741 tgaagtttgt tccctttttc tgggtaaaga ctaccacact acccacctta ggttatacat
13801 tctctcagcc tgatccagat tgcacagaag ttatcctaag ctgatgcccc tgactcatgt
13861 gagatcattg cactgttttc ctgattactc tccaaagttt atttcagatg aatttaggct
13921 actctaaact gtagttcgca gaccggcagc atcagcatta cccaggagct tgtaaggaaa
13981 acaaaatctt gaggctacta cagacttgct gagtgacaat ctgcatttta acaagatctc
14041 caggtgattc aaaggcactt ttaagtttga gaaacacgga ataggtgact ttttattttt
14101 ttattttttt gagacagagt cttgctctgt cccccaggct ggagtgcaat ggcatgatct
14161 aggcttactg caacctctgc ctcctgagtt caagtgattg tcctaaatag ctgggattac
14221 aggcacctgc catcatgccc agctaatttt tgtatttttg tagagaaggg gtttcaccgt
14281 gttggccacg ctggtcttga actcccaacc tcaggtgatc cgccctcctt ggcctcccaa
14341 agtgctggga ttataggcat gagccactgc gcccggtgga ataggtgact tctaaggtcc
14401 ttgcagttgt agatgtctat actactatga aagacatgtc tttgcagttt tatcacttta
14461 acccttagct ctattgttta ctaactgtga agctttggac aaattacttg acctctctgt
14521 gcctttgtta cttcatctgt aaaatggtaa ttcccccaaa gggttgttag gtatgtgctt
14581 agaacactgc cttgttggga ataggccccc aaaatctggc cataaactgg ccccaaaact
14641 ggccataagc aaaatctctg cagcactgtg acatgtttgt gatggccatg acacccacac
14701 tggaaggttg tgggttcacc ggaatgaggg caaggaacac atggcccacc ctgggcagaa
14761 aaccgcttaa aggtattctt aaaccataaa caatagcatg agcgatctgt gccttaagga
14821 catgctcctg ctgcagataa ccagccagag cccatctctt cattttggcc catccctttg
14881 tttcccgtaa ggaatacttt tagttaatct ataaaaacaa tgcttatcac tgacttgctg
14941 tcaataaaca cgtgggtaaa tctctgttcg aggctgtcag ctctgaaggc tgtgagaccc
15001 ctgatttccc actccacacc tctatatttc tgtgtgcgtg tttttaattc ctctagcact
15061 gctgggttag ggtctccttg acagagctgg tctcagcagt gcctggcata aagaaggtgc
15121 cacagaagtg ttgttagctg tcctaatatt gaatatgctt ccatgaatac tatgcagctc
15181 ccagtgccag gtcaggcagg gggaagaaca aattcgagaa ctgacaatga agccacttca
15241 ctggagaatg gagttgtaga ggcttctgca atctaagtgg gagatcagga attttaggct
15301 tgggggctgt actgagcagc ttgctgaggc cctcagtttt ttttttgttt tgttttgttt
15361 tgtttttttt ttttgtgacg gagtttcgct ctgttgccca gactggagtg tgcagtggca
15421 cgaccttggt ttactgcaac ctctgcctcc tgggttcaca ccattctcct gcctcagctt
15481 cccaaatagc taggactaca ggcgcccgcc accactcccg gttaattttt tttttttttt
15541 tgtattttta gtagcgatag ggtttcaccg tgttagcccg gatggtctca atcccctgac
15601 ctcgtgatct gtgcgcctca gcctcccaaa gtgctgggat tacaggcgtg aaccaccaca
15661 cccagcctca ccattttttt ttttttaaga actcaggaca tagagtggat agtgccttct
15721 cccagcaatt cctatgtctg tgacccagtg ctagagctac ctgtaaaaca gatctttgat
15781 tgtgccaggc tgtgcttctt ctaggggctg gaagaagatg attgtgagac aggtgttaga
15841 gggaagcctg tgaagatagg tgggaaatga aaacagcaca aatcttgtgt aaaatagata
15901 agcatctctt attattggac agtctttgtg ggaaggtcta tggcacattg aagatgttag
15961 ttaatatcaa attgctcata ttttctgcaa ggtgccttcc ctattcccag atgagggtgc
16021 tatgtcctct tgctagacta gggcctcagg tcacattttg tgcacacgtc tctccagggc 16081 ctcaagctca gccaacacct ctttgggcag atcctggttg acctgctctg tcaggtagct
16141 ccgaatgtca cgaacctcct gttcccagaa gtccttgggg agggagaaca gctgagtggt
16201 gtctatagct ctgaggccgc tgagatccaa ggctccttcc tttggcacca gcccaatggg
16261 tgtctctcgg gcactgtcct ccccctctaa ccgccggcag atccagtcta gcacccgagc
16321 attctcccca aagcctggcc acaggaagtg ccctgcctcg tcacgccgga accagttgac
16381 atggaagata cggggcagct gggccccctt gcgcccttcc atgctcagcc agtgttccag
16441 gtagtgcccg aagttgtagc caaaaaaggg ccgcatggca aatgggtcgt gcatgatgat
16501 cttccctggg ggggaagcaa gatgggtaag gaatcttcct tctcactggg gtagggaagg
16561 gcaccctgca tccagttgga ggaagctgtg aaaggcttat ggttctgaat atcttcaggg
16621 atggggaaaa gatagaagtg ggaagaggtg gggccatatc agactccagg ggtggacaaa
16681 aggaaggtct ggctcaggaa gggagagagg acgtgctgtg tgcacacaca ggagagggag
16741 gaatggtgag ggtgctcacc tttgtgttct gctgcagcag tggactcaga gcgcatggcg
16801 ctgcccacaa acaccccatg acgccagttg aaggcctcgt ataccagggg tacccctaga
16861 tcaccaatga acagagtcac aggcagccct tttctttgga ccctaactcc agcccttctg
16921 gtgagcttga ctggtactct ctctcctaag acctcggcta tcccattttc agaccctttg
16981 cctcctccca agtttgcatt caccagggga gaactctgga gaaaggtgag atccaggctg
17041 aggctctgga tcagagggag ggaggtaggc cctaatacag agatagccct tttgccaaga
17101 acatggagct catatgttgt ttacctttgg gtctgcggcc accaaagatg atggcgtcaa
17161 tggggacacc ctctggggcc tcccaggctg ggtccatgat ggggcactgg cgagccgggg
17221 cacaaaatcg agagttggga tgtgcacagg gctccttgtc acctggcaga ggaaatacaa
17281 acactattat ttccaaggtc atgtcgaccc ccaacacaca catacatggg cacacattct
17341 tgcagggttc tttttttttt tttgcctcat cagctgccta gaaccttgtg tgataaggag
17401 cagagagagg ggagccaggg catctccaag agctcaggtt gtttagccat gaaggtgcgg
17461 ccagctgagc tatgtgagaa aagagtggga gaggaattgg ggtttggcag ggcactaatg
17521 tttgtgccaa gctactggca cttggcactg accagggctc aagggaatgg ggttagatat
17581 gggcataagg ttataataat ttttccccca gaaactattt cattatttgt gagattatta
17641 tttaaatgaa tacccaaacc taaagcaaaa actgagaatg tcagcttagt acttcagaca
17701 attgactttc cgtcagcaaa ccggggaaga caggttctcc taagttatcc aaatgcaaat
17761 aggaatttat tttatctttt tatttttgag gcagagtctt gctctgttgc ccaggctgta
17821 gtgcagtggt gcaatcttgg cttactgcaa cctccgcctc ccaggttcaa acaattctcc
17881 tacctcagcc tccccagtag ctgggattac aggcacccac caccatgcct ggctgatttt
17941 tttgtatttt taatagagat ggggtttcac catgttggcc aggctggttt caaactcctg
18001 accttaactg atctgcccac cttggcctcc caaagtagta ggattacagg catgagccac
18061 tgcgcctggc ctgattttat ttacttaatt aatttagtta tgagacggag tctcactctg
18121 tcaccaggct ggagtgcagt ggcatgatct tgtctcactg caacctctgc ctcctgggat
18181 caagcaattt tcctgcctcc tgagtagctg ggattacagg catgagccac catgcctggc
18241 taatttttgt attttattgg agacggggtt ttgccatgtt gccaggctgg tctcgaactc
18301 ctgacctcag gtgatccaac tgcctcggcc tcccaaagtg ctgggattac agatgtgagt
18361 cactgtgccc tgcaaggaat tgattttaaa gctaacaaca tgttggtgat ttccctgccc
18421 tgcttagacc ctgatgaagt gatagggctg gaaaaataga gatagggata tcacatgggt
18481 agggataacc tcaggagccc aggtcacact tggcaccttc aggtgtcctg gaggggggtt
18541 gggactaagt cagtggcaca tgtatgaagc accactgtgt ggcccctgag tggacatggt
18601 gccttctctg ctggaggttg ctggtcagac ctggggagtg gggaagccac ggggccaaaa 18661 tccccaccct ctcccatccg ccagcttctg cccgccattg cagataagag ccatccttct
18721 tcagcaccca gtgcagaatc ctaacacagg gtattattct gggaattgaa gctggggaca
18781 agatgcccta gttatgcccc caaatctgga gatgatgaaa gggttgggga actagcctgt
18841 ggggaaagat gaaagtttct tggatttctc agttgggtgg gaaggctgag gggggcttaa
18901 tgatggtgtt agtaaaaata aagggtgatt agatgaagca aggagggtga ctgctaggcc
18961 agcctggcaa acctgaatat aggcttcagt gactacaagg ccagcctccc ctcccatgct
19021 cttctttgcc cctgcctctt ggtgtctgga ctgcctgact gcagaaggcc atggaaagaa
19081 tactgaaggt ccagagtgca gggctgaggg agaggtggga ctcccaggcg cccagggtaa
19141 tgacaggatt cagaaactag cttctgggaa agactcaagc actgacctga ttttgtttgt
19201 aggaaggatt ggggtgaatg ctttggaggg acaggggaag ggtgacggta acaatactga
19261 cctttagaca gtggttatta tacaggggac agtgggagcc aagtggcagg aggagagttg
19321 gagcagagga ggcagctttc ctcttttcct aatgggccaa actttatgga tagtgcttgg
19381 agcccaatac cttctgtaag aatgttcaaa agtccttcct tttcctttca ttaaaaaaaa
19441 atccagcctg tatttattat tgagaattta ctgtgtattt gtcagtgtga taaacccttt
19501 ttatgcacta tttaatcctc caacaatctc atgagatagg tactatcaca actaccctca
19561 ttcaactgat gtggaaacta aagcttaggg aagttgagca acttagccag atcacaaaac
19621 cagtgactgg tggagttggg acatgaactg agattttgcc tgggactgga aactgcaaac
19681 gttcatgact tctgtgcctc ctggcagtcc tagaagatgg ttggaggttg tggagaaagc
19741 ttttccacca ttaaggtgct gaggcctgga ggctgtgcca caccttcccc accgcacata
19801 ccaggtttcc agggtttgcc cagccaggag gtcacagtaa caccaggtgg aagaggctgg
19861 tcaatgccct cccagtacac gccaccatca ctggtctcag ccacattggt aaaaatagtg
19921 ttactctgga ttgtagccat ggcgttggga ttggtggtgg cagaggtacc aggggcaacc
19981 ccaaagaagc cgttctcagg gttgatggcc cggagtcgac ctgttaggag aagtgaaaga
20041 aaggaaggac caaacaagga aaacttgaga tgtaagacca aagaaggtcc tgctccaccc
20101 acccctgtcc tgagatggac ccaagatctg atgaggaaag gctgtctctc gggtggctgg
20161 gctgccagag gaatggagca gggttgggtg ttcaggaaac tttctcactg acaaagtcat
20221 tgtgaacact agagaggaga ccccgaggct ctgacaagag ccagaaccaa gagtatgatc
20281 tgagagtccc tcaccttcac tgtcaaacct catccaagca atatcatccc ccacacactc
20341 cactttccag cctggcagtg caggccgcat catagccagg ttggtcttgc cacaggcact
20401 agggaaggcg gctgccacat agcgcttctt ccctgcaggg ctggtgatgc ccaggatctg
20461 tgcattgggg agagagggaa taagaaagag gtcaccaaaa gtcagggcat ggtctgcatg
20521 gggaagggca gctagggtct aatagggagg accaatgttt attaactata taagtgattg
20581 ccctgccatc aggcctgggt tagtggcagg ggaaacctca acattcagca gcctgaggcc
20641 aaagctttgg gccttcaagt agagtccccg cccaccagcc tggcacctgg caggagggag
20701 gtgaggctga ggcagactgg ccaggcccca cccctgccct gtccccggca gctgccctgc
20761 ttctcaccag gccctcacca gcatgtgctc tgccagccag ccctcatccc gggccagccg
20821 agaggcgatg cgtagggcaa agcacttctt gcccagcagg gagttgccac catagccgct
20881 gccgaaggag atgatctccc gctggtcggg cacgtggcca atcagggttt tctctgggtt
20941 gcacggccac tggctcactg gctcccctgg ggacaatggg gtcatggggc tgctggcagc
21001 agcatcagga actggggtgt cggggccaga gggatcaggg attggcagga gagacacttg
21061 ggagcagtag cagcaccaag aggtggctga agccccccac ctcataataa ccatcagctt
21121 ccatgcccct attcttggac acggattttt ctcaacctag tgcaaagtgc tctgcaaaca
21181 cagccttatc cctctgctgg gactgctgct ctggatcttg ggaattaggt tgccagagag 21241 gacaggttct tagggtctgt ggagaggtag gatttgggat ttcctctgag tacaagaagg
21301 cctctgtgtt ccccttgggg cagagcaggt gcttaccttg tcctgtcagg ggctggccca
21361 cggagtgcag acacttgaca aagtcaccat ctcccagggc ctgaagcaca ggtgtcccca
21421 gtcgggtcat aatacgcatg cttgccacca cataggctga gtcagtgagc tgcaccccga
21481 tgcgggacag cggggagccc acaggaccca tgctgaatgg aagcacatac atggtgcggc
21541 ctgtggagga aggcatcccc tggatgaagg gttccaaacc tgttcacatc ttccgtgccc
21601 ttgccactgt gcccctgccc tggttaccct gcatgcagcc tggaaacctc tcatccacag
21661 ctcgctggaa atcagctggg gacatccagt tgcccagctg cccacgggcc ccaccaggcg
21721 ggagtggtac cgtgtcccgc tgagaaggag ttacaatcac cgtcttgctc tctactcgtg
21781 ccacatcctt ggggtctgtg cgggccagcc agctggggga gaggggattg tcaggaagat
21841 ggtggccagc aggtttccct tgtccctaga cccacttttt caagtccaac tttgactcca
21901 ggtcttctgt tggccttatg tttccccacc caatcacatc tcagtccctt cctccaggct
21961 ttgtcccatc taaggggtgt tccccaaggt cccagccctc tgggggtctc tgcccctggc
22021 aaaagctccc tgaactggtg aggaaaaaaa aaaaaagcaa aggatcttat ttatatcagc
22081 ttcttcattt aacattaaaa taaaatacaa actacaaact aggctgggcg cagtggctca
22141 tgcctgtaat cccagcactt tgggaggctg aggtgggtgg atcacttgag gttaggagtt
22201 tgagaccaac ctggccaaca tggtgaaacc ctgtctctac taaaaataca aaaatcagct
22261 gggtgtggtg gcgcatgctt gtaatcccag ctactccgga ggctgaggca ggagaattgc
22321 ttgagacaat tccccggagg cagaggttgt tgtgagctga aatcatgcca ctgcactcca
22381 gcctgggtga tacagtgaga ctccatctca aaaaaaaaaa aaaatcccag tttctttctt
22441 tttttttttt gagacagagt ttcgctctta ttgcccaggc tggagtgcaa tgacgcgatc
22501 ttggctcact gcaacctccg cctcttgggt ttaagtgatt ctcctgcctc accctcccaa
22561 gtagctggga ttacaggcat gcgctgccat gctgggctaa tttttgtatt tttttttttt
22621 tttttcagta gagacggggt ttctccatgt tggtcaggct ggtcccaaac tcccgacacc
22681 tggtgatcca cccgccttgg cctctcaaag tgctgggatt ataggcgtaa gcaaatccca
22741 gtttctgggt ctgtttaccc caaagctctc attcttgttc attccattgg gatgttctag
22801 ttaagttgat tttgccttgg tgaacccaaa gtggcctcag tgcacctatc ctgcaggttg
22861 tggagcccaa ggcttaccag ttattgtact tggggagctt tcggatgagg ccctgctgct
22921 ccagcagggt cagtgtggca gtattctcag cctcagttcc atcacagatg tggatgccct
22981 ctggttggca caggcgggca ctgtgctcta caaaatctcg aatgccagtg ggaagctggc
23041 ccagatctcc actaagcact cgcagggtct ggatgctacg gcatgatggc cagcccaagg
23101 ggctcagccc atgccagtta agcctatagg agaaacagag gcaatgagct agttgctgtc
23161 atcgagagtg gacaaggcag gtggtggaga gacagaaagc ttgggctgca gcctgctaaa
23221 acatgtctgc atgcagggac catgaagagc aggttgcagt tggtgtgtgg gatgtgttca
23281 ggacacatgt atcttgtagc ctttatgagg cttgaggagg gtgtctcctg ctcagcgagg
23341 gacagatatg gccaaatgag caaaaaaggc acatgcctgg ctgtgtggaa gtatacatgt
23401 aggcatgctg atgttactgc ctgtgtagcc catgcccatg tttaactgtt taatcaacgt
23461 ttagaaataa gtagggagat ggctgggcac ggtggctcat gcctgtaatc ccagcacttt
23521 gggaggctga ggcaggtgga tcatgaggtc aggagatcaa gaccatactg ggcaacatgg
23581 tgaaacccca tctactaaaa atataaaaat tagccggatg tggtggcgtg tgcctctagt
23641 cccagctact caggaggctg aggcaggaga atcgcttgaa cccgggaggt ggaggttgca
23701 gtgagccgag atcgggacac tgcactccaa cctgggcgac agagcaagac tctgtctcaa
23761 aaaaaaaaaa aaaaaaaaaa aaaaaagaaa tgagtagggg cctttggccc aagtgtcaag 23821 acaagaagtt gggcccaggt gacaatttca tatgtctggt atttgaagcc tcatccattt
23881 tatttccatt ttcaagtata gttttttata aattaaaatg gcagctgtgt ttattctttc
23941 cttctggtgt gtatgctgta agactatgaa agccccaagc aaaggtcaca gtctttccag
24001 tgccaggttt ctagatgagg gctcttgcac agagaatagg tgactggatg ctgggcttcc
24061 aggccctgat ctgctgctgc ccacttggac caacaatggt tgcataaaat gttgccctcg
24121 ggtaagtatt tctgaactct gcggaaggtt gaccactggg gaatgagtgt cactggctgg
24181 ggttcatggg cttaattctc aggaggtcag cgtcctgttg tctgtcctct catggccctg
24241 ggagacagag aagcaacgtc tgctctgatt ggcctggact caaggtggag taaacccgag
24301 agagcaaaga ccatgaaggg gatgttactc tcctcctcta tcaaggcctc gcccatcaga
24361 aactgccccc acacccagga ccacgtgacc ccgtgcttcc cctggctctt cttcctagag
24421 gccacatgcc tagagagctt tggtgttggt gggagggtgg aacagcagct tgctggcagc
24481 tcagactcag agggtgttag cctggggaag gaagaaagct cagagcatgg atacgggagc
24541 ttgagtctgt ctggggtaga agctggggtg gtttccgcta aagcaggata gatgatcagt
24601 gtggccccag gggcagggga ggagggctac tgggacctgg gtctgttcct gcctcagagg
24661 gaagttctcc gtgagcatca gttttcaagc acacagtctt gaggacagcc tctctctccc
24721 tggagcctgg ctcacgttat ctcttgtgaa gcccccacac cctcttgcag ccctctaagt
24781 gggacgtttc cttcagagac cacccacaag ggctgcccaa gtggaacggg ctgtgcgaca
24841 gatgtgggtc acttccgact ctgggacaaa agctgagaag agaggcctca gagaataaat
24901 aggagactaa gaggacaggc agacaaacag gacgagcctg ggggctccag gcctggacgg
24961 aggaagaagc cagctatgta agaaacgaag gcaacttggc gccctcctcc caccttgctt
25021 gcctccctcc cctgggccca ggtccctcgg gctgctctgg acttcccgcc aggttccagt
25081 ccttccagtc cgggagaggc cgggaatgga tatttaacct tccaccttct ttagggggct
25141 ctgagcttag tctcccgggg ctcacgtacc cttgtcccca gggccctgct gcctctcgaa
25201 gtaccctggg gcgctggctg agagcccgtt agaggtccga gggaggtatc tgggaaggaa
25261 aggaggatat gcggagacct ggctcagcag agaggagcga ggagagagag gaagttctga
25321 gagtggcaga tagagatcgc gcggtcagag gcgagcgagg cagagaaggg gaggtgcagg
25381 cggaaacgag gagcaccggc cggctgccct cccaagagac gcgcggcgcg ggaggctgga
25441 cccacagcag tcgcccctgc ccgcctccgc ctaggatggg aaacctggcg gaggctgaga
25501 gcaggagagc gccactggca gccccgaggg ggcgagcgca gcggaaggtg cgggtgggcc
25561 ccgggccggg ggtcactcac cgcaggccag ggcggtacaa tgcggccatg gcacctgggc
25621 aggggetgcg gggtggccag gaaccgagcg gagccgggga ggtatggaag gcggggaagg
25681 agggagcgcg gcgaagcgag ccacagcaga ggctggcggg aggcgcttaa aaaggagggg
25741 ggcaggcgcg ggggcggaac ctggtagggc tggcactagc tttcctccgc cccgctggca
25801 ggccagctcc ctcggccccg gggctccagg ctccaggtca gcccagccgc cgccccaacc
25861 cctgcctcca aaccgccaaa cccatctctc ccattggagg actgggtcca ctcttcggcc
25921 cccgacttcg aggccccgcc ccccatccgc caccgccctc ccagccgcac atgatgtaac
25981 tttgaggact cttgctcccg ggagagacac taggtggcaa acaagctagg aacgaggggc
26041 gaggccaggg gcgggagact acaggggcca gacgtctaga agttaggggg ttgggcattg
26101 cctttccagt tcctcctcct ggggacgcga caccctgagt cctgggcctt tctgtagtcc
26161 aagtgcccaa tgctaaggtc cacttagtcc ccaactccta aatccccgtt tctcctcctg
26221 atcaaggctc ctttctgcct tgccatgaaa tggtggagtc tctctacccc tgggtctctt
26281 ccttggtcct ctgatctggt cattctcctc ccccggcaca tcccctcttc ccctgacgga
26341 gtcttactct gtcacccagg ctggagtgcg tgcagtggcg cgatctcggc tcactgcaca 26401 ctccgcctcc cgggttcaag caattctcct gtctcaacct gcagagtagc tggaattaca
26461 ggcgcctgcc accacactcg gctgattttt tgtatttttt gtaaagacgg ggtttctcca
26521 tgctggccaa gctggtctcc aactcctgac ctcgtgatcc gcctgccttg gcctcccaaa
26581 gtgctggaat ttacaggcgt gagccaccac gcccggcctg gtcattcttt ctctccacaa
26641 tccaatgagg aaactcatct gcccacccaa ctaccatcat aaagtcctca ggtgatttct
26701 caagctatac ctccattggg acatctctct ccaacctgag accactggat atcacccaca
26761 atgctatata gcacctcaaa ctcagcatat ctatgatggg tgtctgctca gcatccactc
26821 gccttttctg gtaatagcac cctgattttc ttttggggaa ccatctcctc agtctgtatt
26881 gtcatgtggg tctgatgtca cccctcttgg gggtaggctt gcagcttagc caacttttgt
26941 gttcctcact ctggccacag caatcaagga tgttcaagga tgggcatgag atccctctct
27001 gggacttttt ctaaaacttt ggaagttagc tctctttctg ctgagttgct gagctggtag
27061 aatataagcc tggagctgct gagtgttagc ttggcactgc aaagcaggaa cctggctgag
27121 acagaagcca gcctagagga agcagagcag ggagatggcg agcaatggat tcctgatttc
27181 agttacagga attgatgcat ttcttctctt gctcaagcta attttaattg gagttctgcc
27241 acttgcaaca gaaacagtct tgattctcag atttcttgga gttctatgct ggaacatagt
27301 gggataagga gagctggtct ccagccacgg gcttgctact ggtccccgtc tcttccccct
27361 caggctctag cctacactca acctcaggta tatgtatttg gatctctttc cccccagttc
27421 atagatccaa actctgtcca cacttaccca gctgcaaaca catacctctt ggccaacctt
27481 tgggcctaaa ggtgtgcaca ctggtggcag catggttgac ctgaaggtca tcatcttctc
27541 cataatcctg cacctgctct catggtttcc tacctcagca aatggcacca tcatctggcc
27601 agttgcccca aagggaatca gtctagacta ttcttatcct gcatagctaa tcagatgcca
27661 ggacctttgg aattgtactt ctcaattagc cctcaagtct gcaactatcc ccatggccag
27721 ggccttagtt cagggcttat ctctcacctg gcttcaggtg atagcttcta aggcacttct
27781 tggactcctg cctctccaaa caccaacccc tctccctacc aagccactcc ccacactgtg
27841 catgcaaatc cacttggaaa gttaagagag aagaataatg tttatgctat ggacagtagg
27901 tgccaggctc tgtgtcagca actctgcatg cataatctca ttctgtttca caactatatt
27961 ttacatatgt ggacacgggc ttaaagagtc atttgctcgg tcaccctaag ggaagaatca
28021 aggaaaaagg gaggcaggac cccagaagta tgccaacata taacacccta aatcaaaggt
28081 caaatgccgc acttgacctc caagatgcct gcttgggcct cttccaagtg tactttcctt
28141 tctttcattc ctgctctaaa gctttttaat aaacttccat tcctgttctg aaaaaaaatt
28201 attcatgaat attttatact tttatcctat tatgaatgaa atgttctaat tgtttaccac
28261 aagtacatac aaataaaatt gctttgtgta tattgaaaaa aaaaagagtc atttgctcaa
28321 agtcacacaa atggttagca ggagaaatgg aatctgaatc catatctttc tgactctaat
28381 taccaagtcc ccctctccct ataaatccta tactgtcccc ttgatttacc attaaaaatt
28441 agatcatatc actcttaagc ttaaaatctc ttccaggctc tttccatcac atgatatctt
28501 atgtccttca taatctgact cctatttatc taatgttgtc acccccacat ccccacttgc
28561 ctccttttct cctacgtact gaactctgaa gtttccagag cacttctgtg aactttttct
28621 gggcatctgc actcaaatta aacacacacc atcctggcca acatggtgaa accccgtctc
28681 tactaaaaat acaaaaatta gcttggtgtg gtggcgcacg ccggtagtcc cagctactca
28741 ggaggctgag gcaggagaat cgcttgaacc cgggaggcgg aggttgcagt gagccgagat
28801 cgcaccactg cactccagcc tgggcaacac agtgagactc tgtctctaac acacacacac
28861 acacacacac acacacacac acacacacac acacaggcct tttctgttcg tcccttagaa
28921 tgaacatcta tttcatctgt gttgcttcta tcccatgtat atgcctatat ttttgtactt 28981 tactatactg tagttacttt tatatctctg taatcctcac tagagtgatg atttcagtct
29041 tgtttttctc ctagttccca gcagtacctg gcctataaca ggcacttaat aaaagttggt
29101 tgaataaaag aatgaatgag tgccacgttt ctgaattctt cttccccacc attactttct
29161 tctctagctt taggcagatg gagcaagggg ctcacgtgca gatttccttg cactgctcat
29221 ttccccttat ctgccacaca cttttcttta gttccctgcc gggagagcct ggcccaccag
29281 ctggccctat gtccaaggag taccaccagg gggcagagtg tgatctgcat tgtcctctct
29341 ggggcctctg ggttcatccc tgaagtctca cagcccgagt agtgatgctg tggtgtgtag
29401 cccagattcc cgcttcagga tcatgatgct cattgttcca gctgctgagt gttggctgct
29461 gatagctcac agctgagtac ttccttgagc actatctgtg gccaaaggga gctgtctcac
29521 caaatgcaat gcccgcttcc tgggggcagt atgtatccaa tgaatggttg ttataaagta
29581 cagaggccta gccctttgtc tcagtttggg acaactctga aggtccatcc cagccccaga
29641 gctctttagg ctcagctgat tacaactgca gtgccattca actgttccct ctcttgggtc
29701 ctgctactct ttctttgaaa gtcccccccc gtgccccccc cccccccccg agtaaaccac
29761 ctgcacacaa gtttctgtct cagagtgtgc ttccagttgc aaatattcct caggctcaac
29821 ttggttacgg cattagtcct ctaatctgac tcttatttca ttgttgcctt cctccacaaa
29881 cacaaagtgc tgacatacgt gatccttccg aacacaaatc tgatcacatc atgtctctac
29941 tgaaaaccct tcagtagctt ctccctgctc ttagaataaa gcccaaaccc ttaatgtgac
30001 ctcccaggct ctgcatgatc tggcccctgc tgacttctcc agcctcagct atcactgttc
30061 ttcccacctt ccaggctttc tactctctgg ctacgtggat cttttctcag ttttgtgaac
30121 atgtctacat ctttcctgcc tcacaacctt tgcatatgtt gtttctgccg cctggaattc
30181 ccaccctgtc cacacctcca ggcagggtca cttcttattc acctgaccag tcttggttta
30241 gcatgacttt cttaggcaac ctgtccctgt gatgcatccc ctctggcttt gtattagagt
30301 atgtcttcgt ggaagaaaat ttcatagcac cctgcccttc ttcttcttag cacattcatc
30361 tctgtttaaa tggtttgttt ttatgtagac acatctctaa catatgtagg acctgcggca
30421 ggagtacaaa tagaggccct caaaccttgt gtttaaatat ttaaaatggg ctgggtgtgg
30481 tggctcatgc cttgtaatcc cagcactttg ggaggcagag gctggaggat cacttgagcc
30541 caggagttta agaccagcct gaacaacata gtgagacttc ttctctacaa aaaataaaaa
30601 agtagccagg catggtggtg tgcacctgta gtcccaactg cttgggagac taaagtggga
30661 gatagcttga gcccaggagt tcaaggctgc agtgagctat gattgcacca ctgcactcca
30721 gcctgggtaa cagagcgaga ccctgtctca aaaaaaaaag attaaaatgt ataactcagg
30781 gtcggcgcag tggctcatgc ctataacccc agcgctttgg gaggctgagg cgggtggatc
30841 atttgaggtc aggagttcaa gaccagcctg gccaacatga aaccctgtct ctactaaaaa
30901 tacaaaaatt aggccaggcg cagtggctca cgcctgtaat cccagcactt tgggaggccg
30961 aggcgggcgg atcacgaggt caggagatcg agaccatctt ggctaaccca gtgaaacccc
31021 atctctacta aaaatacaaa aaaaaaatta gccaggcatg gtggcgggtg cctgtagttc
31081 cagccggagt ctgaggcagg agaatggcat gaacctggga ggcggagctt gccgtcagcc
31141 aagatcgcgc cactgccctc cagcctgggg gacagagcaa gactctgtga aaaaaaaaaa
31201 aaaaaaaaaa attagccagg catggtggtg catgtctgct acttgatagg ctgagccagg
31261 agaatcactt gaacccagga gacagaggtt gcagtaagcc gagatcacac cactgcactc
31321 cagccagggc gacagagcta tctcaaaaaa aaaaaaaaaa aagtataatt caggctaaca
31381 aactgttaca caaaatatat tctgttcttc taccttgaca aatatattga caaatacata
31441 cttcacaatg gcctggaagg ccaggttcag atttgtattt tatttggaat cctcagggtt
31501 ctgcaccaga atgtgatggt gtagggggat gtagttttgg ccactggccc tcagctgggc 31561 ccactttgcc tcctacccct gacaccatct tggactgcaa ggggccttgt gtggaaccat
31621 gtggacctcc catcaggcca tcccaagtct gtccacagtc tcctgcaagc agctacccct
31681 tgtctaccct ttgacctcag aatgtgtgaa ccagtcatgt ggcccagccg tgggagggca
31741 aacccaggga agaggttcac gtgggcccta ggagtgggct tgggcctttt ggacagggaa
31801 tgcttagcta tctggagtgt ggtcctgaga ggattaaggt atgggcagag gatagttgga
31861 ctcctcaccc atgtggtggg acatagccag aggaggccag agtggagcct tctaaagcac
31921 agggcccagg gcaggggcca ctcctgcctg ggcctaagga caataattta tttattattt
31981 tttttttgag acagggtttc tttctgtctc caaagctaga gtgcagtggc accatcatgg
32041 cccactgcac cctcatcctc cccaggctcc tgatcctccc acctcagttt ttgtattttt
32101 agtagagaca gggttttgcc atgttgccca ggctggtgtc gaacttctgg gctcaagcga
32161 tccacccatc ttggccttcc aaagtgctag gattacaggc atgagcctct gcacccagcc
32221 aaagggcaat aatttgatgt ttctctgttt catcagtctg taagtttctt gaagtcaggg
32281 ctggtattag tgtaagttac tgaggggtcg ctaatgcctt actcaggatg tggtgcagaa
32341 taggtgttta atatgcattt ttcaaaagaa tgtaggaggt acaccaagaa gaggttgagg
32401 atttggatct attactgaag atctagatac catgagccag aagtaggaat gagaaccagt
32461 ctttcagggt tccaaaaatg agagtgcagg acagaggaga ggaggtagca tcctggaatg
32521 ctgactgtct cattttctct ccttcctctt cattttctac cccactcctg caggcccttt
32581 gcctgcctgc ccctctttcc ccatggtcca atatcactcc atccatatct tgctaccttt
32641 ctgtcctttg gccactgctc ttcctctgtg gcctatgtgt ctatttcttt gtattggtgt
32701 ctaggtcttg gtccccaatc ttatgtcctg tcccttcctt ctaccactct tactgttcta
32761 gtccttgttg tcccctactc ccttcttggt cctctcctgg aagacttcct ttctttatcc
32821 atctcgtcca tgtgcctaca tctttctgtc tcctttaatc caaatcccca tggagaccct
32881 gacttgtcct gtcctctatc tcacatctac acctactgcc tccttagtct ccttcctctg
32941 ttctattatt cctggagtca cactggcttc atctttttca tccctagatg tccttgagcc
33001 cattagtctc agtattcatt tctcagtctc cagtggatat gggagatggg ctctgctttc
33061 tgggtcccca ctgactgcca cagactctcc tctctgtgcc cttggtcctt tcctctggcc
33121 cagactgggc ccaaccctca ctcccccagc tcctttccct ggtttagtgg tgcctggtct
33181 gagccccaag cagctcaact cgcctgagct tgtttagtct gactccctta gcccgttagc
33241 agcttagccc tcccacctct cctttgagcc ctccagtaaa caagaggatc agtgcagacc
33301 tgacagctgc tggttggggg caagtgtctg gccaggccag agcaggcatg aaaaaggggc
33361 tgcactcaac acttcccatt ccttcttcaa ccagggaaat tgtagagtct ctttcctggg
33421 tgtccacttt ggagagctac attccatggg catgtgtgtg gggtcctgcc tctccatgat
33481 cctcattccc attttgtggt tggttcctag gccttaggct tttttattct tttgagaaaa
33541 cagcagtaga tccaggcagt cacacagaga agcttgaatg gtgacgatgg tttctgctcc
33601 ttaaaacaga aacccaggtg tgggaagaga gtgatgtcat ctgatctagg ttttccaata
33661 tgtgtatgga aagcatggta ggagagacca catacacatg cacagacaga catatataca
33721 tgcctcccca gggaagctgg gtagactgca ggcattctgt gcagttctca aactttcttt
33781 cttttctctt cttttttttt tgagatggag tctctctctg ttgcccaagc tggagtgcag
33841 gggcacgatc tcggctcact gcaacctccg cctcccaggt tcaagtgatt ctcctgcctc
33901 agtaggagta gctggcatta caggtgcctg ccactatgcc cagctaattt ttgtattttt
33961 agtagagatg gggtttcacc atgttggcca ggctggtctt gaactcctga cctcaagtga
34021 tccgcccacc ttggcctccc aaaatgctgg gattacaggc gtgcctggcc tttaaacttt
34081 caagcatgtc agacttgctg gaagggcctt aaaacacaga tttctgggcc ccacccccgg 34141 agtttctgac tcagtagatt taaggtgaga tcaggtaaca tgtatttcta gcaagttccc
34201 aggtgatatg gatgctgctg ctctggggac cacacttcag aaaccacctt cttagataat
34261 ctgtatctgc cagcttttcc ccaacatata aggctgggac caggttaagt tttataagtg
34321 atgacctttg gggtctgatg gacacccagg cctctgtgtt gagaaagagg aactattaac
34381 cccatgggag tatttgggtg gcctcagaag gtaggaagtg gcctttaact ccatagaccc
34441 tatttaaaca gcttcggaca ggtttaaaca tctccttgga taattcctag tatccctgtt
34501 cccactccta ctcagggatg atagctctaa gaggtgttag gggattaggc tgaaaatgta
34561 ggtcacccct cagccatctg ggaactagaa tgagtgagag aggagagagg ggcagagaca
34621 cacacaggga aaaggtgaga gaaagcagag ggcatatgag gccagttaca aaagtgtctc
34681 cgacggactg gtggtgatta gatttcaatg tcccttgagg cccagaagga aggaacagag
34741 ttccctgttc tcttttttcc tactctttct cccaagctgg attagcaaga atgggagaga
34801 caaaatatgg tggtcaagtc ctggagatcc cctgtgggaa aagttgcttt cctttctgat
34861 gcgacggcta tgaggggcat aagaccagtc agcatgaaga tggggcagag gtagaaatgt
34921 gaggattctt gaaaatagga aacagatcca aaaggcccgg tgagagtggg cgtgggagag
34981 cttatagtct ccaaagacag atgaggggct gcagggcctt ggaaggtggg ggtgctggga
35041 gtttgtctgg tcctcttttt ccaatcccag gctatgcatg gctagggctg agggttgtgt
35101 tcacatagag gggtggtggt tcagacccat gtttctgtcc gaactgggaa actgagcact
35161 tgggagtcgg atcatcagtg aggagctttg ttggggaaga tgctcccttt ccttctttga
35221 gaataagcac acttgtactc tcctctctct ccatttcccc caaccccagg ccaataagat
35281 atgcaaatga tctccttacc ttattggttg gaggcctcag gaccacagat gacctcagag
35341 agctggccct ttaagaatgc cctttgggct ctgtgcccac agccccctgg agctgagcag
35401 aggcaccagg ccctgctcca tggagccttc agtctcctgg gaagctgtgc ctgtctggct
35461 ctggcactga ccacatcctc tcggccattt ctgaagtgag tatatccagg gcctacctgg
35521 gtgtcaggcc gctcacctag aaccccctct ttaacacctg ctctctgttg tctgttttca
35581 agaatcctaa caccttggta ccctactcca ctcccaccct gactggcctg tgtccctcac
35641 tgctatcacg tcagaaagat aaacaacctt ccccactact ccttctgtac atccagttct
35701 ttctggatac ctctctcagt gtctcaccat ctcctttctg ccaagaccca gttcctttaa
35761 tctgtgtctg tttccatccc ctctgtcctc tcaagggtga caggttccat agagagggca
35821 gcaaccctgc cctggaacag gaagagagag gcctgggtct tcctctttgc ctctctgggt
35881 agagcctggg ggtctgacat gtggttggaa agaaggctac ctaggcttgg ggcatctaga
35941 aggagccgaa gtctaagccc tggggatgaa cactccatgc cgcgcacctt ctgggggtgg
36001 ggtgggagtt actggaattg ggagctggac tagagcttgg acttcaaggc tgggaagggt
36061 atctgaggtc acccagccag aagttcctca ggtgaacatg tgccccatga ttgataacag
36121 acaggagagt tccttggtga cataagttta ggacactttt tgttgaactt gaacagacgg
36181 tttactaaag gattgctcag gttaatatgc tcttgtgcta tgtgcatctg taagaggtag
36241 ggataggagg caacatttct caaagttatc tgagcacaga cctcttcata ggtattgttc
36301 agaatcagtg ttctagagaa cactctttgg tatatgttac aaagtctaac tgccctcatt
36361 gaacagaagg gaaaacgggt cagaagggtg aaggtgatct gccaagttca cacaacgtaa
36421 caagttctga atagaaggaa aatcaatctt ggtctgttcc ccttggagag actggccttg
36481 aggaaagatg gtggccagtt gattctgatc tttctagaac taattctagg acctttcttt
36541 tttccatata aagcctcttg cccctacaaa agggattcat tgattgatta atccatagaa
36601 caaatgtaca ctgagggtct tctataggca aggcacttcc ctgagtgctt tgagagacag
36661 agagctataa gaacacatta tccttggctc ttaaaattca cagcatacat gccttcccac 36721 tCftcctclclcLcL tatacactca ctttgtcaca gttaattaag caatttaaaa aaatggcttg
36781 gaaatggaat gatgcctctt gagatgacag acctctcggc atgtctcagc actagggttg
36841 ggagcactgc catactgctc ttgcttttca tagatcctga ggcatcagtg gggcgagagg
36901 ctgtgctgtc ctcttcctcc ttcaggaatt cagctgcttg tcccctgtca ggagcccctg
36961 ccctctgaaa ggttactctt cagcctggtg gggactctgc agtgaacaga gctgcaccat
37021 ccctctggct ttcccaaact cttgctccag ggcacttggg ctttgaggga agagggactt
37081 ggtgaagagg ggatggcagg tggcctccat gtgctccaga cctctcctcc tctttgcagg
37141 tgcactcctc ccagcccagc tccagaatgg ccctgccccc cagccccctg gccatggaat
37201 atgtcaatga ctttgacttg atgaagtttg aggtaaagcg ggaaccctct gagggccgac
37261 ctggcccccc tacagcctca ctgggctcca caccttacag ctcagtgcct ccttcaccca
37321 ccttcagtga accaggcatg gtgggggcaa ccgagggcac ccggccaggc ctggaggagc
37381 tgtactggct ggctaccctg cagcagcagc tgggggctgg ggaggcattg gggctgagtc
37441 ctgaagaggc catggagctg ctgcagggtc agggcccagt ccctgttgat gggccccatg
37501 gctactaccc agggagccca gaggagacag gagcccagca cgtccaggtg agtggtcagc
37561 aagctggcct gaggggaggc agggcaagga aggaggactg cccaagagag gaaggggagc
37621 tcccagaggg ggttatggac tgggacaggg gacagagggc aggagaaggg gagaaggtcc
37681 cttgaaagca atcagatcga gaaaactaca ttctgcttct cccccttttc ttaaaatgga
37741 gagaaatgag taggctgaac caggaggagc agggagaaga taagattagc agagaatcca
37801 aagggaagaa ttgagctggg gagtgggcga ctccgggggg taaacagata catggtgtgt
37861 ggaaaccagg gaaagggtta tgtgtggagt ggagctgggt taagactggt ttagattggc
37921 cttttcaaga cttcgtgctt cccagccccc aaccttctca ggaaggattg ggactcatcc
37981 tattaattac agacacagat gggggtgttg cgggcattag gatgtaatcc aaatcctgtg
38041 agggtcaccg ggttgcaggc ttcaggacag ggaaacgcag cgcgttggag ggttgggggc
38101 tgtctgggtg cgggtccact ggacacaccc gggcctggag ctggatgccg gggatcccag
38161 agacgagccc ggggtttagg tgcgcgacgg gctcgcctga ccgtggccgg ccctgcaccg
38221 tggggcgccc gcctgactgg agcaacggtc agctgggggg cccggggagc gtcggggcct
38281 ggggcgggct ctggaccgaa acagactgcg tggaagggcg agccttccgg tgaaggtggg
38341 agccggggcg gggctgtccc ggggcggagc caggtagcgt cgggccctca gggcagagcc
38401 gggtgcgacc tggcgctgac ccggtttctg cattctccct ccgcagctgg cagagcggtt
38461 ttccgacgcg gcgctggtct cgatgtctgt gcgggagcta aaccggcagc tgcggggctg
38521 cgggcgcgac gaggcgctgc ggctgaagca gaggcgccgc acgctgaaga accgcggcta
38581 cgcgcaggcc tgtcgctcca agcggctgca gcagcggcgc gggctggagg ccgagcgcgc
38641 ccgcctggcc gcccagctgg acgcgctgcg ggccgaggtg gcccgcctgg cccgggagcg
38701 cgatctctac aaggctcgct gtgaccggct aacctcgagc ggccccgggt ccggggaccc
38761 ctcccacctc ttcctctgag ccgttcagag caccttgtgg tgtagtgggg gctgggtggg
38821 gtggctccgc ccaggaggcg gctgcacggt tctctgcatc gttaccagag cgccttctgg
38881 tcctagccac gccctgtatg accgcgcaaa tatccccaaa gcttttgggt cctcaagtca
38941 tgcccgaatt tagatgctgg tcattttctg gagaggggtc ccctcccctt acgaacacag
39001 aaacccagcc cacatgacta gcacgctgag ctctgcaggg accagtgcca ggcactgggg
39061 ggtggaagtg tggtgacaca gtgaatggga ggtggaggag ggttgcagct cccacctcag
39121 tttagttttt aattcagggt tttcaacctg taacacatta aagctgtaat tagcaatgag
39181 gctgtatttt cattctgaag cttgtaacct ccccatttta gcactacaga attttcaaga
39241 tttcaatatc caacaactag atagattagg acctctatcc gagatgcttt ttccctgccc 39301 aaccctgtgg ccttcagggc tcagagcagc aaaggcctga agagtgagct ctgggggttg
39361 ttggtgtggg ttgggagaga gctgtgtgca gaagtctgga aacctgggtc ctagtcccag
39421 ctcttccatg ggatccccct gtcaccctga gcaaatcagt tgcttcctgg acttgtgtta
39481 cttcatctaa ttctcatgtg gattggacga cttctgctcc ctttccagtt ctggcatctc
39541 cccagtatgg aagtcccggt ggtctcccca agaagtcccc aagacaatct cgccaaaggc
39601 acctcctatc ctgctgcagt ttcccagctg cagcctaggc aggggatgca cagcccaggc
39661 gaggaagcct ggcttctctg tgagcacata cgtgggtcct cggcagctcc ctccaggctg
39721 tctgggcctc cagacctgca cagggtgctc ctgccacctc ccacctctct gagggctgag
39781 gtgagacttc tcctgggatg acaatttgct gagagagtgc agcttttgtg aattaaactt
39841 gaagtccagg cagaattcta atgcaataag ctaaatgttc ttgcaattta agaagtgttc
39901 attctttatc cctgcttcag gctactgttt gtgtgtctgt gtgtgggaga gggagagaga
39961 gggagagaga gagagagcaa gaaaaaggga agtccccacc tggagctggg tggcacatct
40021 gttatggaga gccaatggaa atggggtgga ggggcaggca ttggaacaga tggatcctcc
40081 ccctctcacc accaccacca ccaaactcag aagcctcagt ggcccagctc ggcctgtcag
40141 tggctatcca ggtctcacag tttccatggt aacccagtcc tccagttcag caggctaagg
40201 ggagggcaga tggggcctct gggcagagca caggcgttgt gctgggagca gccgcctcac
40261 gagttactgt catctgtcct ctaccggaca taataaatgg gagaagcttt cgggcatggg
40321 ggaagaggct cccatatgtc cctcttcctt tctaccccct ctctccaccc cctccccagc
40381 tgtctcttct cttcccatca cagttcttgc tccctctttc ccctcctcta tcccagctca
40441 tccctcctcc gcttaggagc ctgcaatggg agtcctctcc tccatcgctc tcagaatttc
40501 tctcgtctcc tctcccttcc ccaccattgg ccactggcca tcctctctgg ctctggattc
40561 tctctctgag gggctcacag aacctttagc ttctctttct tcatcccctt ccacactcat
40621 tgttgaaggg agaggatggg gcagggaggg tccttccggg agcccagctc tttttctctc
40681 actctaaatt tcacctgtgt ctatccttgc ctgccctgga gctgtaattc agacccacta
40741 cttttcttgt tcacttttct cacctgcatg gcacacaaag acagacagaa ccatccatag
40801 acacctgagc acacaactag gccacatata cagtaccata cctgggtctc aaaatgatac
40861 tcctgggtta cctgagtata cttaaaaaaa caaagttgca cactgtggtg attaagagta
40921 gtgctttagg tggggcgcag tggttcctgc ctgtaatccc aacactttgg gaggccaagg
40981 aggaagtttg agaccagcct gggcaacata gcgagaaccc tgtcactaca aaaaaataaa
41041 ataaaataaa ttcagatgta atggcatgca cctggagtcc cacctaccca ggaggctaag
41101 gtggaaggat aacttgagcc caggagttcg gggatgcagt gagccataat cgtgccactg
41161 cattccagcc tgggtggcag agtgagaccc tgtttcaagt tgcagttcta ccagtttttt
41221 gaccatgggt gggttaaaat caagcctcac ttgattgtca gaaaaatggt gaaaataatg
41281 gtaaccacct actgagaata aatgcattta aataagcact tagcataaag ttgacacatg
41341 ctacgtaatg atatttgctg ttgttgctga tgtgattgtt aagtgtgtga atctgtgtgt
41401 tcatgcactg cacatccctg agtccatgag tgtgacccat taaggccatg aacagacaca
41461 cacattgaca cacccgggaa accagactgt ataggcctta gatgctccac tatgttccca
41521 attcactagc agacctgctg ccctccttca gtatccccca gcacctgctc ttggcccgcc
41581 ccacagctgt gtgggggctg gggttcagct cctgggggac tcagcagggc ctctctggag
41641 acagctataa gaaagcttca gcctgccctc ctgacagccc gtaattatcc tcctatctcc
41701 tgtaattatt ctccatggtg cctagacccc ctggggttgg gaggtgaggg agggggetcc
41761 tcagatccca ctggcacata gctggggtaa gactgcagag acagcagcct gcctggggag
41821 ctctgtctca gattttgaaa ggtgctggtc ctcatttctt atggtgtgtg tgggggtgct 41881 gcaggctgcc cagtgggcat ctgaggcatg atggttagag gctgaggtgc taggagcagt
41941 tctctttatt aatggctaga aagtcaggat cacccaagga agtcactgag gggccacagc
42001 attgaagggt atggggtttg gagagatagg agcaggaccc accactcacg tccagaaccc
42061 agggggeaea cctggtccaa gaggtggagg cattggtcac tggagtcacg agggtcagga
42121 caggcacctg ggagggggtg ggagagtcat aagcactctc ttctacacta cacccagcct
42181 agttgggctc taccaagccc cactttgcac cccctgtgtc cactcctttg gaagccccag
42241 gactcactga gaggctgagg gagtgtcggt ccggagggag gcagtcacgg gctagggctg
42301 ggagtcgtag ccagtgtgca gggcctggga gccccagggc tgatgccctg gctggcgtag
42361 tactccacca cctgccgtgg cacctcagcc aggacacact tggcgagtgc agagggggca
42421 gcctagggtg gggacagtga tgtggttagg ggtgagagga agagtagggg aggcagggtc
42481 atctgaggga gaagtggggc ttcagggtgg ccagctgggc tcccgcgtcc ttagcaggac
42541 atcaaatggt ggaagacgaa ggtcagattt ggggggatga gaagctgagg agtccttcag
42601 ccggaagggg cccgggggac tcacatcctt gaagtctcgg aagggcacga actggacaat
42661 gtctcgggct gcaggcaccc ctcgggggca gcgcaagggg ccgtcgtcgc catccagcag
42721 ccgcatgtca gagaagtcag cattgcccac gcctacgatg atgatggaca tgggcaggcg
42781 ggaggcacgc acgatagcag tgcgagtctc agccatgtcg ctcaccacac cgtcagtgag
42841 caccagcagc accgagtact tctgagggca agcagagagg gtggaagggt tggctttgtg
42901 tgcaagggcg ttgacaccgt ttccaccaag gtgcagaccc tggccctggc accacttaaa
42961 gacacatggg acagctcctg tttgcccgcc atgtcttcct accgtggctt ggccggtgct
43021 ctgctcccgc tgggccggct cagccacacg gttgatgatg ggggccacat tggtggggcc
43081 gtagagctgg atctggggca ggcaacgacg gtaggaggcg atgacccctg agatctctgt
43141 gagtgaagag aagttgtgaa gctggcagaa atgagcaggg ccccctcctg acactcctta
43201 aagcaaggaa atgcttccag gtctgaggac tgccctcccc tcgagttcct tcattaagca
43261 gtgggagagt tggatggtcc cttggcaggg agagttgggt gcagatgctg ggcctcggcc
43321 ctggaagcc
SEQ ID NO: 2 has the following nucleobase sequence (5’-3’)
1 cgccgggggt gtgtacgcca tgagggggag gaagccgaga agcacctccc actgaagccg 61 gcggtaaccg ccccacgcga gaccacccac cagccaggag cggtcgcagg acccgcagcg 121 gcgcgaggcc ttgtttacac cgactgccgc cactgcgttg gccaaccgct cctccgtcac 181 gcgcttcgct cgtcacgcat ctcgcggctt cctggccggc gggctgcaaa cgtcacacga 241 cggccccgcc cccttggcca gccaactgga cagcggagca cgatgattga taggccaata 301 agatatgcaa atgatctcct taccttattg gttggaggcc tcaggaccac agatgacctc 361 agagagctgg ccctttaaga atgccctttg ggctctgtgc ccacagcccc ctggagctga 421 gcagaggcac caggccctgc tccatggagc cttcagtctc ctgggaagct gtgcctgtct 481 ggctctggca ctgaccacat cctctcggcc atttctgaag tgcactcctc ccagcccagc 541 tccagaatgg ccctgccccc cagccccctg gccatggaat atgtcaatga ctttgacttg 601 atgaagtttg aggtaaagcg ggaaccctct gagggccgac ctggcccccc tacagcctca 661 ctgggctcca caccttacag ctcagtgcct ccttcaccca ccttcagtga accaggcatg 721 gtgggggcaa ccgagggcac ccggccaggc ctggaggagc tgtactggct ggctaccctg 781 cagcagcagc tgggggctgg ggaggcattg gggctgagtc ctgaagaggc catggagctg 841 ctgcagggtc agggcccagt ccctgttgat gggccccatg gctactaccc agggagccca 901 gaggagacag gagcccagca cgtccagctg gcagagcggt tttccgacgc ggcgctggtc 961 tcgatgtctg tgcgggagct aaaccggcag ctgcggggct gcgggcgcga cgaggcgctg
1021 cggctgaagc agaggcgccg cacgctgaag aaccgcggct acgcgcaggc ctgtcgctcc
1081 aagcggctgc agcagcggcg cgggctggag gccgagcgcg cccgcctggc cgcccagctg
1141 gacgcgctgc gggccgaggt ggcccgcctg gcccgggagc gcgatctcta caaggctcgc
1201 tgtgaccggc taacctcgag cggccccggg tccggggacc cctcccacct cttcctctga
1261 gccgttcaga gcaccttgtg gtgtagtggg ggctgggtgg ggtggctccg cccaggaggc
1321 ggctgcacgg ttctctgcat cgttaccaga gcgccttctg gtcctagcca cgccctgtat
1381 gaccgcgcaa atatccccaa agcttttggg tcctcaagtc atgcccgaat ttagatgctg
1441 gtcattttct ggagaggggt cccctcccct tacgaacaca gaaacccagc ccacatgact
1501 agcacgctga gctctgcagg gaccagtgcc aggcactggg gggtggaagt gtggtgacac
1561 agtgaatggg aggtggagga gggttgcagc tcccacctca gtttagtttt taattcaggg
1621 ttttcaacct gtaacacatt aaagctgtaa ttagcaatga ggctgtattt tcattctgaa
1681 gcttgtaacc tccccatttt agcactacag aattttcaag atttcaatat ccaacaacta
1741 gatagattag gacctctatc cgagatgctt tttccctgcc caaccctgtg gccttcaggg
1801 ctcagagcag caaaggcctg aagagtgagc tctgggggtt gttggtgtgg gttgggagag
1861 agctgtgtgc agaagtctgg aaacctgggt cctagtccca gctcttccat gggatccccc
1921 tgtcaccctg agcaaatcag ttgcttcctg gacttgtgtt acttcatcta attctcatgt
1981 ggattggacg acttctgctc cctttccagt tctggcatct ccccagtatg gaagtcccgg
2041 tggtctcccc aagaagtccc caagacaatc tcgccaaagg cacctcctat cctgctgcag
2101 tttcccagct gcagcctagg caggggatgc acagcccagg cgaggaagcc tggcttctct
2161 gtgagcacat acgtgggtcc tcggcagctc cctccaggct gtctgggcct ccagacctgc
2221 acagggtgct cctgccacct cccacctctc tgagggctga ggtgagactt ctcctgggat
2281 gacaatttgc tgagagagtg cagcttttgt gaattaaact tgaagtccag gcagaattct
2341 aatgcaataa gctaaatgtt cttgcaattt aagaagtgtt cattctttat ccctgcttca
2401 ggctactgtt tgtgtgtctg tgtgtgggag agggagagag agggagagag agagagagca
2461 agaaaaaggg aagtccccac ctggagctgg gtggcacatc tgttatggag agccaatgga
2521 aatggggtgg aggggeagge attggaacag atggatcctc cccctctcac caccaccacc
2581 accaaactca gaagcctcag tggcccagct cggcctgtca gtggctatcc aggtctcaca
2641 gtttccatgg taacccagtc ctccagttca gcaggctaag gggagggcag atggggcctc
2701 tgggcagagc acaggcgttg tgctgggagc agccgcctca cgagttactg tcatctgtcc
2761 tctaccggac ataataaatg ggagaagctt tcgggcatgg gggaagaggc tcccatatgt
2821 ccctcttcct ttctaccccc tctctccacc ccctccccag ctgtctcttc tcttcccatc
2881 acagttcttg ctccctcttt cccctcctct atcccagctc atccctcctc cgcttaggag
2941 cctgcaatgg gagtcctctc ctccatcgct ctcagaattt ctctcgtctc ctctcccttc
3001 cccaccattg gccactggcc atcctctctg gctctggatt ctctctctga ggggctcaca
3061 gaacctttag cttctctttc ttcatcccct tccacactca ttgttgaagg gagaggatgg
3121 ggcagggagg gtccttccgg gagcccagct ctttttctct cactctaaat ttcacctgtg
3181 tctatccttg cctgccctgg agctgtaatt cagacccact acttttcttg ttcacttttc
3241 tcacctgcat ggcacacaaa gacagacaga accatccata gacacctgag cacacaacta
3301 ggccacatat acagtaccat acctgggtct caaaatgata ctcctgggtt acctgagtat
3361 acttaaaaaa acaaagttgc acactgtggt gattaagagt agtgctttag gtggggcgca
3421 gtggttcctg cctgtaatcc caacactttg ggaggccaag gaggaagttt gagaccagcc
3481 tgggcaacat agcgagaacc ctgtcactac aaaaaaataa aataaaataa attcagatgt 3541 aatggcatgc acctggagtc ccacctaccc aggaggctaa ggtggaagga taacttgagc 3601 ccaggagttc ggggatgcag tgagccataa tcgtgccact gcattccagc ctgggtggca 3661 gagtgagacc ctgtttcaag ttgcagttct accagttttt tgaccatggg tgggttaaaa 3721 tcaagcctca cttgattgtc agaaaaatgg tgaaaataat ggtaaccacc tactgagaat 3781 aaatgcattt aaataagcac ttagcataaa
SEQ ID NO: 3 has the following nucleobase sequence (5’-3’)
1 cgccgggggt gtgtacgcca tgagggggag gaagccgaga agcacctccc actgaagccg
61 gcggtaaccg ccccacgcga gaccacccac cagccaggag cggtcgcagg acccgcagcg
121 gcgcgaggcc ttgtttacac cgactgccgc cactgcgttg gccaaccgct cctccgtcac
181 gcgcttcgct cgtcacgcat ctcgcggctt cctggccggc gggctgcaaa cgtcacacga
241 cggccccgcc cccttggcca gccaactgga cagcggagca cgatgattga taggtgcact
301 cctcccagcc cagctccaga atggccctgc cccccagccc cctggccatg gaatatgtca
361 atgactttga cttgatgaag tttgaggtaa agcgggaacc ctctgagggc cgacctggcc
421 cccctacagc ctcactgggc tccacacctt acagctcagt gcctccttca cccaccttca
481 gtgaaccagg catggtgggg gcaaccgagg gcacccggcc aggcctggag gagctgtact
541 ggctggctac cctgcagcag cagctggggg ctggggaggc attggggctg agtcctgaag
601 aggccatgga gctgctgcag ggtcagggcc cagtccctgt tgatgggccc catggctact
661 acccagggag cccagaggag acaggagccc agcacgtcca gctggcagag cggttttccg
721 acgcggcgct ggtctcgatg tctgtgcggg agctaaaccg gcagctgcgg ggctgcgggc
781 gcgacgaggc gctgcggctg aagcagaggc gccgcacgct gaagaaccgc ggctacgcgc
841 aggcctgtcg ctccaagcgg ctgcagcagc ggcgcgggct ggaggccgag cgcgcccgcc
901 tggccgccca gctggacgcg ctgcgggccg aggtggcccg cctggcccgg gagcgcgatc
961 tctacaaggc tcgctgtgac cggctaacct cgagcggccc cgggtccggg gacccctccc
1021 acctcttcct ctgagccgtt cagagcacct tgtggtgtag tgggggctgg gtggggtggc
1081 tccgcccagg aggcggctgc acggttctct gcatcgttac cagagcgcct tctggtccta
1141 gccacgccct gtatgaccgc gcaaatatcc ccaaagcttt tgggtcctca agtcatgccc
1201 gaatttagat gctggtcatt ttctggagag gggtcccctc cccttacgaa cacagaaacc
1261 cagcccacat gactagcacg ctgagctctg cagggaccag tgccaggcac tggggggtgg
1321 aagtgtggtg acacagtgaa tgggaggtgg aggagggttg cagctcccac ctcagtttag
1381 tttttaattc agggttttca acctgtaaca cattaaagct gtaattagca atgaggctgt
1441 attttcattc tgaagcttgt aacctcccca ttttagcact acagaatttt caagatttca
1501 atatccaaca actagataga ttaggacctc tatccgagat gctttttccc tgcccaaccc
1561 tgtggccttc agggctcaga gcagcaaagg cctgaagagt gagctctggg ggttgttggt
1621 gtgggttggg agagagctgt gtgcagaagt ctggaaacct gggtcctagt cccagctctt
1681 ccatgggatc cccctgtcac cctgagcaaa tcagttgctt cctggacttg tgttacttca
1741 tctaattctc atgtggattg gacgacttct gctccctttc cagttctggc atctccccag
1801 tatggaagtc ccggtggtct ccccaagaag tccccaagac aatctcgcca aaggcacctc
1861 ctatcctgct gcagtttccc agctgcagcc taggcagggg atgcacagcc caggcgagga
1921 agcctggctt ctctgtgagc acatacgtgg gtcctcggca gctccctcca ggctgtctgg
1981 gcctccagac ctgcacaggg tgctcctgcc acctcccacc tctctgaggg ctgaggtgag
2041 acttctcctg ggatgacaat ttgctgagag agtgcagctt ttgtgaatta aacttgaagt
2101 ccaggcagaa ttctaatgca ataagctaaa tgttcttgca atttaagaag tgttcattct 2161 ttatccctgc ttcaggctac tgtttgtgtg tctgtgtgtg ggagagggag agagagggag
2221 agagagagag agcaagaaaa agggaagtcc ccacctggag ctgggtggca catctgttat
2281 ggagagccaa tggaaatggg gtggaggggc aggcattgga acagatggat cctccccctc
2341 tcaccaccac caccaccaaa ctcagaagcc tcagtggccc agctcggcct gtcagtggct
2401 atccaggtct cacagtttcc atggtaaccc agtcctccag ttcagcaggc taaggggagg
2461 gcagatgggg cctctgggca gagcacaggc gttgtgctgg gagcagccgc ctcacgagtt
2521 actgtcatct gtcctctacc ggacataata aatgggagaa gctttcgggc atgggggaag
2581 aggctcccat atgtccctct tcctttctac cccctctctc caccccctcc ccagctgtct
2641 cttctcttcc catcacagtt cttgctccct ctttcccctc ctctatccca gctcatccct
2701 cctccgctta ggagcctgca atgggagtcc tctcctccat cgctctcaga atttctctcg
2761 tctcctctcc cttccccacc attggccact ggccatcctc tctggctctg gattctctct
2821 ctgaggggct cacagaacct ttagcttctc tttcttcatc cccttccaca ctcattgttg
2881 aagggagagg atggggcagg gagggtcctt ccgggagccc agctcttttt ctctcactct
2941 aaatttcacc tgtgtctatc cttgcctgcc ctggagctgt aattcagacc cactactttt
3001 cttgttcact tttctcacct gcatggcaca caaagacaga cagaaccatc catagacacc
3061 tgagcacaca actaggccac atatacagta ccatacctgg gtctcaaaat gatactcctg
3121 ggttacctga gtatacttaa aaaaacaaag ttgcacactg tggtgattaa gagtagtgct
3181 ttaggtgggg cgcagtggtt cctgcctgta atcccaacac tttgggaggc caaggaggaa
3241 gtttgagacc agcctgggca acatagcgag aaccctgtca ctacaaaaaa ataaaataaa
3301 ataaattcag atgtaatggc atgcacctgg agtcccacct acccaggagg ctaaggtgga
3361 aggataactt gagcccagga gttcggggat gcagtgagcc ataatcgtgc cactgcattc
3421 cagcctgggt ggcagagtga gaccctgttt caagttgcag ttctaccagt tttttgacca
3481 tgggtgggtt aaaatcaagc ctcacttgat tgtcagaaaa atggtgaaaa taatggtaac
3541 cacctactga gaataaatgc atttaaataa gcacttagca taaa
SEQ ID NO: 4 has the following nucleobase sequence (5’-3’)
1 gcctcagaga ataaatagga gactaagagg acaggcagac aaacaggacg agcctggggg 61 ctccaggcct ggacggagga agaagccagc tatacggggt ttctccatgc tggccaagct 121 ggtctccaac tcctgacctc gtgatccgcc tgccttggcc tcccaaagtg ctggaattta 181 caggcgtgag ccaccacgcc cggcctggtc attctttctc tccacaatcc aatgaggaaa 241 ctcatctgcc cacccaacta ccatcataaa gtcctcaggt gatttctcaa gctatacctc 301 cattgggaca tctctctcca acctgagacc actggatatc acccacaatg ctatatagca 361 cctcaaactc agcatatcta tgatgggtgt ctgctcagca tccactcgcc ttttctggtg 421 cactcctccc agcccagctc cagaatggcc ctgcccccca gccccctggc catggaatat 481 gtcaatgact ttgacttgat gaagtttgag gtaaagcggg aaccctctga gggccgacct 541 ggccccccta cagcctcact gggctccaca ccttacagct cagtgcctcc ttcacccacc 601 ttcagtgaac caggcatggt gggggcaacc gagggcaccc ggccaggcct ggaggagctg 661 tactggctgg ctaccctgca gcagcagctg ggggctgggg aggcattggg gctgagtcct 721 gaagaggcca tggagctgct gcagggtcag ggcccagtcc ctgttgatgg gccccatggc 781 tactacccag ggagcccaga ggagacagga gcccagcacg tccagctggc agagcggttt 841 tccgacgcgg cgctggtctc gatgtctgtg cgggagctaa accggcagct gcggggctgc 901 gggcgcgacg aggcgctgcg gctgaagcag aggcgccgca cgctgaagaa ccgcggctac 961 gcgcaggcct gtcgctccaa gcggctgcag cagcggcgcg ggctggaggc cgagcgcgcc 1021 cgcctggccg cccagctgga cgcgctgcgg gccgaggtgg cccgcctggc ccgggagcgc
1081 gatctctaca aggctcgctg tgaccggcta acctcgagcg gccccgggtc cggggacccc
1141 tcccacctct tcctctgagc cgttcagagc accttgtggt gtagtggggg ctgggtgggg
1201 tggctccgcc caggaggcgg ctgcacggtt ctctgcatcg ttaccagagc gccttctggt
1261 cctagccacg ccctgtatga ccgcgcaaat atccccaaag cttttgggtc ctcaagtcat
1321 gcccgaattt agatgctggt cattttctgg agaggggtcc cctcccctta cgaacacaga
1381 aacccagccc acatgactag cacgctgagc tctgcaggga ccagtgccag gcactggggg
1441 gtggaagtgt ggtgacacag tgaatgggag gtggaggagg gttgcagctc ccacctcagt
1501 ttagttttta attcagggtt ttcaacctgt aacacattaa agctgtaatt agcaatgagg
1561 ctgtattttc attctgaagc ttgtaacctc cccattttag cactacagaa ttttcaagat
1621 ttcaatatcc aacaactaga tagattagga cctctatccg agatgctttt tccctgccca
1681 accctgtggc cttcagggct cagagcagca aaggcctgaa gagtgagctc tgggggttgt
1741 tggtgtgggt tgggagagag ctgtgtgcag aagtctggaa acctgggtcc tagtcccagc
1801 tcttccatgg gatccccctg tcaccctgag caaatcagtt gcttcctgga cttgtgttac
1861 ttcatctaat tctcatgtgg attggacgac ttctgctccc tttccagttc tggcatctcc
1921 ccagtatgga agtcccggtg gtctccccaa gaagtcccca agacaatctc gccaaaggca
1981 cctcctatcc tgctgcagtt tcccagctgc agcctaggca ggggatgcac agcccaggcg
2041 aggaagcctg gcttctctgt gagcacatac gtgggtcctc ggcagctccc tccaggctgt
2101 ctgggcctcc agacctgcac agggtgctcc tgccacctcc cacctctctg agggctgagg
2161 tgagacttct cctgggatga caatttgctg agagagtgca gcttttgtga attaaacttg
2221 aagtccaggc agaattctaa tgcaataagc taaatgttct tgcaatttaa gaagtgttca
2281 ttctttatcc ctgcttcagg ctactgtttg tgtgtctgtg tgtgggagag ggagagagag
2341 ggagagagag agagagcaag aaaaagggaa gtccccacct ggagctgggt ggcacatctg
2401 ttatggagag ccaatggaaa tggggtggag gggcaggcat tggaacagat ggatcctccc
2461 cctctcacca ccaccaccac caaactcaga agcctcagtg gcccagctcg gcctgtcagt
2521 ggctatccag gtctcacagt ttccatggta acccagtcct ccagttcagc aggctaaggg
2581 gagggcagat ggggcctctg ggcagagcac aggcgttgtg ctgggagcag ccgcctcacg
2641 agttactgtc atctgtcctc taccggacat aataaatggg agaagctttc gggcatgggg
2701 gaagaggctc ccatatgtcc ctcttccttt ctaccccctc tctccacccc ctccccagct
2761 gtctcttctc ttcccatcac agttcttgct ccctctttcc cctcctctat cccagctcat
2821 ccctcctccg cttaggagcc tgcaatggga gtcctctcct ccatcgctct cagaatttct
2881 ctcgtctcct ctcccttccc caccattggc cactggccat cctctctggc tctggattct
2941 ctctctgagg ggctcacaga acctttagct tctctttctt catccccttc cacactcatt
3001 gttgaaggga gaggatgggg cagggagggt ccttccggga gcccagctct ttttctctca
3061 ctctaaattt cacctgtgtc tatccttgcc tgccctggag ctgtaattca gacccactac
3121 ttttcttgtt cacttttctc acctgcatgg cacacaaaga cagacagaac catccataga
3181 cacctgagca cacaactagg ccacatatac agtaccatac ctgggtctca aaatgatact
3241 cctgggttac ctgagtatac ttaaaaaaac aaagttgcac actgtggtga ttaagagtag
3301 tgctttaggt ggggcgcagt ggttcctgcc tgtaatccca acactttggg aggccaagga
3361 ggaagtttga gaccagcctg ggcaacatag cgagaaccct gtcactacaa aaaaataaaa
3421 taaaataaat tcagatgtaa tggcatgcac ctggagtccc acctacccag gaggctaagg
3481 tggaaggata acttgagccc aggagttcgg ggatgcagtg agccataatc gtgccactgc
3541 attccagcct gggtggcaga gtgagaccct gtttcaagtt gcagttctac cagttttttg 3601 accatgggtg ggttaaaatc aagcctcact tgattgtcag aaaaatggtg aaaataatgg 3661 taaccaccta ctgagaataa atgcatttaa ataagcactt agcataaa
SEQ ID NO: 5 has the following nucleobase sequence (5’-3’)
1 cgccgggggt gtgtacgcca tgagggggag gaagccgaga agcacctccc actgaagccg
61 gcggtaaccg ccccacgcga gaccacccac cagccaggag cggtcgcagg acccgcagcg
121 gcgcgaggcc ttgtttacac cgactgccgc cactgcgttg gccaaccgct cctccgtcac
181 gcgcttcgct cgtcacgcat ctcgcggctt cctggccggc gggctgcaaa cgtcacacga
241 cggccccgcc cccttggcca gccaactgga cagcggagca cgatgattga taggtgcact
301 cctcccagcc cagctccaga atggccctgc cccccagccc cctggccatg gaatatgtca
361 atgactttga cttgatgaag tttgagctgg cagagcggtt ttccgacgcg gcgctggtct
421 cgatgtctgt gcgggagcta aaccggcagc tgcggggctg cgggcgcgac gaggcgctgc
481 ggctgaagca gaggcgccgc acgctgaaga accgcggcta cgcgcaggcc tgtcgctcca
541 agcggctgca gcagcggcgc gggctggagg ccgagcgcgc ccgcctggcc gcccagctgg
601 acgcgctgcg ggccgaggtg gcccgcctgg cccgggagcg cgatctctac aaggctcgct
661 gtgaccggct aacctcgagc ggccccgggt ccggggaccc ctcccacctc ttcctctgag
721 ccgttcagag caccttgtgg tgtagtgggg gctgggtggg gtggctccgc ccaggaggcg
781 gctgcacggt tctctgcatc gttaccagag cgccttctgg tcctagccac gccctgtatg
841 accgcgcaaa tatccccaaa gcttttgggt cctcaagtca tgcccgaatt tagatgctgg
901 tcattttctg gagaggggtc ccctcccctt acgaacacag aaacccagcc cacatgacta
961 gcacgctgag ctctgcaggg accagtgcca ggcactgggg ggtggaagtg tggtgacaca
1021 gtgaatggga ggtggaggag ggttgcagct cccacctcag tttagttttt aattcagggt
1081 tttcaacctg taacacatta aagctgtaat tagcaatgag gctgtatttt cattctgaag
1141 cttgtaacct ccccatttta gcactacaga attttcaaga tttcaatatc caacaactag
1201 atagattagg acctctatcc gagatgcttt ttccctgccc aaccctgtgg ccttcagggc
1261 tcagagcagc aaaggcctga agagtgagct ctgggggttg ttggtgtggg ttgggagaga
1321 gctgtgtgca gaagtctgga aacctgggtc ctagtcccag ctcttccatg ggatccccct
1381 gtcaccctga gcaaatcagt tgcttcctgg acttgtgtta cttcatctaa ttctcatgtg
1441 gattggacga cttctgctcc ctttccagtt ctggcatctc cccagtatgg aagtcccggt
1501 ggtctcccca agaagtcccc aagacaatct cgccaaaggc acctcctatc ctgctgcagt
1561 ttcccagctg cagcctaggc aggggatgca cagcccaggc gaggaagcct ggcttctctg
1621 tgagcacata cgtgggtcct cggcagctcc ctccaggctg tctgggcctc cagacctgca
1681 cagggtgctc ctgccacctc ccacctctct gagggctgag gtgagacttc tcctgggatg
1741 acaatttgct gagagagtgc agcttttgtg aattaaactt gaagtccagg cagaattcta
1801 atgcaataag ctaaatgttc ttgcaattta agaagtgttc attctttatc cctgcttcag
1861 gctactgttt gtgtgtctgt gtgtgggaga gggagagaga gggagagaga gagagagcaa
1921 gaaaaaggga agtccccacc tggagctggg tggcacatct gttatggaga gccaatggaa
1981 atggggtgga ggggcaggca ttggaacaga tggatcctcc ccctctcacc accaccacca
2041 ccaaactcag aagcctcagt ggcccagctc ggcctgtcag tggctatcca ggtctcacag
2101 tttccatggt aacccagtcc tccagttcag caggctaagg ggagggcaga tggggcctct
2161 gggcagagca caggcgttgt gctgggagca gccgcctcac gagttactgt catctgtcct
2221 ctaccggaca taataaatgg gagaagcttt cgggcatggg ggaagaggct cccatatgtc
2281 cctcttcctt tctaccccct ctctccaccc cctccccagc tgtctcttct cttcccatca 2341 cagttcttgc tccctctttc ccctcctcta tcccagctca tccctcctcc gcttaggagc
2401 ctgcaatggg agtcctctcc tccatcgctc tcagaatttc tctcgtctcc tctcccttcc
2461 ccaccattgg ccactggcca tcctctctgg ctctggattc tctctctgag gggctcacag
2521 aacctttagc ttctctttct tcatcccctt ccacactcat tgttgaaggg agaggatggg
2581 gcagggaggg tccttccggg agcccagctc tttttctctc actctaaatt tcacctgtgt
2641 ctatccttgc ctgccctgga gctgtaattc agacccacta cttttcttgt tcacttttct
2701 cacctgcatg gcacacaaag acagacagaa ccatccatag acacctgagc acacaactag
2761 gccacatata cagtaccata cctgggtctc aaaatgatac tcctgggtta cctgagtata
2821 cttaaaaaaa caaagttgca cactgtggtg attaagagta gtgctttagg tggggcgcag
2881 tggttcctgc ctgtaatccc aacactttgg gaggccaagg aggaagtttg agaccagcct
2941 gggcaacata gcgagaaccc tgtcactaca aaaaaataaa ataaaataaa ttcagatgta
3001 atggcatgca cctggagtcc cacctaccca ggaggctaag gtggaaggat aacttgagcc
3061 caggagttcg gggatgcagt gagccataat cgtgccactg cattccagcc tgggtggcag
3121 agtgagaccc tgtttcaagt tgcagttcta ccagtttttt gaccatgggt gggttaaaat
3181 caagcctcac ttgattgtca gaaaaatggt gaaaataatg gtaaccacct actgagaata
3241 aatgcattta aataagcact tagcataaa
The term “nucleobase,” as used herein, represents a nitrogen-containing heterocyclic ring found at the T position of the ribofuranose/2’-deoxyribofuranose of a nucleoside. Nucleobases are unmodified or modified. As used herein, “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C), and uracil (U). Modified nucleobases include 5-substituted pyrimidines, 6-azapyrimidines, alkyl or alkynyl substituted pyrimidines, alkyl substituted purines, and N-2, N-6 and 0-6 substituted purines, as well as synthetic and natural nucleobases, e.g., 5-methylcytosine, 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-alkyl (e.g., 6-methyl) adenine and guanine, 2-alkyl (e.g., 2-propyl) adenine and guanine, 2-thiouracil, 2- thiothymine, 2-thiocytosine, 5-halouracil, 5-halocytosine, 5-propynyl uracil, 5-propynyl cytosine, 5- trifluoromethyl uracil, 5-trifluoromethyl cytosine, 7-methyl guanine, 7-methyl adenine, 8-azaguanine, 8- azaadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine, 3-deazaadenine. Certain nucleobases are particularly useful for increasing the binding affinity of nucleic acids, e g., 5-substituted pyrimidines; 6- azapyrimidines; N2-, N6-, and/or 06-substituted purines. Nucleic acid duplex stability can be enhanced using, e.g., 5-methylcytosine. Non-limiting examples of nucleobases include: 2-aminopropyladenine, 5- hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-N-methylguanine, 6-N- methyladenine, 2-propyladenine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-propynyl ( — CºC — CH3) uracil, 5-propynylcytosine, 6-azouracil, 6-azocytosine, 6-azothymine, 5-ribosyluracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl, 8-aza and other 8-substituted purines, 5-halo, particularly 5-bromo, 5-trifluoromethyl, 5-halouracil, and 5-halocytosine, 7-methylguanine, 7- methyladenine, 2-F-adenine, 2-aminoadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine, 3- deazaadenine, 6-N-benzoyladenine, 2-N-isobutyrylguanine, 4-N-benzoylcytosine, 4-N-benzoyluracil, 5- methyl 4-N-benzoylcytosine, 5-methyl 4-N-benzoyluracil, universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases. Further modified nucleobases include tricyclic pyrimidines, such as 1 ,3-diazaphenoxazine-2-one, 1 ,3-diazaphenothiazine-2-one and 9-(2- aminoethoxy)-1 ,3-diazaphenoxazine-2-one (G-clamp). Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example, 7-deazaadenine, 7- deazaguanine, 2-aminopyridine, or 2-pyridone. Further nucleobases include those disclosed in Merigan et al., U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, Kroschwitz, J. I., Ed., John Wiley & Sons, 1990, 858-859; Englisch et al., Angewandte Chemie, International Edition, 1991 , 30, 613; Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, Crooke, S. T. and Lebleu, B., Eds., CRC Press, 1993, 273-288; and those disclosed in Chapters 6 and 15, Antisense Drug Technology, Crooke S. T., Ed., CRC Press, 2008, 163-166 and 442- 443.
The term “nucleoside,” as used herein, represents sugar-nucleobase compounds and groups known in the art, as well as modified or unmodified 2’-deoxyribofuranose-nucleobase compounds and groups known in the art. The sugar may be ribofuranose. The sugar may be modified or unmodified.
An unmodified ribofuranose-nucleobase is ribofuranose having an anomeric carbon bond to an unmodified nucleobase. Unmodified ribofuranose-nucleobases are adenosine, cytidine, guanosine, and uridine. Unmodified 2’-deoxyribofuranose-nucleobase compounds are 2’-deoxyadenosine, 2’- deoxycytidine, 2’-deoxyguanosine, and thymidine. The modified compounds and groups include one or more modifications selected from the group consisting of nucleobase modifications and sugar modifications described herein. A nucleobase modification is a replacement of an unmodified nucleobase with a modified nucleobase. A sugar modification may be, e.g., a 2’-substitution, locking, carbocyclization, or unlocking. A 2’-substitution is a replacement of 2’-hydroxyl in ribofuranose with 2’- fluoro, 2’-methoxy, or 2’-(2-methoxy)ethoxy. Alternatively, a 2’-substitution may be a 2’-(ara) substitution, which corresponds to the following structure:
Figure imgf000037_0001
where B is a nucleobase, and R is a 2’-(ara) substituent (e.g., fluoro). 2’-(ara) substituents are known in the art and can be same as other 2’-substituents described herein. In some embodiments, 2’-(ara) substituent is a 2’-(ara)-F substituent (R is fluoro). A locking modification is an incorporation of a bridge between 4’-carbon atom and 2’-carbon atom of ribofuranose. Nucleosides having a locking modification are known in the art as bridged nucleic acids, e.g., locked nucleic acids (LNA), ethylene-bridged nucleic acids (ENA), and cEt nucleic acids. The bridged nucleic acids are typically used as affinity enhancing nucleosides.
The term “nucleotide,” as used herein, represents a nucleoside bonded to an internucleoside linkage or a monovalent group of the following structure -X1-P(X2)(R1)2, where X1 is O, S, or NH, and X2 is absent, =0, or =S, and each R1 is independently -OH, -N(R2)2, or-0-CH2CH2CN, where each R2 is independently an optionally substituted alkyl, or both R2 groups, together with the nitrogen atom to which they are attached, combine to form an optionally substituted heterocyclyl.
The term “oligonucleotide,” as used herein, represents a structure containing 10 or more contiguous nucleosides covalently bound together by internucleoside linkages. An oligonucleotide includes a 5’ end and a 3’ end. The 5’ end of an oligonucleotide may be, e.g., hydroxyl, a hydrophobic moiety, 5’ cap, phosphate, diphosphate, triphosphate, phosphorothioate, diphosphorothioate, triphosphorothioate, phosphorodithioate, diphosphrodithioate, triphosphorodithioate, phosphonate, phosphoramidate, a cell penetrating peptide, an endosomal escape moiety, or a neutral organic polymer. The 3’ end of an oligonucleotide may be, e.g., hydroxyl, a hydrophobic moiety, phosphate, diphosphate, triphosphate, phosphorothioate, diphosphorothioate, triphosphorothioate, phosphorodithioate, disphorodithioate, triphosphorodithioate, phosphonate, phosphoramidate, a cell penetrating peptide, an endosomal escape moiety, or a neutral organic polymer (e.g., polyethylene glycol). An oligonucleotide having a 5’-hydroxyl or 5’-phosphate has an unmodified 5’ terminus. An oligonucleotide having a 5’ terminus other than 5’-hydroxyl or 5’-phosphate has a modified 5’ terminus. An oligonucleotide having a 3’-hydroxyl or 3’-phosphate has an unmodified 3’ terminus. An oligonucleotide having a 3’ terminus other than 3’-hydroxyl or 3’-phosphate has a modified 3’ terminus. Oligonucleotides can be in double- or single- stranded form. Double-stranded oligonucleotide molecules can optionally include one or more single- stranded segments (e.g., overhangs).
All references to “oligonucleotides” include free base forms and also to salts and/or solvates thereof, including pharmaceutically acceptable salts and/or solvates thereof, unless otherwise indicated
The term “oxo,” as used herein, represents a divalent oxygen atom (e.g., the structure of oxo may be shown as =0).
The term “pharmaceutically acceptable,” as used herein, refers to those compounds, materials, compositions, and/or dosage forms, which are suitable for contact with the tissues of an individual (e.g., a human), without excessive toxicity, irritation, allergic response and other problem complications commensurate with a reasonable benefit/risk ratio.
The term “pharmaceutical composition,” as used herein, represents a composition containing an oligonucleotide described herein, formulated with a pharmaceutically acceptable excipient, and manufactured or sold with the approval of a governmental regulatory agency as part of a therapeutic regimen for the treatment of disease in a subject.
The term “pharmaceutically acceptable salt,” as used herein, means any pharmaceutically acceptable salt of a compound (e.g., an oligonucleotide) disclosed herein. Pharmaceutically acceptable salts of any of the compounds described herein may include those that are within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and animals without undue toxicity, irritation, allergic response and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, pharmaceutically acceptable salts are described in: Berge et al., J. Pharmaceutical Sciences 66:1-19, 1977 and in Pharmaceutical Salts: Properties, Selection, and Use, (Eds. P.H. Stahl and C.G. Wermuth), Wiley-VCH, 2008. The salts can be prepared in situ during the final isolation and purification of the compounds described herein or separately by reacting a free base group with a suitable acid. Representative acid addition salts include acetate, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, glucoheptonate, glycerophosphate, hemisulfate, heptonate, hexanoate, hydrobromide, hydrochloride, 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, toluenesulfonate, undecanoate, valerate salts, and the like. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like, as well as nontoxic ammonium, quaternary ammonium, and amine cations, including, but not limited to ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, ethylamine, and the like.
The term “protecting group,” as used herein, represents a group intended to protect a functional group (e.g., a hydroxyl, an amino, or a carbonyl) from participating in one or more undesirable reactions during chemical synthesis. The term “O-protecting group,” as used herein, represents a group intended to protect an oxygen containing (e.g., phenol, hydroxyl or carbonyl) group from participating in one or more undesirable reactions during chemical synthesis. The term “/V-protecting group,” as used herein, represents a group intended to protect a nitrogen containing (e.g., an amino or hydrazine) group from participating in one or more undesirable reactions during chemical synthesis. Commonly used O- and N- protecting groups are disclosed in Greene, “Protective Groups in Organic Synthesis,” 3rd Edition (John Wiley & Sons, New York, 1999), which is incorporated herein by reference. Exemplary O- and N- protecting groups include alkanoyl, aryloyl, or carbamyl groups such as formyl, acetyl, propionyl, pivaloyl, t-butylacetyl, 2-chloroacetyl, 2-bromoacetyl, trifluoroacetyl, trichloroacetyl, phthalyl, o-nitrophenoxyacetyl, ochlorobutyryl, benzoyl, 4-chlorobenzoyl, 4-bromobenzoyl, f-butyldimethylsilyl, tri-/so- propylsilyloxymethyl, 4,4'-dimethoxytrityl, isobutyryl, phenoxyacetyl, 4-isopropylpehenoxyacetyl, dimethylformamidino, and 4-nitrobenzoyl.
Exemplary O-protecting groups for protecting carbonyl containing groups include, but are not limited to: acetals, acylals, 1 ,3-dithianes, 1 ,3-dioxanes, 1 ,3-dioxolanes, and 1 ,3-dithiolanes.
Other O-protecting groups include, but are not limited to: substituted alkyl, aryl, and arylalkyl ethers (e.g., trityl; methylthiomethyl; methoxy methyl; benzyloxymethyl; siloxymethyl; 2,2,2,- trichloroethoxymethyl; tetrahydropyranyl; tetrahydrofuranyl; ethoxyethyl; 1-[2-(trimethylsilyl)ethoxy]ethyl; 2-trimethylsilylethyl; t-butyl ether; p-chlorophenyl, p-methoxyphenyl, p-nitrophenyl, benzyl, p- methoxybenzyl, and nitrobenzyl); silyl ethers (e.g., trimethylsilyl; triethylsilyl; triisopropylsilyl; dimethylisopropylsilyl; t-butyldimethylsilyl; t-butyldiphenylsilyl; tribenzylsilyl; triphenylsilyl; and diphenymethylsilyl); carbonates (e.g., methyl, methoxymethyl, 9-fluorenylmethyl; ethyl; 2,2,2- trichloroethyl; 2-(trimethylsilyl)ethyl; vinyl, allyl, nitrophenyl; benzyl; methoxybenzyl; 3,4-dimethoxybenzyl; and nitrobenzyl).
Other /V-protecting groups include, but are not limited to, chiral auxiliaries such as protected or unprotected D, L or D, L-amino acids such as alanine, leucine, phenylalanine, and the like; sulfonyl- containing groups such as benzenesulfonyl, p-toluenesulfonyl, and the like; carbamate forming groups such as benzyloxycarbonyl, p-chlorobenzyloxycarbonyl, p-methoxybenzyloxycarbonyl, p- nitrobenzyloxycarbonyl, 2-nitrobenzyloxycarbonyl, p-bromobenzyloxycarbonyl, 3,4- dimethoxybenzyloxycarbonyl, 3,5-dimethoxybenzyl oxycarbonyl, 2,4-dimethoxybenzyloxycarbonyl, 4-methoxybenzyloxycarbonyl, 2-nitro-4,5-dimethoxybenzyloxycarbonyl,
3.4.5-trimethoxybenzyloxycarbonyl, 1 -(p-biphenylyl)-l -methylethoxycarbonyl, a,a-dimethyl-
3.5-dimethoxybenzyloxycarbonyl, benzhydroxy carbonyl, t-butyloxycarbonyl, diisopropylmethoxycarbonyl, isopropoxycarbonyl, ethoxycarbonyl, methoxycarbonyl, allyloxycarbonyl, 2,2,2-trichloroethoxycarbonyl, phenoxycarbonyl, 4-nitrophenoxy carbonyl, fluorenyl-9-methoxycarbonyl, cyclopentyloxycarbonyl, adamantyloxycarbonyl, cyclohexyloxycarbonyl, phenylthiocarbonyl, and the like, arylalkyl groups such as benzyl, triphenylmethyl, benzyloxymethyl, and the like and silyl groups such as trimethylsilyl, and the like. The term “skipmer,” as used herein, refers a gapmer, in which alternating internucleoside linkages are phosphate phosphodiester linkages and intervening internucleoside linkages are modified internucleoside linkages.
The term “stereochemically enriched,” as used herein, refers to a local stereochemical preference for one enantiomer of the recited group over the opposite enantiomer of the same group. Thus, an oligonucleotide containing a stereochemically enriched internucleoside linkage is an oligonucleotide, in which a phosphorothioate of predetermined stereochemistry is present in preference to a phosphorothioate of stereochemistry that is opposite of the predetermined stereochemistry. This preference can be expressed numerically using a diastereomeric ratio for the phosphorothioate of the predetermined stereochemistry. The diastereomeric ratio for the phosphorothioate of the predetermined stereochemistry is the molar ratio of the diastereomers having the identified phosphorothioate with the predetermined stereochemistry relative to the diastereomers having the identified phosphorothioate with the stereochemistry that is opposite of the predetermined stereochemistry. The diastereomeric ratio for the phosphorothioate of the predetermined stereochemistry may be greater than or equal to 1.1 (e.g., greater than or equal to 4, greater than or equal to 9, greater than or equal to 19, or greater than or equal to 39).
The term “subject,” as used herein, represents a human or non-human animal (e.g., a mammal) that is suffering from, or is at risk of, disease, disorder, or condition, as determined by a qualified professional (e.g., a doctor or a nurse practitioner) with or without known in the art laboratory test(s) of sample(s) from the subject. Non-limiting examples of diseases, disorders, and conditions include retinitis pigmentosa (e.g., Rho P23H-associated retinitis pigmentosa, PDE6-associated retinitis pigmentosa, MERTK-associated retinitis pigmentosa, BBS1 -associated retinitis pigmentosa, Rho-associated retinitis pigmentosa, MRFP-associated retinitis pigmentosa, RLBP1 -associated retinitis pigmentosa, RP1- associated retinitis pigmentosa, RPGR-X-linked retinitis pigmentosa, NR2E3-associated retinitis pigmentosa, or SPATA7-associated retinitis pigmentosa), Stargardt disease (e.g., ABCA4-associated Stargardt disease), cone-rod dystrophy (e.g., AIPL1 -associated cone-rod dystrophy or RGRIP1- associated cone-rod dystrophy), Leber congenital amaurosis (e.g., AIPL1 -associated Leber congenital amaurosis, GUCY2D-associated Leber congenital amaurosis, RD3-associated Leber congenital amaurosis, RPE65-associated Leber congenital amaurosis, or SPATA7-associated Leber congenital amaurosis), Bardet Biedl syndrome (e.g., BBS1 -associated Bardet Biedl syndrome), macular dystrophy (e.g., BEST1 -associated macular dystrophy), dry macular degeneration, geographic atrophy, atrophic age-related macular degeneration (AMD), advanced dry AMD, retinal dystrophy (e.g., CEP290- associated retinal dystrophy, CDH3-associated retinal dystrophy, CRB1 -associated retinal dystrophy, or PRPH2-associated retinal dystrophy), choroideremia (e.g., CHM-associated choroideremia), Usher syndrome type 1 (e.g., MY07A-associated Usher syndrome), retinoschisis (e.g., RS1-X-linked retinoschisis), Leber hereditary optic neuropathy (e.g., ND4-associated Lebe’rs hereditary optic neuropathy), and achromatopsia (e.g., CNGA3-associated achromatopsia or CNGB3-associated achromatopsia). Non-limiting examples of diseases, disorders, and conditions include ocular diseases, disorders, and conditions associated with a dysfunction of ABCA4, AIPL1 , BBS1 , BEST1 , CEP290,
CDH3, CHM, CNGA3, CNGB3, CRB1 , GUCY2D, MERTK, MRFP, MY07A, ND4, NR2E3, PDE6, PRPH2, RD3, RHO, RLBP1 , RP1 , RPE65, RPGR, RPGRIP1 , RS1 , or SPATA7 gene. A “sugar” or “sugar moiety,” includes naturally occurring sugars having a furanose ring or a structure that is capable of replacing the furanose ring of a nucleoside. Sugars included in the nucleosides of the invention may be non-furanose (or 4'-substituted furanose) rings or ring systems or open systems. Such structures include simple changes relative to the natural furanose ring (e.g., a six- membered ring). Alternative sugars may also include sugar surrogates wherein the furanose ring has been replaced with another ring system such as, e.g., a morpholino or hexitol ring system. Non-limiting examples of sugar moieties useful that may be included in the oligonucleotides of the invention include b- D-ribose, p-D-2'-deoxyribose, substituted sugars (e.g., 2', 5', and bis substituted sugars), 4'-S-sugars (e.g., 4'-S-ribose, 4'-S-2'-deoxyribose, and 4'-S-2'-substituted ribose), bicyclic sugar moieties (e.g., the 2'- O — CH2-4' or2'-0 — (CH2)2-4' bridged ribose derived bicyclic sugars) and sugar surrogates (when the ribose ring has been replaced with a morpholino or a hexitol ring system).
The term “tailmer,” as used herein, refers to an oligonucleotide having an RNase H recruiting region (gap) flanked by a 3’ wing including at least one affinity enhancing nucleoside (e.g., 1 , 2, 3, or 4 affinity enhancing nucleosides).
“Treatment” and "treating," as used herein, refer to the medical management of a subject with the intent to improve, ameliorate, stabilize, or prevent a disease, disorder, or condition (e.g., retinitis pigmentosa). This term includes active treatment (treatment directed to improve retinitis pigmentosa); causal treatment (treatment directed to the cause of associated retinitis pigmentosa); palliative treatment (treatment designed for the relief of symptoms of retinitis pigmentosa); preventative treatment (treatment directed to minimizing or partially or completely inhibiting the development of retinitis pigmentosa); and supportive treatment (treatment employed to supplement another therapy).
The term “unimer,” as used herein, refers to an oligonucleotide having a pattern of structural features characterized by all of the internucleoside linkages having the same structural feature. By same structural feature is meant the same stereochemistry at the internucleoside linkage phosphorus or the same modification at the linkage phosphorus. In instances, where the “same structural feature” refers to the stereochemical configuration of the internucleoside linkages, the unimer is a “stereounimer.”
Enumeration of positions within oligonucleotides and nucleic acids, as used herein and unless specified otherwise, starts with the 5’-terminal nucleoside as 1 and proceeds in the 3’-direction.
The compounds described herein, unless otherwise noted, encompass isotopically enriched compounds (e.g., deuterated compounds), tautomers, and all stereoisomers and conformers (e.g. enantiomers, diastereomers, E/Z isomers, atropisomers, etc.), as well as racemates thereof and mixtures of different proportions of enantiomers or diastereomers, or mixtures of any of the foregoing forms as well as salts (e.g., pharmaceutically acceptable salts).
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows a bar graph quantifying the effect of an Nrl targeting ASO upon rod and cone gene expression. The data were normalized to negative scrambled control. Treatment with the Nrl-targeting ASO decreased Nrl and rod gene expression without decreasing cone gene expression or the expression of Otx2. Otx2 is an upstream transcription factor expressed in both rod and cone photoreceptors.
FIGS. 2A-2J show dosage curves quantifying the mRNA inhibitory effect of the indicated Nrl- targeting oligonucleotides in HEK293 cells expressing high levels of the target homo sapiens (GenBank ID: BC012395.1). The data were normalized to GFP and/or actin and are represented as a percentage of a negative scrambled control. Treatment with Nrl-targeting oligonucleotides resulted in a dose-dependent decrease in Nrl gene expression, relative to the vehicle (DPBS) control. FIG. 2A shows dosage curves for chemically modified version of SEQ ID NO: 7. FIG. 2B shows dosage curves for chemically modified version of SEQ ID NO: 9. FIG. 2C shows dosage curves for chemically modified version of SEQ ID NO:
10. FIG. 2D shows dosage curves for chemically modified version of SEQ ID NO: 11. FIG. 2E shows dosage curves for chemically modified version of SEQ ID NO: 12. FIG. 2F shows dosage curves for chemically modified version of SEQ ID NO: 13. FIG. 2G shows dosage curves for chemically modified version of SEQ ID NO: 14. FIG. 2H shows dosage curves for chemically modified version of SEQ ID NO: 15. FIG. 2I shows dosage curves for chemically modified version of SEQ ID NO: 16. FIG. 2J shows dosage curves for chemically modified version of SEQ ID NO: 17. (See Table 1 , below, regarding chemically modified versions of the sequences described herein.)
FIGS. 3A-3E show dosage curves quantifying the mRNA inhibitory effect of the indicated Nrl- targeting oligonucleotides in HEK293 cells expressing high levels of the target Macaca fascicularis (GenBank ID: XM_015453620.1). The data were normalized to GFP and/or actin and are represented as a percentage of a vehicle (DPBS) control. Treatment with Nrl-targeting oligonucleotides resulted in a dose-dependent decrease in Nrl gene expression, relative to the negative scrambled control. FIG. 3A shows dosage curves for chemically modified version of SEQ ID NO: 9. FIG. 3B shows dosage curves for chemically modified version of SEQ ID NO: 10. FIG. 3C shows dosage curves for chemically modified version of SEQ ID NO: 14. FIG. 3D shows dosage curves for chemically modified version of SEQ ID NO: 15. FIG. 3E shows dosage curves for chemically modified version of SEQ ID NO: 16. (See Table l , below, regarding chemically modified versions of the sequences described herein.)
DETAILED DESCRIPTION
In general, the invention provides oligonucleotides that may be used in the treatment of ocular degeneration disorders (e.g., a retinal degeneration disorder; e.g., retinitis pigmentosa (e.g., Rho P23H- associated retinitis pigmentosa, PDE6-associated retinitis pigmentosa, MERTK-associated retinitis pigmentosa, BBS1 -associated retinitis pigmentosa, Rho-associated retinitis pigmentosa, MRFP- associated retinitis pigmentosa, RLBP1 -associated retinitis pigmentosa, RP1 -associated retinitis pigmentosa, RPGR-X-linked retinitis pigmentosa, NR2E3-associated retinitis pigmentosa, or SPATA7- associated retinitis pigmentosa), Stargardt disease (e.g., ABCA4-associated Stargardt disease), cone-rod dystrophy (e.g., AIPL1 -associated cone-rod dystrophy or RGRIP1 -associated cone-rod dystrophy), Leber congenital amaurosis (e.g., AIPL1 -associated Leber congenital amaurosis, GUCY2D-associated Leber congenital amaurosis, RD3-associated Leber congenital amaurosis, RPE65-associated Leber congenital amaurosis, or SPATA7-associated Leber congenital amaurosis), Bardet Biedl syndrome (e.g., BBS1- associated Bardet Biedl syndrome), macular dystrophy (e.g., BEST1 -associated macular dystrophy), dry macular degeneration, geographic atrophy, atrophic age-related macular degeneration (AMD), advanced dry AMD, retinal dystrophy (e.g., CEP290-associated retinal dystrophy, CDH3-associated retinal dystrophy, CRB1 -associated retinal dystrophy, or PRPH2-associated retinal dystrophy), choroideremia (e.g., CHM-associated choroideremia), Usher syndrome type 1 (e.g., MY07A-associated Usher syndrome), retinoschisis (e.g., RS1-X-linked retinoschisis), Leber hereditary optic neuropathy (e.g., ND4- associated Lebe’rs hereditary optic neuropathy), and achromatopsia (e.g., CNGA3-associated achromatopsia or CNGB3-associated achromatopsia)). Without wishing to be bound by theory, reduction of the expression of NRL in photoreceptor cells can prevent loss of photoreceptor cells, thereby treating an ocular degeneration disorder (e.g., a retinal degeneration disorder).
The invention provides an antisense approach to reducing expression of NRL in cells as described herein. Typically, an antisense activity may be observed directly or indirectly. Observation or detection of an antisense activity involves observation or detection of a change in an amount of a target nucleic acid or protein encoded by such target nucleic acid, a change in the ratio of splice variants of a nucleic acid or protein, and/or a phenotypic change in a cell or animal.
I. Antisense
In one approach, the invention provides a single-stranded oligonucleotide having a nucleobase sequence with at least 6 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 or a modified version thereof (e.g., SEQ ID NOs: 18-29). In some embodiments, the single-stranded oligonucleotide may be delivered to a patient as a double stranded oligonucleotide, where the oligonucleotide of the invention is hybridized to another oligonucleotide (e.g., an oligonucleotide having a total of 12 to 30 nucleotides).
An antisense oligonucleotide of the invention (e.g., a single-stranded oligonucleotide of the invention) includes a nucleobase sequence having at least 6 (e.g., at least 7, 8, 9, 10, 11 , 12, 13, 14, 15, or 16) contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 or a modified version thereof (e.g., SEQ ID NOs: 18-29). For example, the oligonucleotide may include a total of at least 7 (e.g., at least 8, at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, or at least 16) interlinked nucleotides, e.g., the oligonucleotide may include a total a total of 25 interlinked nucleotides or fewer (e.g., 20 interlinked nucleotides or fewer, 19 interlinked nucleotides or fewer, 18 interlinked nucleotides or fewer, 17 interlinked nucleotides or fewer, 16 interlinked nucleotides or fewer, 15 interlinked nucleotides or fewer, 14 interlinked nucleotides or fewer,
13 interlinked nucleotides or fewer, 12 interlinked nucleotides or fewer, or 11 interlinked nucleotides or fewer). Thus, the single-stranded oligonucleotide may include, e.g., at least 8 (e.g., at least 9, at least 10, at least 11 , at least 12, at least 13, at least 14, at least 15, or at least 16) contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 or a modified version thereof (e.g., SEQ ID NOs: 18-29).
An antisense oligonucleotide of the invention (e.g., a single-stranded oligonucleotide of the invention) may be a gapmer, headmer, ortailmer. Gapmers are oligonucleotides having an RNase H recruiting region (gap) flanked by a 5' wing and 3' wing, each of the wings including at least one affinity enhancing nucleoside (e.g., 1, 2, 3, or 4 affinity enhancing nucleosides). Headmers are oligonucleotides having an RNase H recruiting region (gap) flanked by a 5’ wing including at least one affinity enhancing nucleoside (e.g., 1 , 2, 3, or 4 affinity enhancing nucleosides). Tailmers are oligonucleotides having an RNase H recruiting region (gap) flanked by a 3’ wing including at least one affinity enhancing nucleoside (e.g., 1 , 2, 3, or 4 affinity enhancing nucleosides). In certain embodiments, each wing includes 1-5 nucleosides. In some embodiments, each nucleoside of each wing is a modified nucleoside. In particular embodiments, the gap includes 7-12 nucleosides. Typically, the gap region includes a plurality of contiguous, unmodified deoxyribonucleotides. For example, all nucleotides in the gap region are unmodified deoxyribonucleotides (2’-deoxyribofuranose-based nucleotides). Preferably, an antisense oligonucleotide of the invention (e.g., a single-stranded oligonucleotide of the invention) is a gapmerwith 30-38% of the nucleotides being LNAs.
The 5'-wing may consists of, e.g., 1 to 8 nucleosides. The 5'-wing may consist of, e.g., 1 to 7 nucleosides. The 5'-wing may consist of, e.g., 1 to 6 linked nucleosides. The 5'-wing may consist of, e.g., 1 to 5 linked nucleosides. The 5'-wing may consist of, e.g., 2 to 5 linked nucleosides. The 5'-wing may consist of, e.g., 3 to 5 linked nucleosides. The 5'-wing may consist of, e.g., 4 or 5 linked nucleosides. The 5'-wing may consist of, e.g., 1 to 4 linked nucleosides. The 5'-wing may consist of, e.g., 1 to 3 linked nucleosides. The 5'-wing may consist of, e.g., 1 or 2 linked nucleosides. The 5'-wing may consist of, e.g., 2 to 4 linked nucleosides. The 5'-wing may consist of, e.g., 2 or 3 linked nucleosides. The 5'-wing may consist of, e.g., 3 or 4 linked nucleosides. The 5'-wing may consist of, e.g., 1 nucleoside. The 5'-wing may consist of, e.g., 2 linked nucleosides. The 5'-wing may consist of, e.g., 3 linked nucleosides. The 5'-wing may consist of, e.g., 4 linked nucleosides. The 5'-wing may consist of, e.g., 5 linked nucleosides. The 5'-wing may consist of, e.g., 6 linked nucleosides.
The 3’-wing may consists of, e.g., 1 to 8 nucleosides. The 3’-wing may consist of, e.g., 1 to 7 nucleosides. The 3’-wing may consist of, e.g., 1 to 6 linked nucleosides. The 3’-wing may consist of, e.g., 1 to 5 linked nucleosides. The 3’-wing may consist of, e.g., 2 to 5 linked nucleosides. The 3’-wing may consist of, e.g., 3 to 5 linked nucleosides. The 3’-wing may consist of, e.g., 4 or 5 linked nucleosides. The 3’-wing may consist of, e.g., 1 to 4 linked nucleosides. The 3’-wing may consist of, e.g., 1 to 3 linked nucleosides. The 3’-wing may consist of, e.g., 1 or 2 linked nucleosides. The 3’-wing may consist of, e.g., 2 to 4 linked nucleosides. The 3’-wing may consist of, e.g., 2 or 3 linked nucleosides. The 3’-wing may consist of, e.g., 3 or 4 linked nucleosides. The 3’-wing may consist of, e.g., 1 nucleoside. The 3’-wing may consist of, e.g., 2 linked nucleosides. The 3’-wing may consist of, e.g., 3 linked nucleosides. The 3’-wing may consist of, e.g., 4 linked nucleosides. The 3’-wing may consist of, e.g., 5 linked nucleosides. The 3’-wing may consist of, e.g., 6 linked nucleosides.
The 5'-wing may include, e.g., at least one bridged nucleoside. The 5'-wing may include, e.g., at least two bridged nucleosides. The 5'-wing may include, e.g., at least three bridged nucleosides. The 5'- wing may include, e.g., at least four bridged nucleosides. The 5'-wing may include, e.g., at least one constrained ethyl (cEt) nucleoside. The 5'-wing may include, e.g., at least one LNA nucleoside. Each nucleoside of the 5'-wing may be, e.g., a bridged nucleoside. Each nucleoside of the 5'-wing may be, e.g., a constrained ethyl (cEt) nucleoside. Each nucleoside of the 5'-wing may be, e.g., a LNA nucleoside.
The 3’-wing may include, e.g., at least one bridged nucleoside. The 3’-wing may include, e.g., at least two bridged nucleosides. The 3’-wing may include, e.g., at least three bridged nucleosides. The 3’- wing may include, e.g., at least four bridged nucleosides. The 3’-wing may include, e.g., at least one constrained ethyl (cEt) nucleoside. The 3’-wing may include, e.g., at least one LNA nucleoside. Each nucleoside of the 3’-wing may be, e.g., a bridged nucleoside. Each nucleoside of the 3’-wing may be, e.g., a constrained ethyl (cEt) nucleoside. Each nucleoside of the 3’-wing may be, e.g., a LNA nucleoside.
The 5'-wing may include, e.g., at least one non-bicyclic modified nucleoside. The 5'-wing may include, e.g., at least one 2'-substituted nucleoside. The 5'-wing may include, e.g., at least one 2'-MOE nucleoside. The 5'-wing may include, e.g., at least one 2'-OMe nucleoside. Each nucleoside of the 5'- wing may be, e.g., a non-bicyclic modified nucleoside. Each nucleoside of the 5'-wing may be, e.g., a 2'- substituted nucleoside. Each nucleoside of the 5'-wing may be, e.g., a 2'-MOE nucleoside. Each nucleoside of the 5'-wing may be, e.g., a 2'-OMe nucleoside.
The 3’-wing may include, e.g., at least one non-bicyclic modified nucleoside. The 3’-wing may include, e.g., at least one 2'-substituted nucleoside. The 3’-wing may include, e.g., at least one 2'-MOE nucleoside. The 3’-wing may include, e.g., at least one 2'-OMe nucleoside. Each nucleoside of the 3’- wing may be, e.g., a non-bicyclic modified nucleoside. Each nucleoside of the 3’-wing may be, e.g., a 2'- substituted nucleoside. Each nucleoside of the 3’-wing may be, e.g., a 2'-MOE nucleoside. Each nucleoside of the 3’-wing may be, e.g., a 2'-OMe nucleoside.
The gap may consist of, e.g., 6 to 20 linked nucleosides. The gap may consist of, e.g., 6 to 15 linked nucleosides. The gap may consist of, e.g., 6 to 12 linked nucleosides. The gap may consist of, e.g., 6 to 10 linked nucleosides. The gap may consist of, e.g., 6 to 9 linked nucleosides. The gap may consist of, e.g., 6 to 8 linked nucleosides. The gap may consist of, e.g., 6 or 7 linked nucleosides. The gap may consist of, e.g., 7 to 10 linked nucleosides. The gap may consist of, e.g., 7 to 9 linked nucleosides. The gap may consist of, e.g., 7 or 8 linked nucleosides. The gap may consist of, e.g., 8 to 10 linked nucleosides. The gap may consist of, e.g., 8 or 9 linked nucleosides. The gap may consist of, e.g., 6 linked nucleosides. The gap may consist of, e.g., 7 linked nucleosides. The gap may consist of, e.g., 8 linked nucleosides. The gap may consist of, e.g., 9 linked nucleosides. The gap may consist of, e.g., 10 linked nucleosides. The gap may consist of, e.g., 11 linked nucleosides. The gap may consist of, e.g., 12 linked nucleosides.
Each nucleoside of the gap may be, e.g., a 2'-deoxynucleoside. The gap may include, e.g., one or more modified nucleosides. Each nucleoside of the gap may be, e.g., a 2'-deoxynucleoside or may be, e.g., a modified nucleoside that is “DNA-like.” In such embodiments, “DNA-like” means that the nucleoside has similar characteristics to DNA, such that a duplex including the gapmer and an RNA molecule is capable of activating RNase H. For example, under certain conditions, 2'-(ara)-F may support RNase H activation, and thus is DNA-like. In certain embodiments, one or more nucleosides of the gap is not a 2'-deoxynucleoside and is not DNA-like. In certain such embodiments, the gapmer nonetheless supports RNase H activation (e.g., by virtue of the number or placement of the non-DNA nucleosides).
In certain embodiments, gaps include a stretch of unmodified 2'-deoxynucleoside interrupted by one or more modified nucleosides, thus resulting in three sub-regions (two stretches of one or more 2'- deoxynucleosides and a stretch of one or more interrupting modified nucleosides). In certain embodiments, no stretch of unmodified 2'-deoxynucleosides is longer than 5, 6, or 7 nucleosides. In certain embodiments, such short stretches is achieved by using short gap regions. In certain embodiments, short stretches are achieved by interrupting a longer gap region.
The gap may include, e.g., one or more modified nucleosides. The gap may include, e.g., one or more modified nucleosides selected from among cEt, FHNA, LNA, and 2-thio-thymidine. The gap may include, e.g., one modified nucleoside. The gap may include, e.g., a 5'-substituted sugar moiety selected from the group consisting of 5'-Me and 5'-(R)-Me. The gap may include, e.g., two modified nucleosides. The gap may include, e.g., three modified nucleosides. The gap may include, e.g., four modified nucleosides. The gap may include, e.g., two or more modified nucleosides and each modified nucleoside is the same. The gap may include, e.g., two or more modified nucleosides and each modified nucleoside is different. The gap may include, e.g., one or more modified internucleoside linkages. The gap may include, e.g., one or more methyl phosphonate linkages. In certain embodiments the gap may include, e.g., two or more modified internucleoside linkages. The gap may include, e.g., one or more modified linkages and one or more modified nucleosides. The gap may include, e.g., one modified linkage and one modified nucleoside. The gap may include, e.g., two modified linkages and two or more modified nucleosides.
An antisense oligonucleotide of the invention (e.g., a single-stranded oligonucleotide of the invention) may include one or more mismatches. For example, the mismatch may be specifically positioned within a gapmer, headmer, ortailmer. The mismatch may be, e.g., at position 1 , 2, 3, 4, 5, 6,
7, or 8 (e.g., at position 1 , 2, 3, or 4) from the 3’-end of the gap region. Alternatively or additionally, the mismatch may be, e.g., at position 9, 8, 7, 6, 5, 4, 3, 2, or 1 (e.g., at position 4, 3, 2, or 1) from the 3'-end of the gap region. In some embodiments, the 5’ wing and/or 3’wing do not include mismatches.
An antisense oligonucleotide of the invention (e.g., a single-stranded oligonucleotide of the invention) may be a morpholino.
An antisense oligonucleotide of the invention (e.g., a single-stranded oligonucleotide of the invention) may be include a total of X to Y interlinked nucleosides, where X represents the fewest number of nucleosides in the range and Y represents the largest number nucleosides in the range. In these embodiments, X and Y are each independently selected from the group consisting of 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, and 50; provided that X<Y. For example, an oligonucleotide of the invention may include a total of 12 to 13, 12 to 14, 12 to 15, 12 to 16, 12 to 17, 12 to 18, 12 to 19, 12 to 20, 12 to 21 , 12 to 22, 12 to 23, 12 to 24, 12 to 25, 12 to 26, 12 to 27, 12 to 28, 12 to 29, 12 to 30, 13 to
14, 13 to 15, 13 to 16, 13 to 17, 13 to 18, 13 to 19, 13 to 20, 13 to 21 , 13 to 22, 13 to 23, 13 to 24, 13 to
25, 13 to 26, 13 to 27, 13 to 28, 13 to 29, 13 to 30, 14 to 15, 14 to 16, 14 to 17, 14 to 18, 14 to 19, 14 to
20, 14 to 21 , 14 to 22, 14 to 23, 14 to 24, 14 to 25, 14 to 26, 14 to 27, 14 to 28, 14 to 29, 14 to 30, 15 to
16, 15 to 17, 15 to 18, 15 to 19, 15 to 20, 15 to 21 , 15 to 22, 15 to 23, 15 to 24, 15 to 25, 15 to 26, 15 to
27, 15 to 28, 15 to 29, 15 to 30, 16 to 17, 16 to 18, 16 to 19, 16 to 20, 16 to 21 , 16 to 22, 16 to 23, 16 to
24, 16 to 25, 16 to 26, 16 to 27, 16 to 28, 16 to 29, 16 to 30, 17 to 18, 17 to 19, 17 to 20, 17 to 21 , 17 to
22, 17 to 23, 17 to 24, 17 to 25, 17 to 26, 17 to 27, 17 to 28, 17 to 29, 17 to 30, 18 to 19, 18 to 20, 18 to
21 , 18 to 22, 18 to 23, 18 to 24, 18 to 25, 18 to 26, 18 to 27, 18 to 28, 18 to 29, 18 to 30, 19 to 20, 19 to
21 , 19 to 22, 19 to 23, 19 to 24, 19 to 25, 19 to 26, 19 to 29, 19 to 28, 19 to 29, 19 to 30, 20 to 21 , 20 to
22, 20 to 23, 20 to 24, 20 to 25, 20 to 26, 20 to 27, 20 to 28, 20 to 29, 20 to 30, 21 to 22, 21 to 23, 21 to
24, 21 to 25, 21 to 26, 21 to 27, 21 to 28, 21 to 29, 21 to 30, 22 to 23, 22 to 24, 22 to 25, 22 to 26, 22 to
27, 22 to 28, 22 to 29, 22 to 30, 23 to 24, 23 to 25, 23 to 26, 23 to 27, 23 to 28, 23 to 29, 23 to 30, 24 to
25, 24 to 26, 24 to 27, 24 to 28, 24 to 29, 24 to 30, 25 to 26, 25 to 27, 25 to 28, 25 to 29, 25 to 30, 26 to
27, 26 to 28, 26 to 29, 26 to 30, 27 to 28, 27 to 29, 27 to 30, 28 to 29, 28 to 30, or 29 to 30 interlinked nucleosides.
In some embodiments, an antisense oligonucleotide of the invention (e.g., a single-stranded oligonucleotide of the invention) includes at least one modified internucleoside linkage. A modified internucleoside linkage may be, e.g., a phosphorothioate internucleoside linkage (e.g., a phosphorothioate diester or phosphorothioate triester).
In some embodiments, an antisense oligonucleotide of the invention (e.g., a single-stranded oligonucleotide of the invention) includes at least one stereochemically enriched phosphorothioate-based internucleoside linkage. In some embodiments, an antisense oligonucleotide of the invention (e.g., a single-stranded oligonucleotide of the invention) includes a pattern of stereochemically enriched phosphorothioate internucleoside linkages described herein (e.g., a 5’-RpSpSp-3’). These patterns may enhance target NRL nucleic acid cleavage by RNase H relative to a stereorandom corresponding oligonucleotide. In some embodiments, inclusion and/or location of particular stereochemically enriched linkages within an oligonucleotide may alter the cleavage pattern of a target nucleic acid, when such an oligonucleotide is utilized for cleaving the nucleic acid. For example, a pattern of internucleoside linkage P-stereogenic centers may increase cleavage efficiency of a target nucleic acid. A pattern of internucleoside linkage P-stereogenic centers may provide new cleavage sites in a target nucleic acid. A pattern of internucleoside linkage P-stereogenic centers may reduce the number of cleavage sites, for example, by blocking certain existing cleavage sites. Moreover, in some embodiments, a pattern of internucleoside linkage P-stereogenic centers may facilitate cleavage at only one site within the target sequence that is complementary to an oligonucleotide utilized for the cleavage. Cleavage efficiency may be increased by selecting a pattern of internucleoside linkage P-stereogenic centers that reduces the number of cleavage sites in a target nucleic acid.
Purity of an oligonucleotide may be expressed as the percentage of oligonucleotide molecules that are of the same oligonucleotide type within an oligonucleotide composition. At least about 10% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 20% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 30% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 40% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 50% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 60% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 70% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 80% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 90% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 92% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 94% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 95% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 96% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 97% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 98% of the oligonucleotides may be, e.g., of the same oligonucleotide type. At least about 99% of the oligonucleotides may be, e.g., of the same oligonucleotide type.
An oligonucleotide may include one or more stereochemically enriched internucleoside linkages. An oligonucleotide may include two or more stereochemically enriched internucleoside linkages. An oligonucleotide may include three or more stereochemically enriched internucleoside linkages. An oligonucleotide may include four or more stereochemically enriched internucleoside linkages. An oligonucleotide may include five or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 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 stereochemically enriched internucleoside linkages. An oligonucleotide may include 5 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 6 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 7 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 8 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 9 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 10 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 11 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 12 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 13 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 14 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 15 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 16 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 17 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 18 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 19 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 20 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 21 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 22 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 23 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 24 or more stereochemically enriched internucleoside linkages. An oligonucleotide may include 25 or more stereochemically enriched internucleoside linkages.
An oligonucleotide may include at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% stereochemically enriched internucleoside linkages. Exemplary such stereochemically enriched internucleoside linkages are described herein. An oligonucleotide may include at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% stereochemically enriched internucleoside linkages in the Sp configuration.
A stereochemically enriched internucleoside linkage may be, e.g., a stereochemically enriched phosphorothioate internucleoside linkage. A provided oligonucleotide comprises at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% stereochemically enriched phosphorothioate internucleoside linkages. All stereochemically enriched linkages may be, e.g., stereochemically enriched phosphorothioate internucleoside linkages. At least 10, 20, 30, 40, 50, 60, 70, 80, or 90% stereochemically enriched phosphorothioate internucleoside linkages have the Sp stereochemical configuration. At least 10% stereochemically enriched phosphorothioate internucleoside linkages have the Sp stereochemical configuration. At least 20% stereochemically enriched phosphorothioate internucleoside linkages have the Sp stereochemical configuration. At least 30% stereochemically enriched phosphorothioate internucleoside linkages have the Sp stereochemical configuration. At least 40% stereochemically enriched phosphorothioate internucleoside linkages have the Sp stereochemical configuration. At least 50% stereochemically enriched phosphorothioate internucleoside linkages have the Sp stereochemical configuration. At least 60% stereochemically enriched phosphorothioate internucleoside linkages have the Sp stereochemical configuration. At least 70% stereochemically enriched phosphorothioate internucleoside linkages have the Sp stereochemical configuration. At least 80% stereochemically enriched phosphorothioate internucleoside linkages have the Sp stereochemical configuration. At least 90% stereochemically enriched phosphorothioate internucleoside linkages have the Sp stereochemical configuration. At least 95% stereochemically enriched phosphorothioate internucleoside linkages have the Sp stereochemical configuration. At least 10, 20, 30, 40, 50, 60, 70, 80, or 90% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. At least 10% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. At least 20% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. At least 30% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. At least 40% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. At least 50% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. At least 60% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. At least 70% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. At least 80% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. At least 90% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. At least 95% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. In some embodiments, less than 10, 20, 30, 40, 50, 60, 70, 80, or 90% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. In some embodiments, less than 10% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. In some embodiments, less than 20% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. In some embodiments, less than 30% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. In some embodiments, less than 40% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. In some embodiments, less than 50% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. In some embodiments, less than 60% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. In some embodiments, less than 70% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. In some embodiments, less than 80% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. In some embodiments, less than 90% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. In some embodiments, less than 95% stereochemically enriched phosphorothioate internucleoside linkages have the Rp stereochemical configuration. An oligonucleotide may have, e.g., only one Rp stereochemically enriched phosphorothioate internucleoside linkages. An oligonucleotide may have, e.g., only one Rp stereochemically enriched phosphorothioate internucleoside linkages, where all internucleoside linkages are stereochemically enriched phosphorothioate internucleoside linkages. A stereochemically enriched phosphorothioate internucleoside linkage may be, e.g., a stereochemically enriched phosphorothioate diester linkage. In some embodiments, each stereochemically enriched phosphorothioate internucleoside linkage is independently a stereochemically enriched phosphorothioate diester linkage. In some embodiments, each internucleoside linkage is independently a stereochemically enriched phosphorothioate diester linkage. In some embodiments, each internucleoside linkage is independently a stereochemically enriched phosphorothioate diester linkage, and only one is Rp.
The gap region may include, e.g., a stereochemically enriched internucleoside linkage. The gap region may include, e.g., stereochemically enriched phosphorothioate internucleoside linkages. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry, where the repeating pattern is (Sp)mRp or Rp(Sp)m, where m is 2, 3, 4, 5, 6, 7 or 8. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry, where the repeating pattern is (Sp)mRp or Rp(Sp)m, where m is 2, 3, 4, 5, 6, 7 or 8. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry, where the repeating pattern is (Sp)mRp, where m is 2, 3, 4, 5, 6, 7 or 8. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry, where the repeating pattern is Rp(Sp)m, where m is 2, 3, 4, 5, 6, 7 or 8. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry, where the repeating pattern is (Sp)mRp or Rp(Sp)m, where m is 2, 3, 4, 5, 6, 7 or 8. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry, where the repeating pattern is a motif including at least 33% of internucleoside linkages with the Sp stereochemical identify. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry, where the repeating pattern is a motif including at least 50% of internucleoside linkages with the Sp stereochemical identify. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry, where the repeating pattern is a motif including at least 66% of internucleoside linkages with the Sp stereochemical identify. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry, where the repeating pattern is a repeating triplet motif selected from RpRpSp and SpSpRp. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry, where the repeating pattern is a repeating RpRpSp. The gap region may have, e.g., a repeating pattern of internucleoside linkage stereochemistry, where the repeating pattern is a repeating SpSpRp.
An oligonucleotide may include a pattern of internucleoside P-stereogenic centers in the gap region including (Sp)mRp or Rp(Sp)m. An oligonucleotide may include a pattern of internucleoside P- stereogenic centers in the gap region including Rp(Sp)m. An oligonucleotide may include a pattern of P- stereogenic centers in the gap region including (Sp)mRp. In some embodiments, m is 2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers in the gap region including RP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers in the gap region including (SP)2RP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers in the gap region including (RP)2RP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers in the gap region including RPSPRP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers in the gap region including SPRPRP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers in the gap region including ( SP)2RP
An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (Sp)mRp or Rp(Sp)m. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including Rp(Sp)m. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (Sp)mRp. In some embodiments, m is 2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including RP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (SP)2RP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (RP)2RP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including RPSPRP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including SPRPRP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (SP)2RP.
In the embodiments of internucleoside P-stereogenic center patterns, m is 2, 3, 4, 5, 6, 7 or 8, unless specified otherwise. In some embodiments of internucleoside P-stereogenic center patterns, m is
3, 4, 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, m is 4, 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, m is 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, m is 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, m is 7 or 8. In some embodiments of internucleoside P- stereogenic center patterns, m is 2. In some embodiments of internucleoside P-stereogenic center patterns, m is 3. In some embodiments of internucleoside P-stereogenic center patterns, m is 4. In some embodiments of internucleoside P-stereogenic center patterns, m is 5. In some embodiments of internucleoside P-stereogenic center patterns, m is 6. In some embodiments of internucleoside P- stereogenic center patterns, m is 7. In some embodiments of internucleoside P-stereogenic center patterns, m is 8.
A repeating pattern may be, e.g., (Sp)m(Rp)n, where n is independently 1 , 2, 3, 4, 5, 6, 7 or 8, and m is independently as described herein. An oligonucleotide may include a pattern of internucleoside P- stereogenic centers including (Sp)m(Rp)n. An oligonucleotide may include a pattern of internucleoside P- stereogenic centers including (Sp)m(Rp)n. A repeating pattern may be, e.g., (Rp)n(Sp)m, where n is independently 1 , 2, 3, 4, 5, 6, 7 or 8, and m is independently as described herein. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (Rp)n(Sp)m. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers in the gap region including (Rp)n(Sp)m. In some embodiments, (Rp)n(Sp)m is (RP)(SP)2. In some embodiments, (Sp)n(Rp)m is (SP)2(RP).
A repeating pattern may be, e.g., (Sp)m(Rp)n(Sp)t, where each of n and t is independently 1 , 2, 3,
4, 5, 6, 7 or 8, and m is as described herein. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (Sp)m(Rp)n(Sp)t. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (Sp)m(Rp)n(Sp)t. A repeating pattern may be, e.g., (Sp)t(Rp)n(Sp)m, where each of n and t is independently 1 , 2, 3, 4, 5, 6, 7 or 8, and m is as described herein. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (Sp)t(Rp)n(Sp)m. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers in the gap region including (Sp)t(Rp)n(Sp)m.
A repeating pattern is (Np)t(Rp)n(Sp)m, where each of n and t is independently 1 , 2, 3, 4, 5, 6, 7 or 8, Np is independently Rp or Sp, and m is as described herein. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (Np)t(Rp)n(Sp)m. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers in the gap region including (Np)t(Rp)n(Sp)m. A repeating pattern may be, e.g., (Np)t(Rp)n(Sp)m, where each of n and t is independently 1 , 2, 3, 4, 5, 6, 7 or 8, Np is independently Rp or Sp, and m is as described herein. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (Np)t(Rp)n(Sp)m. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers in the gap region including (Np)t(Rp)n(Sp)m. In some embodiments, Np is Rp. In some embodiments, Np is Sp. All Np may be, e.g., same. All Np may be, e.g., Sp. At least one Np may be, e.g., different from another Np. In some embodiments, t is 2.
In the embodiments of internucleoside P-stereogenic center patterns, n is 1 , 2, 3, 4, 5, 6, 7 or 8.
In some embodiments of internucleoside P-stereogenic center patterns, n is 2, 3, 4, 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, n is 3, 4, 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, n is 4, 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, n is 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, n is 6, 7 or 8. In some embodiments of internucleoside P- stereogenic center patterns, n is 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, n is 1. In some embodiments of internucleoside P-stereogenic center patterns, n is 2. In some embodiments of internucleoside P-stereogenic center patterns, n is 3. In some embodiments of internucleoside P-stereogenic center patterns, n is 4. In some embodiments of internucleoside P- stereogenic center patterns, n is 5. In some embodiments of internucleoside P-stereogenic center patterns, n is 6. In some embodiments of internucleoside P-stereogenic center patterns, n is 7. In some embodiments of internucleoside P-stereogenic center patterns, n is 8.
In the embodiments of internucleoside P-stereogenic center patterns, t is 1 , 2, 3, 4, 5, 6, 7 or 8.
In some embodiments of internucleoside P-stereogenic center patterns, t is 2, 3, 4, 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, t is 3, 4, 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, t is 4, 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, t is 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, t is 6, 7 or 8. In some embodiments of internucleoside P- stereogenic center patterns, t is 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, t is 1. In some embodiments of internucleoside P-stereogenic center patterns, t is 2. In some embodiments of internucleoside P-stereogenic center patterns, t is 3. In some embodiments of internucleoside P-stereogenic center patterns, t is 4. In some embodiments of internucleoside P- stereogenic center patterns, t is 5. In some embodiments of internucleoside P-stereogenic center patterns, t is 6. In some embodiments of internucleoside P-stereogenic center patterns, t is 7. In some embodiments of internucleoside P-stereogenic center patterns, t is 8.
At least one of m and t may be, e.g., greater than 2. At least one of m and t may be, e.g., greater than 3. At least one of m and t may be, e.g., greater than 4. At least one of m and t may be, e.g., greater than 5. At least one of m and t may be, e.g., greater than 6. At least one of m and t may be, e.g., greater than 7. In some embodiments, each of m and t is greater than 2. In some embodiments, each of m and t is greater than 3. In some embodiments, each of m and t is greater than 4. In some embodiments, each of m and t is greater than 5. In some embodiments, each of m and t is greater than 6. In some embodiments, each of m and t is greater than 7.
In some embodiments of internucleoside P-stereogenic center patterns, n is 1 , and at least one of m and t is greater than 1 . In some embodiments of internucleoside P-stereogenic center patterns, n is 1 and each of m and t is independent greater than 1. In some embodiments of internucleoside P- stereogenic center patterns, m>n and t>n. In some embodiments, (Sp)m(Rp)n(Sp)t is (SP)2RP(SP)2. In some embodiments, (Sp)t(Rp)n(Sp)m is (SP)2RP(SP)2. In some embodiments, (Sp)t(Rp)n(Sp)m is SPRP(SP)2.
In some embodiments, (Np)t(Rp)n(Sp)m is (Np)tRp(Sp)m. In some embodiments, (Np)t(Rp)n(Sp)m is (Np)2Rp(Sp)m. In some embodiments, (Np)t(Rp)n(Sp)m is (Rp)2Rp(Sp)m. In some embodiments, (Np)t(Rp)n(Sp)m is (Sp)2Rp(Sp)m. In some embodiments, (Np)t(Rp)n(Sp)m is RpSpRp(Sp)m. In some embodiments, (Np)t(Rp)n(Sp)m is SpRpRp(Sp)m.
In some embodiments, (Sp)t(Rp)n(Sp)m is SpRpSpSp. In some embodiments, (Sp)t(Rp)n(Sp)m is (SP)2RP(SP)2. In some embodiments, (Sp)t(Rp)n(Sp)m is (SP)3RP(SP)3. In some embodiments, (Sp)t(Rp)n(Sp)m is (SP)4RP(SP)4. In some embodiments, (Sp)t(Rp)n(Sp)m is (Sp)tRp(Sp)5. In some embodiments, (Sp)t(Rp)n(Sp)m is SpRp(Sp)s. In some embodiments, (Sp)t(Rp)n(Sp)m is (SP)2RP(SP)5. In some embodiments, (Sp)t(Rp)n(Sp)m is (SP)3RP(SP)5. In some embodiments, (Sp)t(Rp)n(Sp)m is (SP)4RP(SP)5. In some embodiments, (Sp)t(Rp)n(Sp)m is (SP)5RP(SP)5.
In some embodiments, (Sp)m(Rp)n(Sp)t is (SP)2RP(SP)2. In some embodiments, (Sp)m(Rp)n(Sp)t is (SP)3RP(SP)3. In some embodiments, (Sp)m(Rp)n(Sp)t is (SP)4RP(SP)4. In some embodiments, (Sp)m(Rp)n(Sp)t is (Sp)mRp(Sp)5. In some embodiments, (Sp)m(Rp)n(Sp)t is (SP)2RP(SP)5. In some embodiments, (Sp)m(Rp)n(Sp)t is (SP)3RP(SP)5. In some embodiments, (Sp)m(Rp)n(Sp)t is (SP)4RP(SP)5. In some embodiments, (Sp)m(Rp)n(Sp)t is (SP)5RP(SP)5.
The gap region may include, e.g., at least one Rp internucleoside linkage. The gap region may include, e.g., at least one Rp phosphorothioate internucleoside linkage. The gap region may include, e.g., at least two Rp internucleoside linkages. The gap region may include, e.g., at least two Rp phosphorothioate internucleoside linkages. The gap region may include, e.g., at least three Rp internucleoside linkages. The gap region may include, e.g., at least three Rp phosphorothioate internucleoside linkages. The gap region may include, e.g., at least 4, 5, 6, 7, 8, 9, or 10 Rp internucleoside linkages. The gap region may include, e.g., at least 4, 5, 6, 7, 8, 9, or 10 Rp phosphorothioate internucleoside linkages.
A gapmer may include a wing-gap-wing motif that is a 5-10-5 motif, where the nucleosides in each wing region are 2'-MOE-modified nucleosides. A wing-gap-wing motif of a gapmer may be, e.g., a 5-10-5 motif where the nucleosides in the gap region are 2'-deoxyribonucleosides. A wing-gap-wing motif of a gapmer may be, e.g., a 5-10-5 motif, where all internucleoside linkages are phosphorothioate internucleoside linkages. A wing-gap-wing motif of a gapmer may be, e.g., a 5-10-5 motif, where all internucleoside linkages are stereochemically enriched phosphorothioate internucleoside linkages. A wing-gap-wing motif of a gapmer may be, e.g., a 5-10-5 motif, where the nucleosides in each wing region are 2'-MOE-modified nucleosides, the nucleosides in the gap region are 2'-deoxyribonucleosides, and all internucleoside linkages are stereochemically enriched phosphorothioate internucleoside linkages.
In certain embodiments, a wing-gap-wing motif is a 5-10-5 motif where the residues at each wing region are not 2'-MOE-modified residues. In certain embodiments, a wing-gap-wing motif is a 5-10-5 motif where the residues in the gap region are 2'-deoxyribonucleotide residues. In certain embodiments, a wing-gap-wing motif is a 5-10-5 motif, where all internucleosidic linkages are phosphorothioate internucleosidic linkages. In certain embodiments, a wing-gap-wing motif is a 5-10-5 motif, where all internucleoside linkages are stereochemically enriched phosphorothioate internucleoside linkages. In certain embodiments, a wing- gap-wing motif is a 5-10-5 motif where the residues at each wing region are not 2'-MOE-modified residues, the residues in the gap region are 2'-deoxyribonucleotide, and all internucleoside linkages are stereochemically enriched phosphorothioate internucleoside linkages.
An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth, and twentieth internucleoside linkages being a P-stereogenic linkage (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least two of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., stereogenic. At least three of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least four of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least five of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least six of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least seven of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least eight of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least nine of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). One of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Two of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Three of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Four of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Five of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Six of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Seven of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Eight of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Nine of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Ten of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages being P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least two of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least three of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least four of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least five of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least six of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least seven of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). One of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Two of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Three of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Four of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Five of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Six of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Seven of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Eight of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester).
An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester), and at least one internucleoside linkage being non-stereogenic. An oligonucleotide may include a region in which at least one of the first, second, third, fifth, seventh, eighteenth, nineteenth, and twentieth internucleoside linkages being P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester), and at least one internucleoside linkage being non-stereogenic. At least two internucleoside linkages may be, e.g., non-stereogenic. At least three internucleoside linkages may be, e.g., non-stereogenic. At least four internucleoside linkages may be, e.g., non-stereogenic. At least five internucleoside linkages may be, e.g., non-stereogenic. At least six internucleoside linkages may be, e.g., non-stereogenic. At least seven internucleoside linkages may be, e.g., non-stereogenic. At least eight internucleoside linkages may be, e.g., non-stereogenic. At least nine internucleoside linkages may be, e.g., non-stereogenic. At least 10 internucleoside linkages may be, e.g., non-stereogenic. At least 11 internucleoside linkages may be, e.g., non-stereogenic. At least 12 internucleoside linkages may be, e.g., non-stereogenic. At least 13 internucleoside linkages may be, e.g., non-stereogenic. At least 14 internucleoside linkages may be, e.g., non-stereogenic. At least 15 internucleoside linkages may be, e.g., non-stereogenic. At least 16 internucleoside linkages may be, e.g., non-stereogenic. At least 17 internucleoside linkages may be, e.g., non-stereogenic. At least 18 internucleoside linkages may be, e.g., non-stereogenic. At least 19 internucleoside linkages may be, e.g., non-stereogenic. At least 20 internucleoside linkages may be, e.g., non-stereogenic. In some embodiments, one internucleoside linkage is non-stereogenic. In some embodiments, two internucleoside linkages are non-stereogenic. In some embodiments, three internucleoside linkages are non-stereogenic. In some embodiments, four internucleoside linkages are non-stereogenic. In some embodiments, five internucleoside linkages are non-stereogenic. In some embodiments, six internucleoside linkages are non-stereogenic. In some embodiments, seven internucleoside linkages are non-stereogenic. In some embodiments, eight internucleoside linkages are non-stereogenic. In some embodiments, nine internucleoside linkages are non-stereogenic. In some embodiments, 10 internucleoside linkages are non-stereogenic. In some embodiments, 11 internucleoside linkages are non-stereogenic. In some embodiments, 12 internucleoside linkages are non-stereogenic. In some embodiments, 13 internucleoside linkages are non-stereogenic. In some embodiments, 14 internucleoside linkages are non-stereogenic. In some embodiments, 15 internucleoside linkages are non-stereogenic. In some embodiments, 16 internucleoside linkages are non-stereogenic. In some embodiments, 17 internucleoside linkages are non-stereogenic. In some embodiments, 18 internucleoside linkages are non-stereogenic. In some embodiments, 19 internucleoside linkages are non-stereogenic. In some embodiments, 20 internucleoside linkages are non-stereogenic. An oligonucleotide may include a region in which all internucleoside linkages, except at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages which is P-stereogenic, are non-stereogenic.
An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic, and at least one internucleoside linkage being phosphate phosphodiester. An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic, and at least one internucleoside linkage being phosphate phosphodiester. At least two internucleoside linkages may be, e.g., phosphate phosphodiesters. At least three internucleoside linkages may be, e.g., phosphate phosphodiesters. At least four internucleoside linkages may be, e.g., phosphate phosphodiesters. At least five internucleoside linkages may be, e.g., phosphate phosphodiesters. At least six internucleoside linkages may be, e.g., phosphate phosphodiesters. At least seven internucleoside linkages may be, e.g., phosphate phosphodiesters. At least eight internucleoside linkages may be, e.g., phosphate phosphodiesters. At least nine internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 10 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 11 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 12 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 13 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 14 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 15 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 16 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 17 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 18 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 19 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 20 internucleoside linkages may be, e.g., phosphate phosphodiesters. In some embodiments, one internucleoside linkage is phosphate phosphodiesters. In some embodiments, two internucleoside linkages are phosphate phosphodiesters.
In some embodiments, three internucleoside linkages are phosphate phosphodiesters. In some embodiments, four internucleoside linkages are phosphate phosphodiesters. In some embodiments, five internucleoside linkages are phosphate phosphodiesters. In some embodiments, six internucleoside linkages are phosphate phosphodiesters. In some embodiments, seven internucleoside linkages are phosphate phosphodiesters. In some embodiments, eight internucleoside linkages are phosphate phosphodiesters. In some embodiments, nine internucleoside linkages are phosphate phosphodiesters.
In some embodiments, 10 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 11 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 12 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 13 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 14 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 15 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 16 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 17 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 18 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 19 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 20 internucleoside linkages are phosphate phosphodiesters. An oligonucleotide may include a region with all internucleoside linkages, except at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic, being phosphate phosphodiesters.
An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic, and at least 10% of all internucleoside linkages in the region being non-stereogenic. An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic, and at least 10% of all internucleoside linkages in the region being non-stereogenic. At least 20% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 30% of all the internucleoside linkages in the region may be, e.g., non- stereogenic. At least 40% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 50% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 60% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 70% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 80% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 90% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 50% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. A non-stereogenic internucleoside linkage may be, e.g., a phosphate phosphodiester. In some embodiments, each non-stereogenic internucleoside linkage is a phosphate phosphodiester. The first internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The first internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The second internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The second internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The third internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The third internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The fifth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The fifth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The seventh internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The seventh internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The eighth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The eighth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The ninth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The ninth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The eighteenth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The eighteenth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The nineteenth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The nineteenth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The twentieth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The twentieth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage.
The region may have a length of, e.g., at least 21 bases. The region may have a length of, e.g., 21 bases.
In some embodiments, each stereochemically enriched internucleoside linkage in an oligonucleotide is a phosphorothioate phosphodiester.
An oligonucleotide may have, e.g., at least 25% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 30% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 35% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 40% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 45% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 50% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 55% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 60% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 65% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 70% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 75% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 80% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 85% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 90% of its internucleoside linkages in Sp configuration.
An oligonucleotide may include at least two internucleoside linkages having different stereochemical configuration and/or different P-modifications relative to one another. The oligonucleotide may have a structure represented by the following formula:
[SBnl RBn2SBn3RBn4. . . SBnxRBny] where: each RB independently represents a block of nucleotide units having the Rp configuration at the internucleoside linkage phosphorus atom; each SB independently represents a block of nucleotide units having the Sp configuration at the internucleoside linkage phosphorus atom; each of n1 to ny is zero or an integer, provided that at least one odd n and at least one even n must be non-zero so that the oligonucleotide includes at least two internucleoside linkages with different stereochemistry relative to one another; and where the sum of n1 to ny is between 2 and 200.
In some embodiments, the sum of n1 to ny is between a lower limit selected from the group consisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, and more, and the upper limit selected from the group consisting of 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, and 200, the upper limit being greater than the lower limit. In some of these embodiments, each n has the same value. In some embodiments, each even n has the same value as each other even n. In some embodiments, each odd n has the same value each other odd n. At least two even ns may have, e.g., different values from one another. At least two odd ns may have, e.g., different values from one another.
At least two adjacent ns may be, e.g., equal to one another, so that an oligonucleotide includes adjacent blocks of Sp linkages and Rp linkages of equal lengths. In some embodiments, an oligonucleotide includes repeating blocks of Sp and Rp linkages of equal lengths. In some embodiments, an oligonucleotide includes repeating blocks of Sp and Rp linkages, where at least two such blocks are of different lengths from one another. In some such embodiments, each Sp block is of the same length and is of a different length from each Rp block, where all Rp blocks may optionally be of the same length as one another.
At least two skip-adjacent ns may be, e.g., equal to one another, so that a provided oligonucleotide includes at least two blocks of internucleoside linkages of a first stereochemistry that are equal in length to one another and are separated by a separating block of internucleoside linkages of the opposite stereochemistry, where the separating block may be of the same length or a different length from the blocks of first stereochemistry.
In some embodiments, ns associated with linkage blocks at the ends of an oligonucleotide are of the same length. In some embodiments, an oligonucleotide has terminal blocks of the same linkage stereochemistry. In some such embodiments, the terminal blocks are separated from one another by a middle block of the opposite linkage stereochemistry.
An oligonucleotide of formula [SBni RBn2SBn3RBn4. . . SBnxRBny] may be, e.g., a stereoblockmer.
An oligonucleotide of formula [SBni RBn2SBn3RBn4. . . SBnxRBny] may be, e.g., a stereoskipmer. An oligonucleotide of formula [SBni RBn2SBn3RBn4. . . SBnxRBny] may be, e.g., a stereoaltmer. An oligonucleotide of formula [SBni RBn2SBn3RBn4. . . SBnxRBny] may be, e.g., a gapmer.
An oligonucleotide of formula [SB ni RBn2SBn3RBn4. . . SBnxRBny] may be, e.g., of any of the above described patterns and may further include, e.g., patterns of P-modifications. For instance, an oligonucleotide of formula [SBni RBn2SBn3RBn4. . . SBnxRBny] may be, e.g., a stereoskipmer and a P- modification skipmer. An oligonucleotide of formula [SB n i RBn2SBn3RBn4. . . SBnxRBny] may be, e.g., a stereoblockmer and a P-modification altmer. An oligonucleotide of formula [SB niRBn2SBn3RBn4. . .
SBnxRBny] may be, e.g., a stereoaltmer and a P-modification blockmer.
An oligonucleotide may include, e.g., at least one phosphate phosphodiester and at least two consecutive modified internucleoside linkages. An oligonucleotide may include, e.g., at least one phosphate phosphodiester and at least two consecutive phosphorothioate triesters.
An oligonucleotide may be, e.g., a blockmer. An oligonucleotide may be, e.g., a stereoblockmer. An oligonucleotide may be, e.g., a P-modification blockmer. An oligonucleotide may be, e.g., a linkage blockmer.
An oligonucleotide may be, e.g., an altmer. An oligonucleotide may be, e.g., a stereoaltmer. An oligonucleotide may be, e.g., a P-modification altmer. An oligonucleotide may be, e.g., a linkage altmer.
An oligonucleotide may be, e.g., a unimer. An oligonucleotide may be, e.g., a stereounimer. An oligonucleotide may be, e.g., a P-modification unimer. An oligonucleotide may be, e.g., a linkage unimer.
An oligonucleotide may be, e.g., a skipmer.
II. Complementarity
It is possible to introduce mismatch bases without eliminating activity. Accordingly an oligonucleotide of the invention may include (i) a nucleobase sequence having at least 6 contiguous nucleobases complementary to an equal-length portion within an NRL target nucleic acid and (ii) a nucleobase sequence having a plurality of nucleobases including one or more nucleobases complementary to an NRL target nucleic acid and one or more mismatches.
In some embodiments, oligonucleotides of the invention are complementary to an NRL target nucleic acid over the entire length of the oligonucleotide. In other embodiments, oligonucleotides are 99%, 95%, 90%, 85%, or 80% complementary to the NRL target nucleic acid. In further embodiments, oligonucleotides are at least 80% complementary to the NRL target nucleic acid over the entire length of the oligonucleotide and include a nucleobase sequence that is fully complementary to an NRL target nucleic acid. The nucleobase sequence that is fully complementary may be, e.g., 6 to 20, 10 to 18, or 18 to 20 contiguous nucleobases in length.
An oligonucleotide of the invention may include one or more mismatched nucleobases relative to the target nucleic acid. In certain embodiments, an antisense or RNAi activity against the target is reduced by such mismatch, but activity against a non-target is reduced by a greater amount. Thus, the off-target selectivity of the oligonucleotides may be improved.
III. Oligonucleotide Modifications
An oligonucleotide of the invention may be a modified oligonucleotide. A modified oligonucleotide of the invention includes one or more modifications, e.g., a nucleobase modification (e.g., SEQ ID NOs: 18-29), a sugar modification, an internucleoside linkage modification, or a terminal modification.
Nucleobase Modifications
Oligonucleotides of the invention may include one or more modified nucleobases. Unmodified nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C), and uracil (U). Modified nucleobases include 5-substituted pyrimidines, 6- azapyrimidines, alkyl or alkynyl substituted pyrimidines, alkyl substituted purines, and N-2, N-6 and 0-6 substituted purines, as well as synthetic and natural nucleobases, e.g., 5-methylcytosine, 5- hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-alkyl (e.g., 6-methyl) adenine and guanine, 2-alkyl (e.g., 2-propyl) adenine and guanine, 2-thiouracil, 2-thiothymine, 2-thiocytosine, 5- halouracil, 5-halocytosine, 5-propynyl uracil, 5-propynyl cytosine, 5-trifluoromethyl uracil, 5-trifluoromethyl cytosine, 7-methyl guanine, 7-methyl adenine, 8-azaguanine, 8-azaadenine, 7-deazaguanine, 7- deazaadenine, 3-deazaguanine, 3-deazaadenine. Certain nucleobases are particularly useful for increasing the binding affinity of nucleic acids, e g., 5-substituted pyrimidines; 6-azapyrimidines; N2-, N6-, and/or 06-substituted purines. Nucleic acid duplex stability can be enhanced using, e.g., 5- methylcytosine. Non-limiting examples of nucleobases include: 2-aminopropyladenine, 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-N-methylguanine, 6-N-methyladenine, 2- propyladenine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-propynyl ( — CºC — CH3) uracil, 5- propynylcytosine, 6-azouracil, 6-azocytosine, 6-azothymine, 5-ribosyluracil (pseudouracil), 4-thiouracil, 8- halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl, 8-aza and other 8-substituted purines, 5-halo, particularly 5- bromo, 5-trifluoromethyl, 5-halouracil, and 5-halocytosine, 7-methylguanine, 7-methyladenine, 2-F- adenine, 2-aminoadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine, 3-deazaadenine, 6-N- benzoyladenine, 2-N-isobutyrylguanine, 4-N-benzoylcytosine, 4-N-benzoyluracil, 5-methyl 4-N- benzoylcytosine, 5-methyl 4-N-benzoyluracil, universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases. Further modified nucleobases include tricyclic pyrimidines, such as 1 ,3-diazaphenoxazine-2-one, 1 ,3-diazaphenothiazine-2-one and 9-(2-aminoethoxy)-1 ,3- diazaphenoxazine-2-one (G-clamp). Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deazaadenine, 7-deazaguanine, 2- aminopyridine and 2-pyridone. Further nucleobases include those disclosed in Merigan et al., U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, Kroschwitz, J. I., Ed., John Wiley & Sons, 1990, 858-859; Englisch et al., Angewandte Chemie, International Edition, 1991 , 30, 613; Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, Crooke, S. T. and Lebleu, B., Eds., CRC Press, 1993, 273-288; and those disclosed in Chapters 6 and 15, Antisense Drug Technology, Crooke S. T., Ed., CRC Press, 2008, 163-166 and 442-443
Sugar Modifications
Oligonucleotides of the invention may include one or more sugar modifications in nucleosides. Nucleosides having an unmodified sugar include a sugar moiety that is a furanose ring as found in ribonucleosides and 2’-deoxyribonucleosides.
Sugars included in the nucleosides of the invention may be non-furanose (or 4'-substituted furanose) rings or ring systems or open systems. Such structures include simple changes relative to the natural furanose ring (e.g., a six-membered ring). Alternative sugars may also include sugar surrogates wherein the furanose ring has been replaced with another ring system such as, e.g., a morpholino or hexitol ring system. Non-limiting examples of sugar moieties useful that may be included in the oligonucleotides of the invention include b-D-ribose, p-D-2'-deoxyribose, substituted sugars (e.g., 2', 5', and bis substituted sugars), 4'-S-sugars (e.g., 4'-S-ribose, 4'-S-2'-deoxyribose, and 4'-S-2'-substituted ribose), bridged sugars (e.g., the 2'-0 — CH2-4' or 2'-0 — (CH2)2-4' bridged ribose derived bicyclic sugars) and sugar surrogates (when the ribose ring has been replaced with a morpholino or a hexitol ring system). The nucleosides and nucleotides containing bridged sugars having 2'-0 — CH2-4' are referred to herein as locked nucleic acids (LNA).
Typically, a sugar modification may be, e.g., a 2’-substitution, locking, carbocyclization, or unlocking. A 2’-substitution is a replacement of 2’-hydroxyl in ribofuranose with 2’-fluoro, 2’-methoxy, or 2’-(2-methoxy)ethoxy. Alternatively, a 2’-substitution may be a 2’-(ara) substitution, which corresponds to the following structure:
Figure imgf000062_0001
where B is a nucleobase, and R is a 2’-(ara) substituent (e.g., fluoro). 2’-(ara) substituents are known in the art and can be same as other 2’-substituents described herein. In some embodiments, 2’-(ara) substituent is a 2’-(ara)-F substituent (R is fluoro). A locking modification is an incorporation of a bridge between 4’-carbon atom and 2’-carbon atom of ribofuranose. Nucleosides having a sugar with a locking modification are known in the art as bridged nucleic acids, e.g., locked nucleic acids (LNA), ethylene- bridged nucleic acids (ENA), and cEt nucleic acids. The bridged nucleic acids are typically used as affinity enhancing nucleosides.
Internucleoside Linkage Modifications
Oligonucleotides of the invention may include one or more internucleoside linkage modifications. The two main classes of internucleoside linkages are defined by the presence or absence of a phosphorus atom. Non-limiting examples of phosphorus-containing internucleoside linkages include phosphodiester linkages, phosphotriester linkages, phosphorothioate diester linkages, phosphorothioate triester linkages, morpholino internucleoside linkages, methylphosphonates, and phosphoramidate. Nonlimiting examples of non-phosphorus internucleoside linkages include methylenemethylimino ( — CH2 — N(CH3) — O — CH2 — ), thiodiester (— O— C(O)— S— ), thionocarbamate (— O— C(0)(NH)— S— ), siloxane (— O— Si(H)2— O— ), and N,N'-dimethylhydrazine ( — C H2 — N (C H 3) — N (C H 3) — ) . Modified linkages, compared to natural phosphodiester linkages, can be used to alter, typically increase, nuclease resistance of the oligonucleotide. Methods of preparation of phosphorous-containing and non- phosphorous-containing internucleoside linkages are known in the art.
Internucleoside linkages may be stereochemically enriched. For example, phosphorothioate- based internucleoside linkages (e.g., phosphorothioate diester or phosphorothioate triester) may be stereochemically enriched. The stereochemically enriched internucleoside linkages including a stereogenic phosphorus are typically designated Sp or Rp to identify the absolute stereochemistry of the phosphorus atom. Wthin an oligonucleotide, Sp phosphorothioate indicates the following structure:
Figure imgf000062_0002
Within an oligonucleotide, Rp phosphorothioate indicates the following structure:
Figure imgf000062_0003
The oligonucleotides of the invention may include one or more neutral internucleoside linkages. Non-limiting examples of neutral internucleoside linkages include phosphotriesters, phosphorothioate triesters, methylphosphonates, methylenemethylimino (3'-CH2 — N(CH3) — 0-3’), amide-3 (3'-CH2 —
C(=0) — N(H)-3’), amide-4 (3'-CH2 — N(H) — C(=0)-3’), formacetal (3'-0— CH2— 0-3’), and thioformacetal (3'-S — CH2 — 0-3’). Further neutral internucleoside linkages include nonionic linkages including siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester, and amides (See for example: Carbohydrate Modifications in Antisense Research; Y. S. Sanghvi and P. D. Cook, Eds., ACS Symposium Series 580; Chapters 3 and 4, 40-65).
Oligonucleotides may include, e.g., modified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or modified internucleoside linkage motif. Oligonucleotides may include, e.g., a region having an alternating internucleoside linkage motif. In certain embodiments, oligonucleotides of the present disclosure include a region of uniformly modified internucleoside linkages. In certain such embodiments, the oligonucleotide may include, e.g., a region that is uniformly linked by phosphorothioate internucleoside linkages. The oligonucleotide may be, e.g., uniformly linked by phosphorothioate internucleoside linkages. Each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate. Each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate and at least one internucleoside linkage is phosphorothioate.
The oligonucleotide may include, e.g., at least 6 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least 7 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least 8 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least 9 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least 10 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least 11 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least 12 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least 13 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least 14 phosphorothioate internucleoside linkages.
The oligonucleotide may include, e.g., at least one block of at least 6 consecutive phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least one block of at least 7 consecutive phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least one block of at least 8 consecutive phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least one block of at least 9 consecutive phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least one block of at least 10 consecutive phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., at least one block of at least 12 consecutive phosphorothioate internucleoside linkages. In certain such embodiments, at least one such block is located at the 3' end of the oligonucleotide. In certain such embodiments, at least one such block is located within 3 nucleosides of the 3' end of the oligonucleotide. The oligonucleotide may include, e.g., fewer than 15 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., fewer than 14 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., fewer than 13 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., fewer than 12 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., fewer than 11 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., fewer than 10 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., fewer than 9 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., fewer than 8 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., fewer than 7 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., fewer than 6 phosphorothioate internucleoside linkages. The oligonucleotide may include, e.g., fewer than 5 phosphorothioate internucleoside linkages. In some embodiments, at least one phosphorothioate internucleoside linkage is a phosphorothioate diester. In some embodiments, each phosphorothioate internucleoside linkage is a phosphorothioate diester. In some embodiments, at least one phosphorothioate internucleoside linkage is a phosphorothioate triester. In some embodiments, each phosphorothioate internucleoside linkage is a phosphorothioate triester. In some embodiments, each internucleoside linkage is independently a phosphodiester (e.g., phosphate phosphodiester or phosphorothioate diester).
An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (Sp)mRp or Rp(Sp)m. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including Rp(Sp)m. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (Sp)mRp. In some embodiments, m is 2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including RP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (SP)2RP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (RP)2RP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including RPSPRP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including SPRPRP(SP)2. An oligonucleotide may include a pattern of internucleoside P-stereogenic centers including (SP)2RP.
In the embodiments of internucleoside P-stereogenic center patterns, m is 2, 3, 4, 5, 6, 7 or 8, unless specified otherwise. In some embodiments of internucleoside P-stereogenic center patterns, m is 3, 4, 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, m is 4, 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, m is 5, 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, m is 6, 7 or 8. In some embodiments of internucleoside P-stereogenic center patterns, m is 7 or 8. In some embodiments of internucleoside P- stereogenic center patterns, m is 2. In some embodiments of internucleoside P-stereogenic center patterns, m is 3. In some embodiments of internucleoside P-stereogenic center patterns, m is 4. In some embodiments of internucleoside P-stereogenic center patterns, m is 5. In some embodiments of internucleoside P-stereogenic center patterns, m is 6. In some embodiments of internucleoside P- stereogenic center patterns, m is 7. In some embodiments of internucleoside P-stereogenic center patterns, m is 8.
An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth, and twentieth internucleoside linkages being a P-stereogenic linkage (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least two of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., stereogenic. At least three of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least four of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least five of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least six of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least seven of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least eight of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least nine of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). One of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Two of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Three of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Four of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Five of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Six of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Seven of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Eight of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Nine of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Ten of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester).
An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages being P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least two of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least three of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least four of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least five of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least six of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). At least seven of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). One of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Two of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Three of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Four of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Five of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Six of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Seven of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester). Eight of the first, second, third, fifth, seventh, eighteenth, nineteenth and twentieth internucleoside linkages may be, e.g., P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester).
An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester), and at least one internucleoside linkage being non-stereogenic. An oligonucleotide may include a region in which at least one of the first, second, third, fifth, seventh, eighteenth, nineteenth, and twentieth internucleoside linkages being P- stereogenic (e.g., phosphorothioate phosphodiester or phosphorothioate phosphotriester), and at least one internucleoside linkage being non-stereogenic. At least two internucleoside linkages may be, e.g., non-stereogenic. At least three internucleoside linkages may be, e.g., non-stereogenic. At least four internucleoside linkages may be, e.g., non-stereogenic. At least five internucleoside linkages may be, e.g., non-stereogenic. At least six internucleoside linkages may be, e.g., non-stereogenic. At least seven internucleoside linkages may be, e.g., non-stereogenic. At least eight internucleoside linkages may be, e.g., non-stereogenic. At least nine internucleoside linkages may be, e.g., non-stereogenic. At least 10 internucleoside linkages may be, e.g., non-stereogenic. At least 11 internucleoside linkages may be, e.g., non-stereogenic. At least 12 internucleoside linkages may be, e.g., non-stereogenic. At least 13 internucleoside linkages may be, e.g., non-stereogenic. At least 14 internucleoside linkages may be, e.g., non-stereogenic. At least 15 internucleoside linkages may be, e.g., non-stereogenic. At least 16 internucleoside linkages may be, e.g., non-stereogenic. At least 17 internucleoside linkages may be, e.g., non-stereogenic. At least 18 internucleoside linkages may be, e.g., non-stereogenic. At least 19 internucleoside linkages may be, e.g., non-stereogenic. At least 20 internucleoside linkages may be, e.g., non-stereogenic. In some embodiments, one internucleoside linkage is non-stereogenic. In some embodiments, two internucleoside linkages are non-stereogenic. In some embodiments, three internucleoside linkages are non-stereogenic. In some embodiments, four internucleoside linkages are non-stereogenic. In some embodiments, five internucleoside linkages are non-stereogenic. In some embodiments, six internucleoside linkages are non-stereogenic. In some embodiments, seven internucleoside linkages are non-stereogenic. In some embodiments, eight internucleoside linkages are non-stereogenic. In some embodiments, nine internucleoside linkages are non-stereogenic. In some embodiments, 10 internucleoside linkages are non-stereogenic. In some embodiments, 11 internucleoside linkages are non-stereogenic. In some embodiments, 12 internucleoside linkages are non-stereogenic. In some embodiments, 13 internucleoside linkages are non-stereogenic. In some embodiments, 14 internucleoside linkages are non-stereogenic. In some embodiments, 15 internucleoside linkages are non-stereogenic. In some embodiments, 16 internucleoside linkages are non-stereogenic. In some embodiments, 17 internucleoside linkages are non-stereogenic. In some embodiments, 18 internucleoside linkages are non-stereogenic. In some embodiments, 19 internucleoside linkages are non-stereogenic. In some embodiments, 20 internucleoside linkages are non-stereogenic. An oligonucleotide may include a region in which all internucleoside linkages, except at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth and twentieth internucleoside linkages which is P-stereogenic, are non-stereogenic.
An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic, and at least one internucleoside linkage being phosphate phosphodiester. An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic, and at least one internucleoside linkage being phosphate phosphodiester. At least two internucleoside linkages may be, e.g., phosphate phosphodiesters. At least three internucleoside linkages may be, e.g., phosphate phosphodiesters. At least four internucleoside linkages may be, e.g., phosphate phosphodiesters. At least five internucleoside linkages may be, e.g., phosphate phosphodiesters. At least six internucleoside linkages may be, e.g., phosphate phosphodiesters. At least seven internucleoside linkages may be, e.g., phosphate phosphodiesters. At least eight internucleoside linkages may be, e.g., phosphate phosphodiesters. At least nine internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 10 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 11 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 12 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 13 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 14 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 15 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 16 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 17 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 18 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 19 internucleoside linkages may be, e.g., phosphate phosphodiesters. At least 20 internucleoside linkages may be, e.g., phosphate phosphodiesters. In some embodiments, one internucleoside linkage is phosphate phosphodiesters. In some embodiments, two internucleoside linkages are phosphate phosphodiesters.
In some embodiments, three internucleoside linkages are phosphate phosphodiesters. In some embodiments, four internucleoside linkages are phosphate phosphodiesters. In some embodiments, five internucleoside linkages are phosphate phosphodiesters. In some embodiments, six internucleoside linkages are phosphate phosphodiesters. In some embodiments, seven internucleoside linkages are phosphate phosphodiesters. In some embodiments, eight internucleoside linkages are phosphate phosphodiesters. In some embodiments, nine internucleoside linkages are phosphate phosphodiesters. In some embodiments, 10 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 11 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 12 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 13 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 14 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 15 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 16 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 17 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 18 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 19 internucleoside linkages are phosphate phosphodiesters. In some embodiments, 20 internucleoside linkages are phosphate phosphodiesters. An oligonucleotide may include a region with all internucleoside linkages, except at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic, being phosphate phosphodiesters.
An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighth, ninth, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic, and at least 10% of all internucleoside linkages in the region being non-stereogenic. An oligonucleotide may include a region with at least one of the first, second, third, fifth, seventh, eighteenth, nineteenth, and twentieth internucleoside linkages being P-stereogenic, and at least 10% of all internucleoside linkages in the region being non-stereogenic. At least 20% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 30% of all the internucleoside linkages in the region may be, e.g., non- stereogenic. At least 40% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 50% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 60% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 70% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 80% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 90% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. At least 50% of all the internucleoside linkages in the region may be, e.g., non-stereogenic. A non-stereogenic internucleoside linkage may be, e.g., a phosphate phosphodiester. In some embodiments, each non-stereogenic internucleoside linkage is a phosphate phosphodiester.
The first internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The first internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The second internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The second internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The third internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The third internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The fifth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The fifth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The seventh internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The seventh internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The eighth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The eighth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The ninth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The ninth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The eighteenth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The eighteenth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The nineteenth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The nineteenth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage. The twentieth internucleoside linkage of the region may be, e.g., an Sp internucleoside linkage. The twentieth internucleoside linkage of the region may be, e.g., an Rp internucleoside linkage.
The region may have a length of, e.g., at least 21 bases. The region may have a length of, e.g., 21 bases.
In some embodiments, each stereochemically enriched internucleoside linkage in an oligonucleotide is a phosphorothioate phosphodiester.
An oligonucleotide may have, e.g., at least 25% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 30% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 35% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 40% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 45% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 50% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 55% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 60% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 65% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 70% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 75% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 80% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 85% of its internucleoside linkages in Sp configuration. An oligonucleotide may have, e.g., at least 90% of its internucleoside linkages in Sp configuration.
An oligonucleotide may include, e.g., at least one phosphate phosphodiester and at least two consecutive modified internucleoside linkages. An oligonucleotide may include, e.g., at least one phosphate phosphodiester and at least two consecutive phosphorothioate triesters.
An oligonucleotide may be, e.g., a blockmer. An oligonucleotide may be, e.g., a stereoblockmer. An oligonucleotide may be, e.g., a P-modification blockmer. An oligonucleotide may be, e.g., a linkage blockmer.
An oligonucleotide may be, e.g., an altmer. An oligonucleotide may be, e.g., a stereoaltmer. An oligonucleotide may be, e.g., a P-modification altmer. An oligonucleotide may be, e.g., a linkage altmer.
An oligonucleotide may be, e.g., a unimer. An oligonucleotide may be, e.g., a stereounimer. An oligonucleotide may be, e.g., a P-modification unimer. An oligonucleotide may be, e.g., a linkage unimer. An oligonucleotide may be, e.g., a skipmer.
Terminal Modifications
Oligonucleotides of the invention may include a terminal modification. The terminal modification is a 5’-terminal modification or a 3’-terminal modification.
The 5’ end of an oligonucleotide may be, e.g., hydroxyl, a hydrophobic moiety, 5’ cap, phosphate, diphosphate, triphosphate, phosphorothioate, diphosphorothioate, triphosphorothioate, phosphorodithioate, diphosphrodithioate, triphosphorodithioate, phosphonate, phosphoramidate, a cell penetrating peptide, an endosomal escape moiety, or a neutral organic polymer. An unmodified 5’- terminus is hydroxyl or phosphate. An oligonucleotide having a 5’ terminus other than 5’-hydroxyl or 5’- phosphate has a modified 5’ terminus.
The 3’ end of an oligonucleotide may be, e.g., hydroxyl, a hydrophobic moiety, phosphate, diphosphate, triphosphate, phosphorothioate, diphosphorothioate, triphosphorothioate, phosphorodithioate, disphorodithioate, triphosphorodithioate, phosphonate, phosphoramidate, a cell penetrating peptide, an endosomal escape moiety, or a neutral organic polymer (e.g., polyethylene glycol). An unmodified 3’-terminuns is hydroxyl or phosphate. An oligonucleotide having a 3’ terminus other than 3’-hydroxyl or 3’-phosphate has a modified 3’ terminus.
The terminal modification (e.g., 5’-terminal modification) may be, e.g., a hydrophobic moiety. Advantageously, an oligonucleotide including a hydrophobic moiety may exhibit superior cellular uptake, as compared to an oligonucleotide lacking the hydrophobic moiety. Oligonucleotides including a hydrophobic moiety may therefore be used in compositions that are substantially free of transfecting agents. A hydrophobic moiety is a monovalent group (e.g., a bile acid (e.g., cholic acid, taurocholic acid, deoxycholic acid, oleyl lithocholic acid, or oleoyl cholenic acid), glycolipid, phospholipid, sphingolipid, isoprenoid, vitamin, saturated fatty acid, unsaturated fatty acid, fatty acid ester, triglyceride, pyrene, porphyrine, texaphyrine, adamantine, acridine, biotin, coumarin, fluorescein, rhodamine, Texas-Red, digoxygenin, dimethoxytrityl, f-butydimethylsilyl, f-butyldiphenylsilyl, cyanine dye (e.g., Cy3 or Cy5), Hoechst 33258 dye, psoralen, or ibuprofen) covalently linked to the terminus of the oligonucleotide backbone (e.g., 5’-terminus). Non-limiting examples of the monovalent group include ergosterol, stigmasterol, b-sitosterol, campesterol, fucosterol, saringosterol, avenasterol, coprostanol, cholesterol, vitamin A, vitamin D, vitamin E, cardiolipin, and carotenoids. The linker connecting the monovalent group to the oligonucleotide may be an optionally substituted Ci-eo aliphatic (e.g., optionally substituted Ci-eo alkylene) or an optionally substituted C2-60 heteroaliphatic (e.g., optionally substituted C2-60 heteroalkylene), where the linker may be optionally interrupted with one, two, or three instances independently selected from the group consisting of an optionally substituted arylene, optionally substituted heterocyclylene, and optionally substituted cycloalkylene. The linker may be bonded to an oligonucleotide through, e.g., an oxygen atom attached to a 5’-terminal carbon atom, a 3’-terminal carbon atom, a 5’-terminal phosphate or phosphorothioate, a 3’-terminal phosphate or phosphorothioate, or an internucleoside linkage.
IV. Pharmaceutical Compositions
An oligonucleotide of the invention (e.g., a pharmaceutically acceptable salt thereof) may be included in a pharmaceutical composition. A pharmaceutical composition typically includes a pharmaceutically acceptable diluent or carrier. A pharmaceutical composition may include (e.g., consist of), e.g., a sterile saline solution and an oligonucleotide of the invention. The sterile saline is typically a pharmaceutical grade saline. A pharmaceutical composition may include (e.g., consist of), e.g., sterile water and an oligonucleotide of the invention. The sterile water is typically a pharmaceutical grade water. A pharmaceutical composition may include (e.g., consist of), e.g., phosphate-buffered saline (PBS) and an oligonucleotide of the invention. The sterile PBS is typically a pharmaceutical grade PBS.
In certain embodiments, pharmaceutical compositions include one or more oligonucleotides and one or more excipients. In certain embodiments, excipients are selected from water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylase, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose and polyvinylpyrrolidone.
In certain embodiments, oligonucleotides may be admixed with pharmaceutically acceptable active and/or inert substances for the preparation of pharmaceutical compositions or formulations. Compositions and methods for the formulation of pharmaceutical compositions depend on a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.
In certain embodiments, pharmaceutical compositions including an oligonucleotide encompass any pharmaceutically acceptable salts of the oligonucleotide, esters of the oligonucleotide, or salts of such esters. In certain embodiments, pharmaceutical compositions including an oligonucleotide, upon administration to a subject (e.g., a human), are capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. Accordingly, for example, the disclosure is also drawn to pharmaceutically acceptable salts of oligonucleotides, prodrugs, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents. Suitable pharmaceutically acceptable salts include, but are not limited to, sodium and potassium salts. In certain embodiments, prodrugs include one or more conjugate group attached to an oligonucleotide, wherein the conjugate group is cleaved by endogenous nucleases within the body.
Lipid moieties have been used in nucleic acid therapies in a variety of methods. In certain such methods, the nucleic acid, such as an oligonucleotide, is introduced into preformed liposomes or lipoplexes made of mixtures of cationic lipids and neutral lipids. In certain methods, DNA complexes with mono- or poly-cationic lipids are formed without the presence of a neutral lipid. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to a particular cell or tissue. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to fat tissue. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to muscle tissue.
In certain embodiments, pharmaceutical compositions include a delivery system. Examples of delivery systems include, but are not limited to, liposomes and emulsions. Certain delivery systems are useful for preparing certain pharmaceutical compositions including those including hydrophobic compounds. In certain embodiments, certain organic solvents such as dimethylsulfoxide are used.
In certain embodiments, pharmaceutical compositions include one or more tissue-specific delivery molecules designed to deliver the one or more pharmaceutical agents of the present invention to specific tissues or cell types. For example, in certain embodiments, pharmaceutical compositions include liposomes coated with a tissue-specific antibody.
In certain embodiments, pharmaceutical compositions include a co-solvent system. Certain of such co-solvent systems include, for example, benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase. In certain embodiments, such co-solvent systems are used for hydrophobic compounds. A non-limiting example of such a co-solvent system is the VPD co-solvent system, which is a solution of absolute ethanol including 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant Polysorbate 80™ and 65% w/v polyethylene glycol 300. The proportions of such co-solvent systems may be varied considerably without significantly altering their solubility and toxicity characteristics. Furthermore, the identity of co-solvent components may be varied: for example, other surfactants may be used instead of Polysorbate 80™; the fraction size of polyethylene glycol may be varied; other biocompatible polymers may replace polyethylene glycol, e.g., polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose.
In certain embodiments, pharmaceutical compositions are prepared for oral administration. In certain embodiments, pharmaceutical compositions are prepared for buccal administration. In certain embodiments, a pharmaceutical composition is prepared for administration by injection (e.g., intraocular (e.g., intravitreal), intravenous, subcutaneous, intramuscular, intrathecal, intracerebroventricular, etc.). In certain of such embodiments, a pharmaceutical composition includes a carrier and is formulated in aqueous solution, such as water or physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer. In certain embodiments, other ingredients are included (e.g., ingredients that aid in solubility or serve as preservatives). In certain embodiments, injectable suspensions are prepared using appropriate liquid carriers, suspending agents and the like. Certain pharmaceutical compositions for injection are presented in unit dosage form, e.g., in ampoules or in multidose containers. Certain pharmaceutical compositions for injection are suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Certain solvents suitable for use in pharmaceutical compositions for injection include, but are not limited to, lipophilic solvents and fatty oils, such as sesame oil, synthetic fatty acid esters, such as ethyl oleate or triglycerides, and liposomes. Aqueous injection suspensions may contain.
V. Methods of the Invention
The invention provides methods of using oligonucleotides (e.g., pharmaceutically salts thereof) and pharmaceutical compositions of the invention.
A method of the invention may be a method of inhibiting or reducing the production of an NRL protein in a cell including an NRL gene by contacting the cell with the oligonucleotide (e.g., a pharmaceutically salt thereof) of the invention. The cell may be present in a subject (e.g., in a subject’s eye). The cell may be a photoreceptor cell.
A method of the invention may be a method of treating a subject having a disease, disorder, or condition (e.g., retinitis pigmentosa) by administering to the subject a therapeutically effective amount of an oligonucleotide of the invention or a pharmaceutical composition of the invention. The diseases, disorders, and conditions that may be treated using methods of the invention include retinitis pigmentosa (e.g., Rho P23H-associated retinitis pigmentosa, PDE6-associated retinitis pigmentosa, MERTK- associated retinitis pigmentosa, BBS1 -associated retinitis pigmentosa, Rho-associated retinitis pigmentosa, MRFP-associated retinitis pigmentosa, RLBP1 -associated retinitis pigmentosa, RP1- associated retinitis pigmentosa, RPGR-X-linked retinitis pigmentosa, NR2E3-associated retinitis pigmentosa, or SPATA7-associated retinitis pigmentosa), Stargardt disease (e.g., ABCA4-associated Stargardt disease), cone-rod dystrophy (e.g., AIPL1 -associated cone-rod dystrophy or RGRIP1- associated cone-rod dystrophy), Leber congenital amaurosis (e.g., AIPL1 -associated Leber congenital amaurosis, GUCY2D-associated Leber congenital amaurosis, RD3-associated Leber congenital amaurosis, RPE65-associated Leber congenital amaurosis, or SPATA7-associated Leber congenital amaurosis), Bardet Biedl syndrome (e.g., BBS1 -associated Bardet Biedl syndrome), macular dystrophy (e.g., BEST1 -associated macular dystrophy), dry macular degeneration, geographic atrophy, atrophic age-related macular degeneration (AMD), advanced dry AMD, retinal dystrophy (e.g., CEP290- associated retinal dystrophy, CDH3-associated retinal dystrophy, CRB1 -associated retinal dystrophy, or PRPH2-associated retinal dystrophy), choroideremia (e.g., CHM-associated choroideremia), Usher syndrome type 1 (e.g., MY07A-associated Usher syndrome), retinoschisis (e.g., RS1-X-linked retinoschisis), Leber hereditary optic neuropathy (e.g., ND4-associated Lebe’rs hereditary optic neuropathy), and achromatopsia (e.g., CNGA3-associated achromatopsia or CNGB3-associated achromatopsia). Methods of the invention may be used to treat subjects having a disease, disorder, or condition associated with a dysfunction of ABCA4, AIPL1 , BBS1 , BEST1 , CEP290, CDH3, CHM, CNGA3, CNGB3, CRB1 , GUCY2D, MERTK, MRFP, MY07A, ND4, NR2E3, PDE6, PRPH2, RD3, RHO, RLBP1 , RP1 , RPE65, RPGR, RPGRIP1 , RS1 , or SPAT A7 gene. Advantageously, because the oligonucleotides of the invention target NR2E3 and not ABCA4, AIPL1 , BBS1 , BEST1 , CEP290, CDH3, CHM, CNGA3, CNGB3, CRB1 , GUCY2D, MERTK, MRFP, MY07A, ND4, PDE6, PRPH2, RD3, RHO, RLBP1 , RP1 , RPE65, RPGR, RPGRIP1 , RS1 , or SPATA7, the therapeutic activity of the oligonucleotides of the invention does not depend on the type of the mutation responsible for the dysfunctional ABCA4, AIPL1 , BBS1 , BEST1 , CEP290, CDH3, CHM, CNGA3, CNGB3, CRB1 , GUCY2D, MERTK, MRFP, MY07A,
ND4, NR2E3, PDE6, PRPH2, RD3, RHO, RLBP1 , RP1 , RPE65, RPGR, RPGRIP1 , RS1 , or SPATA7 gene.
The oligonucleotide of the invention (e.g., a pharmaceutically salt thereof) or the pharmaceutical composition of the invention may be administered to the subject using methods known in the art. For example, the oligonucleotide of the invention (e.g., a pharmaceutically salt thereof) or the pharmaceutical composition of the invention may be administered topically to the eye of the subject. Additionally or alternatively, the oligonucleotide (e.g., a pharmaceutically salt thereof) of the invention or the pharmaceutical composition of the invention may be administered to the subject intraocularly (e.g., intravitreally).
VI. Preparation of Oligonucleotides
Oligonucleotides of the invention may be prepared using techniques and methods known in the art for the oligonucleotide synthesis. For example, oligonucleotides of the invention may be prepared using a phosphoramidite-based synthesis cycle. This synthesis cycle includes the steps of (1) deblocking a 5’-protected nucleotide to produce a 5’-deblocked nucleotide, (2) coupling the 5’-deblocked nucleotide with a 5’-protected nucleoside phosphoramidite to produce nucleosides linked through a phosphite, (3) repeating steps (1) and (2) one or more times as needed, (4) capping the 5’-terminus, and (5) oxidation orsulfurization of internucleoside phosphites. The reagents and reaction conditions useful for the oligonucleotide synthesis are known in the art.
The oligonucleotides disclosed herein may be linked to solid support as a result of solid-phase synthesis. Cleavable solid supports that may be used with the oligonucleotides are known in the art. Non-limiting examples of the solid support include, e.g., controlled pore glass or macroporous polystyrene bonded to a strand through a cleavable linker (e.g., succinate-based linker) known in the art (e.g., UnyLinker™). An oligonucleotide linked to solid support may be removed from the solid support by cleaving the linker connecting an oligonucleotide and solid support. The following examples are meant to illustrate the invention. They are not meant to limit the invention in any way.
EXAMPLES
Example 1. Preparation of Single-Stranded Oligonucleotides Oligonucleotides may be prepared using techniques and methods known in the art. Single- stranded oligonucleotides of SEQ ID NOs: 6-17 may be, e.g., gapmers with all internucleoside linkages being phosphorothioate diesters. The antisense oligonucleotides (SEQ ID NOs: 6-17) and modified versions thereof (SEQ ID NOs: 18-29) are listed in Table 1.
Table 1: Nrl-targeting oligonucleotides
Figure imgf000074_0001
Chemical modifications above include the following: Each “+” refers to an LNA nucleotide, such that +A refers to an LNA nucleotide having adenine nucleobase. Each “*” refers to a phosphorothioate internucleoside linkage. Each “iMe-dC” refers to 5-methyl-dC nucleotide. All nucleosides in Table 1 are deoxyribonucleosides, unless otherwise noted (e.g., LNA).
Example 2. Inhibition of Target Nucleic Acid Expression In Vitro
Oligonucleotides were assessed for their ability to knockdown a target NRL nucleic acid in cultured HEK293 cells expressing high levels of the target homo sapiens NRL (GenBank ID:
BC012395.1) or macaca fascicularis NRL (GenBank ID: XM_015453620.1). Select oligonucleotides from Table 1 above (SEQ ID NOs: 19 and 21-29) were incubated with the cultured cells expressing high levels of the target NRL nucleic acid. Relative target NRL protein (the product of the NRL nucleic acid) reduction was determined using standard techniques useful for quantification of protein (Western blots). The measured target NRL protein was normalized to housekeeping gene (actin) or a constitutively expressed marker (GFP). For comparison, the measured target NRL protein levels was normalized to target NRL protein levels in the same cell line treated with a vehicle control (DPBS).
Dose response analysis was conducted in the selected cell lines (FIG. 2 and FIG. 3), demonstrating that the Nrl-targeting oligonucleotides are effective at reducing the expression of the target NRL. From the dose response analysis, the half maximal inhibitory concentration (IC50) was calculated. The IC50 values of all tested oligonucleotides, normalized to actin or GFP, in HEK293 cells expressing Homo sapiens and/or Macaca fascicularis NRL are indicated in Table 2 below. The relative nucleotide positions and regions for oligonucleotide binding to NRL are also shown below in Table 2.
Table 2: Relative location and IC50 of Nrl-targeting oligonucleotides
Figure imgf000075_0001
Example 3. Inhibition of Target Nucleic Acid Expression In Vitro
Oligonucleotides may be assessed for their ability to knockdown a target NRL nucleic acid in cultured cell line expressing high levels of the target NRL nucleic acid. Selected oligonucleotides may be incubated with a cultured cell line expressing high levels of the target NRL nucleic acid. Relative target NRL protein (a product of the NRL nucleic acid) reduction may be determined using standard techniques useful for quantification of proteins. For comparison, the measured target NRL nucleic acid levels may be normalized to target NRL protein levels in a cell treated with a vehicle control. Alternatively, the measured target NRL nucleic acid levels may be normalized to housekeeping gene levels.
A positive control oligonucleotide may be transfected to ensure appropriate cell transfection efficacy. The transfection may be effected using a transfection agent, e.g., LIPOFECTAMINE.
Dose response analysis may be conducted in the selected cell line. Dose-responsive reduction in the target NRL nucleic acid levels indicates that an oligonucleotide is effective at reducing the expression of the target NRL nucleic acid. Example 4. Functional Testing of Oligonucleotides in Explanted Retinal Cells
An oligonucleotide may be tested in a physiologically relevant primary culture assay using, e.g., intact retinas from wt mice. In this assay, suppression of Rho expression may be used as a read out. After a culture period with media containing vehicle or an oligonucleotide, the retinas may be collected and assessed for Rho expression. Rho is a well-described target of NRL in rod photoreceptors. Oligonucleotides of the invention may cause a substantial reduction in the Rho expression compared to a vehicle in retinal explants from mice. NRL loss-of-function mutations typically lead to a reduction in rod gene expression. To determine whether the same was true for our oligos, explant cultures of murine retinas treated as described above may also be assayed for rod photoreceptor genes, e.g., NRL, NR2E3, GNAT1 , PDE6A, PDE6B, RHO, GNB1 , and CRX. After a culture period (e.g., after 2, 3, 4, 5, 6, or 7 days), an oligonucleotide may decrease the expression of the rod specific genes compared to vehicle treatment.
Intact retinas from adult wild type C57BL/6J mice were explanted on 0.4 pm pore tissue culture inserts (Millicell) in media (Neurobasal-A containing 1% FBS, 1% N2, 1% B27, 1% Pen/Strep, and 0.5% L-Glutamine) containing scrambled negative control (AACACGTCTATACGC) or Nrl targeting (CACGATGCTCAGAAGT) antisense oligonucleotide (ASO) at 10 or 20 pM. In the sequences of the negative control and the ASO, bold, italicized, capital letters designate LNA nucleotides, and plain capital letters designed deoxyribonucleotides. In the sequences of the negative control and the ASO, all internucleoside linkages were phosphorothioate diesters. After 48h in vitro, RNA from the retinas was isolated using Qiazol (Qiagen) and cDNA was synthesized using the iScript cDNA synthesis kit (Bio- Rad). SYBR green PCR master mix (Applied Biosystems) was used for quantitative real-time PCR using a StepOnePlus real-time PCR system (Applied Biosystems). For analysis, values were normalized to Gapdh (DCT) and DDCT between control and ASO-treated samples was expressed as percent of controls (100*2ADDCt). The following primer sequences were used (in order set forth as SEQ ID NOs: 30-49):
Gapdh (F: GGCATT GCT CT CAAT G ACAA, R: CTTGCTCAGT GTCCTT GCT G) ,
Nrl (F: TCCCAGTCCCTTGGCTATGG, R: CACCGAGCTGTATGGTGTG),
Nr2e3 (F: GCAGTGGATCCCACAGAGTT, R: GAGCAATTTCCCAAACCTCA)
Rhodopsin (F: CCCTTCTCCAACGTCACAGG, R: TGAGGAAGTTGATGGGGAAGC),
Gnatl (F: TGACCAATAATGAAGCCATGCT, R: TCTTTGCCCATGGTTGATCA),
S Opsin (F: CAGCATCCGCTTCAACTCCAA, R: GCAGATGAGGGAAAGAGGAATGA),
M Opsin (F: TTGCTGACCTAGCAGAGACCA, R: AGCCTTCAAT G AC AC AC AG AG) ,
Gnat2 (F: TCCACCTCAGTATCTGTTTTCC, R: TT GAG GT C AAGG AACT G ACT CTT) ,
Gnb3 (F: CACTGGCCATGAGTCAGACA, R: GCAGGAGGCGTCATCTGAG), and Otx2 (F: CCGCCTTACGCAGTCAATG, R: GAGGGATGCAGCAAGTCCATA).
The results of this study are shown in FIG. 1. The data summarized in FIG. 1 shows that treatment with the Nrl-targeting ASO decreased Nrl and rod gene expression without decreasing cone gene expression or the expression of Otx2. Otx2 is an upstream transcription factor expressed in both rod and cone photoreceptors. Example 5. Rhodopsin Expression Reduction in the Retinas of Adult Mice
Oligonucleotides may be tested for their effect on adult photoreceptor gene expression in vivo. Oligonucleotide compositions may be administered intravitreally to one eye of an adult mouse (>P21). After a predetermined period of time (e.g., 1 week, 1 month, 3 months, and/or 6 months following the administration), expression of photoreceptor genes may be measured in the treated eye and in the untreated eye. The photoreceptor gene expressions in the treated eye may then be compared to those in the untreated eye. Treatment with oligonucleotides of the invention may reduce the expression of Rho and rod specific genes, e.g., NRL, NR2E3, GNAT1 , PDE6A, PDE6B, GNB1 , and CRX. The Rho and the other rod specific gene expressions may be assessed by qPCR (nucleic acid) and by Western blot (proteins) analyses. The oligonucleotides may also increase the expression of some cone photoreceptor genes (e.g., GNAT 2, PDE6C, GNB3, OPN 1 SW, OPN 1 MW, ARR3, and/or THRB) in the adult retinas.
Example 6. Rod Degeneration in Mutant Rhodopsin Retinas
The effect of the oligonucleotides of the invention on Rho expression in adult rods may have potential as a way to slow the degeneration of these cells in dominant forms of retinitis pigmentosa, e.g., Rho P23H. In this disease, the affected individuals express a mutant form of rhodopsin that is likely inappropriately processed and ultimately leads to the death of the rods. Reducing the NRL expression using oligonucleotides of the invention may slow the degeneration of the rods.
The assay for assessing the effect of an oligonucleotide of the invention on retinitis pigmentosa may be performed as follows. Retina from RhoP23H transgenic mice at P8 may be explanted and maintained in media containing vehicle or an oligonucleotide of the invention. The majority of rod cell deaths in the RhoP23H transgenic line typically occurs between P14 and P21 . Therefore, explants of retinas from RhoP23H mice at P12 were made and treated the explants with vehicle or an oligonucleotide of the invention. Here, designations P8, P12, P14, and P21 refer to the post-natal age of the test mice.
In these tests, P8 explants allow for the assessment of the activity of the oligonucleotides of the invention in decreasing the level of expression of Rho, and P12 explants allow for the assessment of the activity of the oligonucleotides of the invention in preserving the cells in the outer nuclear layer (ONL).
After an extended culture period, the retinas may be subjected to histologic analysis. The number of nuclei may be counted in the outer nuclear layer (ONL) of each retina in the central region. Retinas treated with an oligonucleotide of the invention may have a greater number of rod photoreceptors in the ONL than vehicle-treated controls.
Example 7. Rod Degeneration in Mutant RPE Retinas
Oligonucleotides of the invention may slow the degeneration of adult rod cells in recessive forms of retinitis pigmentosa, driven by mutations in genes like Phosphodiesterase 6 (PDE6). PDE6 is highly concentrated in the retina. It is most abundant in the internal membranes of retinal photoreceptors, where it reduces cytoplasmic levels of cyclic guanosine monophosphate (cGMP) in rod and cone outer segments in response to light. In this disease, the affected individuals express a mutant form of PDE6 that ultimately leads to the death of the rods and cones.
Oligonucleotides of the invention may be assayed to assess their effect on the degeneration of the photoreceptor cells as follows. Retina from rd10 mice, carrying a spontaneous PDE mutation, at P8 may be explanted and maintained in media containing vehicle or an oligonucleotide of the invention. The mutant rods may then be assayed for the rhodopsin expression levels, and the rhodopsin expression levels may be compared to those in the wild-type retina. Rod degeneration in these mice starts around P18. Therefore, explants of retinas from rd10 mice at P16 may be made. The explants may be treated with vehicle or an oligonucleotide of the invention. Here, designations P8, P16, and P18 refer to the postnatal age of the test mice. In these tests, P8 explants allow for the assessment of the activity of the oligonucleotides of the invention in decreasing the level of expression of RHO, and P16 explants allow for the assessment of the activity of the oligonucleotides of the invention in preserving the cells in the outer nuclear layer (ONL).
After an extended culture period, the retinas may be subjected to histologic analysis. The number of nuclei may be counted in the ONL of each retina in the central region. Retinas treated with an oligonucleotide of the invention may have a greater number of rod photoreceptors in the ONL than vehicle-treated controls.
The studies described herein demonstrate that the oligonucleotides of the invention may be useful in the treatment of multiple inherited retinal degenerations (IRDs) in a mutation independent manner. The inherited retinal degenerations include, e.g., diseases, disorders, and conditions associated with a of ABCA4, AIPL1 , BBS1 , BEST1 , CEP290, CDH3, CHM, CNGA3, CNGB3, CRB1 , GUCY2D, MERTK, MRFP, MY07A, ND4, NRL, PDE6, PRPH2, RD3, RHO, RLBP1 , RP1 , RPE65, RPGR,
RPGRIP1 , RS1 , or SPATA7 gene. Non-limiting examples of the diseases, disorders, and conditions that may be treated using oligonucleotides of the invention include retinitis pigmentosa, Stargardt disease, cone-rod dystrophy, Leber congenital amaurosis, Bardet Biedl syndrome, macular dystrophy, dry macular degeneration, geographic atrophy, atrophic age-related macular degeneration (AMD), advanced dry AMD, retinal dystrophy, choroideremia, Usher syndrome type 1 , retinoschisis, Leber hereditary optic neuropathy, and achromatopsia.
Example 8. Primary Culture Assay for Assessing Photoreceptor Gene Expression in Human Retinas
An oligonucleotide may be tested in a physiologically relevant primary culture assay using intact human retinas. In this assay, suppression of NRL and additional rod genes (e.g., NR2E3, RHO, GNAT1 , PDE6A, PDE6B, GNB1 , and/or CRX) may be used as a read out. After a culture period (e.g., 2, 3, 4, 5,
6, or 7 days) with media containing vehicle or an oligonucleotide, the retinal tissue may be collected and assessed for rod gene expression. NR2E3, RHO, GNAT1 , PDE6A, PDE6B, and GNB1 are targets of NRL in photoreceptors, and oligonucleotides described herein may cause a substantial reduction of their expression. NRL loss-of-function mutations lead to a reduction in rod gene expression. To determine whether the same is true for oligonucleotides described herein, cultures of human retinas may be explanted and treated as described in Example 4.
Some embodiments of the invention are within the description provided above. Some embodiments are within the description of the following numbered paragraphs.
1. A single-stranded oligonucleotide comprising a total of 12 to 50 interlinked nucleotides and having a nucleobase sequence comprising at least 6 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof. 2. A single-stranded oligonucleotide comprising a total of 12 to 50 interlinked nucleotides and having a nucleobase sequence comprising at least 6 contiguous nucleobases complementary to the target sequence of any one of SEQ ID NOs: 6-17.
3. The oligonucleotide of paragraph 1 or 2, wherein the oligonucleotide comprises at least one modified nucleobase.
4. The oligonucleotide of paragraph 3, wherein at least one modified nucleobase is 5- methylcytosine.
5. The oligonucleotide of paragraph 3 or 4, wherein at least one modified nucleobase is 7- deazaguanine.
6. The oligonucleotide of any one of paragraphs 3 to 5, wherein at least one modified nucleobase is 6-thioguanine.
7. The oligonucleotide of any one of paragraphs 1 to 6, wherein the oligonucleotide comprises at least one modified internucleoside linkage.
8. The oligonucleotide of paragraph 7, wherein the modified internucleoside linkage is a phosphorothioate linkage.
9. The oligonucleotide of paragraph 8, wherein the phosphorothioate linkage is a stereochemically enriched phosphorothioate linkage.
10. The oligonucleotide of any one of paragraphs 7 to 9, wherein at least 50% of internucleoside linkages in the oligonucleotide are each independently the modified internucleoside linkage.
11. The oligonucleotide of paragraph 10, wherein at least 70% of internucleoside linkages in the oligonucleotide are each independently the modified internucleoside linkage.
12. The oligonucleotide of any one of paragraphs 1 to 11 , wherein the oligonucleotide comprises at least one modified sugar nucleoside.
13. The oligonucleotide of paragraph 12, wherein at least one modified sugar nucleoside is a bridged nucleic acid.
14. The oligonucleotide of paragraph 13, wherein the bridged nucleic acid is a locked nucleic acid (LNA), ethylene-bridged nucleic acid (ENA), or cEt nucleic acid.
15. The oligonucleotide of paragraph 14, wherein the oligonucleotide is a gapmer.
16. The oligonucleotide of any one of paragraphs 12 to 15, wherein at least one modified sugar nucleoside is a 2’-modified sugar nucleoside.
17. The oligonucleotide of paragraph 16, wherein at least one 2’-modified sugar nucleoside comprises a 2’-modification selected from the group consisting of 2’-fluoro, 2’-methoxy, and 2’- methoxyethoxy.
18. The oligonucleotide of any one of paragraphs 1 to 17, wherein the oligonucleotide comprises deoxy ribonucleotides.
19. The oligonucleotide of any one of paragraphs 1 to 18, wherein the oligonucleotide comprises ribonucleotides.
20. The oligonucleotide of any one of paragraphs 1 to 6, wherein the oligonucleotide is a morpholino oligomer.
21. The oligonucleotide of any one of paragraphs 1 to 20, wherein the oligonucleotide comprises a hydrophobic moiety covalently attached at a 5’-terminus, 3’-terminus, or internucleoside linkage of the oligonucleotide. 22. The oligonucleotide of any one of paragraphs 1 to 21 , wherein the oligonucleotide comprises a region complementary to a coding sequence within the NRL target nucleic acid.
23. The oligonucleotide of any one of paragraphs 1 to 22, wherein the oligonucleotide comprises a total of at least 7 interlinked nucleotides.
24. The oligonucleotide of paragraph 23, wherein the single-stranded oligonucleotide comprises at least 7 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
25. The oligonucleotide of any one of paragraphs 1 to 24, wherein the oligonucleotide comprises a total of at least 8 interlinked nucleotides.
26. The oligonucleotide of paragraph 25, wherein the single-stranded oligonucleotide comprises at least 8 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
27. The oligonucleotide of any one of paragraphs 1 to 22, wherein the oligonucleotide comprises a total of at least 9 interlinked nucleotides.
28. The oligonucleotide of paragraph 22, wherein the single-stranded oligonucleotide comprises at least 9 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
29. The oligonucleotide of any one of paragraphs 1 to 22, wherein the oligonucleotide comprises a total of at least 10 interlinked nucleotides.
30. The oligonucleotide of paragraph 29, wherein the single-stranded oligonucleotide comprises at least 10 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
31 . The oligonucleotide of any one of paragraphs 1 to 30, wherein the oligonucleotide comprises a total of 10 interlinked nucleotides or fewer.
32. The oligonucleotide of any one of paragraphs 1 to 22, wherein the oligonucleotide comprises a total of at least 11 interlinked nucleotides.
33. The oligonucleotide of paragraph 32, wherein the single-stranded oligonucleotide comprises at least 11 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
34. The oligonucleotide of any one of paragraphs 1 to 22, wherein the oligonucleotide comprises a total of at least 12 interlinked nucleotides.
35. The oligonucleotide of paragraph 34, wherein the single-stranded oligonucleotide comprises at least 12 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
36. The oligonucleotide of any one of paragraphs 1 to 22, wherein the oligonucleotide comprises a total of at least 13 interlinked nucleotides.
37. The oligonucleotide of paragraph 36, wherein the single-stranded oligonucleotide comprises at least 13 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
38. The oligonucleotide of any one of paragraphs 1 to 22, wherein the oligonucleotide comprises a total of at least 14 interlinked nucleotides. 39. The oligonucleotide of paragraph 38, wherein the single-stranded oligonucleotide comprises at least 14 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
40. The oligonucleotide of any one of paragraphs 1 to 22, wherein the oligonucleotide comprises a total of at least 15 interlinked nucleotides.
41 . The oligonucleotide of paragraph 40, wherein the single-stranded oligonucleotide comprises at least 15 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
42. The oligonucleotide of any one of paragraphs 1 to 22, wherein the oligonucleotide comprises a total of at least 16 interlinked nucleotides.
43. The oligonucleotide of paragraph 42, wherein the single-stranded oligonucleotide comprises at least 16 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
44. The oligonucleotide of any one of paragraphs 1 to 43, wherein the oligonucleotide comprises a total of 25 interlinked nucleotides or fewer.
45. The oligonucleotide of any one of paragraphs 1 to 43, wherein the oligonucleotide comprises a total of 20 interlinked nucleotides or fewer.
46. The oligonucleotide of any one of paragraphs 1 to 43, wherein the oligonucleotide comprises a total of 19 interlinked nucleotides or fewer.
47. The oligonucleotide of any one of paragraphs 1 to 43, wherein the oligonucleotide comprises a total of 18 interlinked nucleotides or fewer.
48. The oligonucleotide of any one of paragraphs 1 to 43, wherein the oligonucleotide comprises a total of 17 interlinked nucleotides or fewer.
49. The oligonucleotide of any one of paragraphs 1 to 43, wherein the oligonucleotide comprises a total of 16 interlinked nucleotides or fewer.
50. The oligonucleotide of any one of paragraphs 1 to 41 , wherein the oligonucleotide comprises a total of 15 interlinked nucleotides or fewer.
51 . The oligonucleotide of any one of paragraphs 1 to 39, wherein the oligonucleotide comprises a total of 14 interlinked nucleotides or fewer.
52. The oligonucleotide of any one of paragraphs 1 to 37, wherein the oligonucleotide comprises a total of 13 interlinked nucleotides or fewer.
53. The oligonucleotide of any one of paragraphs 1 to 36, wherein the oligonucleotide comprises a total of 12 interlinked nucleotides or fewer.
54. The oligonucleotide of any one of paragraphs 1 to 33, wherein the oligonucleotide comprises a total of 11 interlinked nucleotides or fewer.
55. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 6.
56. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 7.
57. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 8. 58. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 9.
59. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 10.
60. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 11.
61 . The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 12.
62. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 13.
63. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 14.
64. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 15.
65. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 16.
66. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 17.
67. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 18.
68. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 19.
69. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 20.
70. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 21.
71 . The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 22.
72. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 23.
73. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 24.
74. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 25.
75. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 26.
76. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 27.
77. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 28.
78. The oligonucleotide of any one of paragraphs 1 to 54, wherein the nucleotide sequence is set forth in SEQ ID NO: 29. 79. The oligonucleotide of any one of paragraphs 55 to 78, wherein the sequence of the oligonucleotide comprises or consists of the nucleotide sequence referenced in the paragraph.
80. An oligonucleotide having a nucleotide sequence that comprises the sequence of any one of SEQ ID NOs: 6-29 or a chemically modified version thereof.
81. The oligonucleotide of paragraph 80, having a nucleotide sequence that consists of the sequence of any one of SEQ ID NOs: 6-29 or a chemically modified version thereof.
82. The oligonucleotide of paragraph 80 or 81 , which comprises a feature or modification as set forth in any one of paragraphs 3 to 23.
83. A pharmaceutically acceptable salt of an oligonucleotide of any one of paragraphs 1 to 82.
84. A pharmaceutical composition comprising the oligonucleotide of any one of paragraph 1 to 83 and a pharmaceutically acceptable excipient.
85. A method of inhibiting or reducing the production of an NRL protein in a cell comprising an NRL gene, the method comprising contacting the cell with the oligonucleotide of any one of paragraphs 1 to
82, the pharmaceutically acceptable salt of paragraph 83, or the pharmaceutically acceptable composition of paragraph 84.
86. The method of paragraph 85, wherein the cell is in a subject.
87. The method of paragraph 86, wherein the cell is in the subject’s eye.
88. A method of treating a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of the oligonucleotide of any one of paragraphs 1 to 82, the pharmaceutically acceptable salt of paragraph 83, or the pharmaceutically acceptable composition of paragraph 84.
89. The method of any one of paragraphs 85 to 88, wherein the oligonucleotide or pharmaceutical composition is administered intraocularly or topically to the eye of the subject.
90. The method of any one of paragraphs 85 to 89, wherein the subject is in need of a treatment for an ocular disease, disorder, or condition associated with a dysfunction of ABCA4, AIPL1 , BBS1 , BEST1 , CEP290, CDH3, CHM, CNGA3, CNGB3, CRB1 , GUCY2D, MERTK, MRFP, MY07A, ND4, NR2E3,
PDE6, PRPH2, RD3, RHO, RLBP1 , RP1 , RPE65, RPGR, RPGRIP1 , RS1 , or SPATA7 gene.
91. The method of any one of paragraphs 85 to 90, wherein the subject is in need of a treatment for retinitis pigmentosa, Stargardt disease, cone-rod dystrophy, Leber congenital amaurosis, Bardet Biedl syndrome, macular dystrophy, dry macular degeneration, geographic atrophy, atrophic age-related macular degeneration (AMD), advanced dry AMD, retinal dystrophy, choroideremia, Usher syndrome type 1 , retinoschisis, Leber hereditary optic neuropathy, and achromatopsia.
92. The method of paragraph 91 , wherein the subject is in need of a treatment for retinitis pigmentosa.
93. The method of paragraph 92, wherein retinitis pigmentosa is Rho P23H-associated retinitis pigmentosa, PDE6-associated retinitis pigmentosa, MERTK-associated retinitis pigmentosa, BBS1- associated retinitis pigmentosa, Rho-associated retinitis pigmentosa, MRFP-associated retinitis pigmentosa, RLBP1 -associated retinitis pigmentosa, RP1 -associated retinitis pigmentosa, RPGR-X- linked retinitis pigmentosa, NR2E3-associated retinitis pigmentosa, or SPATA7-associated retinitis pigmentosa.
94. A double-stranded oligonucleotide including an oligonucleotide of paragraph 1 or 2 hybridized to a complementary oligonucleotide, wherein optionally (a) the complementary oligonucleotide has the same length as the oligonucleotide of paragraph 1 or 2, or (b) the complementary oligonucleotide has a length that is at least, e.g., ±1 , ±2, ±3, ±4, or ±5 nucleotides relative to the number of nucleotides in the oligonucleotide of paragraph 1 or 2. OTHER EMBODIMENTS
Various modifications and variations of the described invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention that are obvious to those skilled in the art are intended to be within the scope of the invention.
Other embodiments are in the claims.

Claims

WHAT IS CLAIMED IS:
1. A single-stranded oligonucleotide comprising a total of 12 to 50 interlinked nucleotides and having a nucleobase sequence comprising at least 6 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
2. A single-stranded oligonucleotide comprising a total of 12 to 50 interlinked nucleotides and having a nucleobase sequence comprising at least 6 contiguous nucleobases complementary to the target sequence of any one of SEQ ID NOs: 6-17.
3. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises at least one modified nucleobase.
4. The oligonucleotide of claim 3, wherein at least one modified nucleobase is 5-methylcytosine.
5. The oligonucleotide of claim 3, wherein at least one modified nucleobase is 7-deazaguanine.
6. The oligonucleotide of claim 3, wherein at least one modified nucleobase is 6-thioguanine.
7. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises at least one modified internucleoside linkage.
8. The oligonucleotide of claim 7, wherein the modified internucleoside linkage is a phosphorothioate linkage.
9. The oligonucleotide of claim 8, wherein the phosphorothioate linkage is a stereochemically enriched phosphorothioate linkage.
10. The oligonucleotide of claim 7, wherein at least 50% of internucleoside linkages in the oligonucleotide are each independently the modified internucleoside linkage.
11 . The oligonucleotide of claim 10, wherein at least 70% of internucleoside linkages in the oligonucleotide are each independently the modified internucleoside linkage.
12. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises at least one modified sugar nucleoside.
13. The oligonucleotide of claim 12, wherein at least one modified sugar nucleoside is a bridged nucleic acid.
14. The oligonucleotide of claim 13, wherein the bridged nucleic acid is a locked nucleic acid (LNA), ethylene-bridged nucleic acid (ENA), or cEt nucleic acid.
15. The oligonucleotide of claim 14, wherein the oligonucleotide is a gapmer.
16. The oligonucleotide of claim 12, wherein at least one modified sugar nucleoside is a 2’-modified sugar nucleoside.
17. The oligonucleotide of claim 16, wherein at least one 2’-modified sugar nucleoside comprises a 2’-modification selected from the group consisting of 2’-fluoro, 2’-methoxy, and 2’-methoxyethoxy.
18. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises deoxyribonucleotides.
19. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises ribonucleotides.
20. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide is a morpholino oligomer.
21 . The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a hydrophobic moiety covalently attached at a 5’-terminus, 3’-terminus, or internucleoside linkage of the oligonucleotide.
22. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a region complementary to a coding sequence within the NRL target nucleic acid.
23. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of at least 7 interlinked nucleotides.
24. The oligonucleotide of claim 23, wherein the single-stranded oligonucleotide comprises at least 7 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6- 17 and chemically modified versions thereof.
25. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of at least 8 interlinked nucleotides.
26. The oligonucleotide of claim 25, wherein the single-stranded oligonucleotide comprises at least 8 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6- 17 and chemically modified versions thereof.
27. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of at least 9 interlinked nucleotides.
28. The oligonucleotide of claim 22, wherein the single-stranded oligonucleotide comprises at least 9 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6- 17 and chemically modified versions thereof.
29. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of at least 10 interlinked nucleotides.
30. The oligonucleotide of claim 29, wherein the single-stranded oligonucleotide comprises at least
10 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
31 . The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 10 interlinked nucleotides or fewer.
32. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of at least 11 interlinked nucleotides.
33. The oligonucleotide of claim 32, wherein the single-stranded oligonucleotide comprises at least
11 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
34. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of at least 12 interlinked nucleotides.
35. The oligonucleotide of claim 34, wherein the single-stranded oligonucleotide comprises at least
12 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
36. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of at least 13 interlinked nucleotides.
37. The oligonucleotide of claim 36, wherein the single-stranded oligonucleotide comprises at least
13 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
38. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of at least 14 interlinked nucleotides.
39. The oligonucleotide of claim 38, wherein the single-stranded oligonucleotide comprises at least
14 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
40. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of at least 15 interlinked nucleotides.
41 . The oligonucleotide of claim 40, wherein the single-stranded oligonucleotide comprises at least
15 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
42. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of at least 16 interlinked nucleotides.
43. The oligonucleotide of claim 42, wherein the single-stranded oligonucleotide comprises at least
16 contiguous nucleobases in a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6-17 and chemically modified versions thereof.
44. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 25 interlinked nucleotides or fewer.
45. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 20 interlinked nucleotides or fewer.
46. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 19 interlinked nucleotides or fewer.
47. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 18 interlinked nucleotides or fewer.
48. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 17 interlinked nucleotides or fewer.
49. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 16 interlinked nucleotides or fewer.
50. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 15 interlinked nucleotides or fewer.
51 . The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 14 interlinked nucleotides or fewer.
52. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 13 interlinked nucleotides or fewer.
53. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 12 interlinked nucleotides or fewer.
54. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide comprises a total of 11 interlinked nucleotides or fewer.
55. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO: 6.
56. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
7.
57. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
8.
58. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
9.
59. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
10.
60. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO: 11.
61 . The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO: 12.
62. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
13.
63. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
14.
64. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
15.
65. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
16.
66. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
17.
67. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
18.
68. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
19.
69. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
20.
70. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO: 21.
71 . The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO: 22.
72. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
23.
73. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
24.
74. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
25.
75. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
26.
76. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
27.
77. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO:
28.
78. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence is set forth in SEQ ID NO: 29.
79. The oligonucleotide of claim 55, wherein the sequence of the oligonucleotide comprises or consists of the nucleotide sequence referenced in the claim.
80. An oligonucleotide having a nucleotide sequence that comprises the sequence of any one of SEQ ID NOs: 6-29 or a chemically modified version thereof.
81 . The oligonucleotide of claim 80, having a nucleotide sequence that consists of the sequence of any one of SEQ ID NOs: 6-29 or a chemically modified version thereof.
82. The oligonucleotide of claim 80, which comprises a feature or modification as set forth herein.
83. A pharmaceutically acceptable salt of an oligonucleotide of claim 1 or 2.
84. A pharmaceutical composition comprising the oligonucleotide of claim 1 and a pharmaceutically acceptable excipient.
85. A method of inhibiting or reducing the production of an NRL protein in a cell comprising an NRL gene, the method comprising contacting the cell with the oligonucleotide of claim 1 or 2, a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising said oligonucleotide or said pharmaceutically acceptable salt.
86. The method of claim 85, wherein the cell is in a subject.
87. The method of claim 86, wherein the cell is in the subject’s eye.
88. A method of treating a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of the oligonucleotide of claim 1 or 2, a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising said oligonucleotide or said pharmaceutically acceptable salt.
89. The method of claim 85, wherein the oligonucleotide or pharmaceutical composition is administered intraocularly or topically to the eye of the subject.
90. The method of claim 85, wherein the subject is in need of a treatment for an ocular disease, disorder, or condition associated with a dysfunction of ABCA4, AIPL1 , BBS1 , BEST1 , CEP290, CDH3, CHM, CNGA3, CNGB3, CRB1 , GUCY2D, MERTK, MRFP, MY07A, ND4, NR2E3, PDE6, PRPH2, RD3, RHO, RLBP1 , RP1 , RPE65, RPGR, RPGRIP1 , RS1 , or SPATA7 gene.
91 . The method of claim 85, wherein the subject is in need of a treatment for retinitis pigmentosa, Stargardt disease, cone-rod dystrophy, Leber congenital amaurosis, Bardet Biedl syndrome, macular dystrophy, dry macular degeneration, geographic atrophy, atrophic age-related macular degeneration (AMD), advanced dry AMD, retinal dystrophy, choroideremia, Usher syndrome type 1 , retinoschisis, Leber hereditary optic neuropathy, and achromatopsia.
92. The method of claim 91 , wherein the subject is in need of a treatment for retinitis pigmentosa.
93. The method of claim 92, wherein retinitis pigmentosa is Rho P23H-associated retinitis pigmentosa, PDE6-associated retinitis pigmentosa, MERTK-associated retinitis pigmentosa, BBS1- associated retinitis pigmentosa, Rho-associated retinitis pigmentosa, MRFP-associated retinitis pigmentosa, RLBP1 -associated retinitis pigmentosa, RP1 -associated retinitis pigmentosa, RPGR-X- linked retinitis pigmentosa, NR2E3-associated retinitis pigmentosa, or SPATA7-associated retinitis pigmentosa.
94. The method of claim 88, wherein the oligonucleotide or pharmaceutical composition is administered intraocularly or topically to the eye of the subject.
95. The method claim 88, wherein the subject is in need of a treatment for an ocular disease, disorder, or condition associated with a dysfunction of ABCA4, AIPL1 , BBS1 , BEST 1 , CEP290, CDH3, CHM, CNGA3, CNGB3, CRB1 , GUCY2D, MERTK, MRFP, MY07A, ND4, NR2E3, PDE6, PRPH2, RD3, RHO, RLBP1 , RP1 , RPE65, RPGR, RPGRIP1, RS1 , or SPATA7 gene.
96. The method of claim 88, wherein the subject is in need of a treatment for retinitis pigmentosa, Stargardt disease, cone-rod dystrophy, Leber congenital amaurosis, Bardet Biedl syndrome, macular dystrophy, dry macular degeneration, geographic atrophy, atrophic age-related macular degeneration (AMD), advanced dry AMD, retinal dystrophy, choroideremia, Usher syndrome type 1 , retinoschisis,
Leber hereditary optic neuropathy, and achromatopsia.
97. The method of claim 96, wherein the subject is in need of a treatment for retinitis pigmentosa.
98. The method of claim 97, wherein retinitis pigmentosa is Rho P23H-associated retinitis pigmentosa, PDE6-associated retinitis pigmentosa, MERTK-associated retinitis pigmentosa, BBS1- associated retinitis pigmentosa, Rho-associated retinitis pigmentosa, MRFP-associated retinitis pigmentosa, RLBP1 -associated retinitis pigmentosa, RP1 -associated retinitis pigmentosa, RPGR-X- linked retinitis pigmentosa, NR2E3-associated retinitis pigmentosa, or SPATA7-associated retinitis pigmentosa.
99. A double-stranded oligonucleotide including an oligonucleotide of claim 1 or 2 hybridized to a complementary oligonucleotide, wherein optionally (a) the complementary oligonucleotide has the same length as the oligonucleotide of claim 1 or 2, or (b) the complementary oligonucleotide has a length that is at least, e.g., ±1 , ±2, ±3, ±4, or ±5 nucleotides relative to the number of nucleotides in the oligonucleotide of claim 1 or 2.
PCT/US2021/043716 2020-07-29 2021-07-29 Nrl antisense oligonucleotides, compositions containing the same, and methods of their use WO2022026719A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202063058296P 2020-07-29 2020-07-29
US63/058,296 2020-07-29

Publications (2)

Publication Number Publication Date
WO2022026719A2 true WO2022026719A2 (en) 2022-02-03
WO2022026719A3 WO2022026719A3 (en) 2022-03-17

Family

ID=80036742

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2021/043716 WO2022026719A2 (en) 2020-07-29 2021-07-29 Nrl antisense oligonucleotides, compositions containing the same, and methods of their use

Country Status (1)

Country Link
WO (1) WO2022026719A2 (en)

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20180346981A1 (en) * 2014-11-20 2018-12-06 Massachusetts Eye And Ear Infirmary Panel-based Genetic Diagnostic Testing for Inherited Eye Diseases
KR102321425B1 (en) * 2019-01-18 2021-11-04 올릭스 주식회사 Asymmetric siRNA Inhibiting Expression of NRL

Also Published As

Publication number Publication date
WO2022026719A3 (en) 2022-03-17

Similar Documents

Publication Publication Date Title
DK2742135T3 (en) BINDING MODIFIED GAPPED OLIGOMERIC COMPOUNDS AND APPLICATIONS THEREOF
AU2016234914B2 (en) Selective reduction of allelic variants
DK2906256T3 (en) SELECTIVE ANTISENSE COMPOUNDS AND APPLICATIONS THEREOF
CN106459972B (en) Compositions for modulating SOD-1 expression
CN109790543B (en) Compounds and methods for reducing TAU expression
KR20190018515A (en) A nucleic acid molecule for reducing PAPD5 or PAPD7 mRNA to treat hepatitis B infection
US20040180847A1 (en) Antisense modulation of kinesin-like 1 expression
KR20060116848A (en) Antisense oligonucleotide modulation of stat3 expression
KR20190076025A (en) Compounds and Methods for Reducing ATXN3 Expression
KR20210008497A (en) Compounds and methods for reducing ATXN3 expression
CN107267517A (en) Noval chemical compound for treating, delaying and/or preventing human genetic disease&#39;s such as type of steirert-Batten-Gibb syndrome 1
RU2766360C2 (en) Nucleic acid molecules for reducing papd5 or papd7 mrna levels for treating infectious hepatitis b
AU2017234678A1 (en) Methods of modulating KEAP1
WO2021202557A1 (en) Spherical nucleic acids (snas) for regulation of frataxin
CN111655851A (en) Antisense oligonucleotides targeting SREBP1
US6448080B1 (en) Antisense modulation of WRN expression
KR20230043914A (en) Compounds and methods for reducing APP expression
WO2022026719A2 (en) Nrl antisense oligonucleotides, compositions containing the same, and methods of their use
US20030232771A1 (en) Antisense modulation of MARK3 expression
US20030158144A1 (en) Antisense modulation of estrogen receptor beta expression
US20220098595A1 (en) Nr2e3 expression reducing oligonucleotides, compositions containing the same, and methods of their use
TW202317765A (en) Compounds and methods for reducing ifnar1 expression
TW202313976A (en) Oligonucleotide progranulin agonists
TW202216171A (en) Methods of safe administration of an irf5 antisense oligonucleotide
US20040115637A1 (en) Modulation of PPAR-alpha expression

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 21851439

Country of ref document: EP

Kind code of ref document: A2

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 21851439

Country of ref document: EP

Kind code of ref document: A2