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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
  • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
  • A61K31/7088—Compounds having three or more nucleosides or nucleotides
  • A61K31/713—Double-stranded nucleic acids or oligonucleotides
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
  • C12N15/113—Non-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
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  • C12N2310/00—Structure or type of the nucleic acid
  • C12N2310/30—Chemical structure
  • C12N2310/32—Chemical structure of the sugar
  • C12N2310/323—Chemical structure of the sugar modified ring structure
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  • C12N2310/00—Structure or type of the nucleic acid
  • C12N2310/30—Chemical structure
  • C12N2310/34—Spatial arrangement of the modifications
  • C12N2310/344—Position-specific modifications, e.g. on every purine, at the 3'-end
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  • C12N2320/00—Applications; Uses
  • C12N2320/50—Methods for regulating/modulating their activity
  • C12N2320/51—Methods for regulating/modulating their activity modulating the chemical stability, e.g. nuclease-resistance

Definitions

• the invention relates to modified oligonucleotides that are advantageous for inhibition of target gene expression, as well as compositions suitable for therapeutic use. Additionally, the invention provides methods of inhibiting the expression of a target gene by administering these modified oligonucleotides, e.g., for the treatment of various diseases.
• RNA interference or “RNAi” is a term initially coined by Fire and co-workers to describe the observation that double-stranded RNAi (dsRNA) can block gene expression (Fire et al. (1998) Nature 391, 806-811; Elbashir et al. (2001) Genes Dev. 15, 188-200).
• Short dsRNA directs gene-specific, post-transcriptional silencing in many organisms, including vertebrates, and has provided a new tool for studying gene function.
• RNAi is mediated by RNA-induced silencing complex (RISC), a sequence-specific, multi-component nuclease that destroys messenger RNAs homologous to the silencing trigger.
• RISC RNA-induced silencing complex
• RISC is known to contain short RNAs (approximately 22 nucleotides) derived from the double-stranded RNA trigger, but the protein components of this activity remained unknown.
• RNA interference RNA interference
• RNAi RNA interference
• sequence-specific target recognition makes off-target toxicity less of a concern.
• RNAi based strategies that use different classes of RNA for efficient knockdown.
• Short interfering RNAs are one type that are fully complementary to the target sequence on the transcript and are introduced into target cells as a duplex. After entering cells, the siRNA is loaded into an RNA-induced silencing complex (RISC). During the loading process, the passenger (sense) strand is removed and the guide (antisense) strand remains within the RISC where it binds to its complementary site on the target mRNA. The bound mRNA can then be cleaved by the nuclease activity of RISC and then further degraded by cellular nucleases.
• RISC RNA-induced silencing complex
• ANAs Altritol-modified nucleic acids support RNA-like A-form strcutures when included in double-stranded nucleic acid strcutres anmd improve nuclease stability. While ANA modifications can improve efficacy when placed at 3′-end of the sense strand in an siRNA, ANA modicifcations result in complete loss of activity when placed at 5′-end of the anstrand strand. See, Chem. Eur. J. 1999, 5, 2424-2431; Nucleic Acids Res. 2007, 35, 1064-1074; Eur. J. Pharm. 2009, 606, 38-44; and Nucleic Acids Res. 2012, 40, 7573-7583.
• This invention provides effective nucleotide or chemical motifs for dsRNA molecules, which are advantageous for inhibition of target gene expression as well as RNAi compositions suitable for therapeutic use.
• dsRNA molecules comprising one or more altritol nucleotides at certain positions, e.g., in the seed region of the antisense strand and/or the sense strand, are surprisingly more effective and/or not detrimental in mediating RNA interference.
• a dsRNA molecule capable of inhibiting the expression of a target gene.
• the dsRNA molecule comprises a sense strand and an antisense strand, wherein the antisense strand has sufficient complementarity to a target sequence to mediate RNA interference, and the dsRNA molecule comprises at least one hexopyranose nucleotide or a cyclohexene nucleotide.
• the hexopyranose nucleoside is of the following structure:
• B is a modified or unmodified nucleobase
• R 1 , R 2 , R 3 , R 4 , R 5 and R 6 independently are H, halogen, OH, protected OH, NH2, NHMe, NMe2, OR 9 , C 1 -C 6 alkyl (e.g., methyl, ethyl, propyl, etc%), branched lipids or amino alkyl
• R 7 and R 8 independently are H, C 1 -C 6 alkyl (e.g., methyl, ethyl, propyl, etc...), or OR 9
• R 9 is C 1 -C 20 alkyl, C 2 -C 20 alkenyl, C 2 -C 20 alkynyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar.
• Exemplary hexopyranose nucleotides include, but are not limited to allopyranose nucleotide, altropyranose nucleotide (altriol nucleotide), glucopyranose nucleotide, mannopyranose nucleotide, gulopyranose nucleotide, idopyranose nucleotide, galactopyranose nucleotide, and talopyranose nucleotide.
• the hexopyranose nucleotide is a deoxyhexopyranose nucleotide, e.g., a 6-deoxyhexopyranose nucleotide.
• Exmplary deoxyhexapyranose nucleotides include, but are not limited fucopyranose nucleotide, rhamopyranose nucleotide, quinovopyranose nucleotide, and pneumopyranose nucleotide.
• the hexopyranose nucleotide or the cyclohexene nucleoside is selected from thos shown in FIGS.12 and 13.
• the hexopyranose nucleotide is an altritol nucleotide.
• the hexopyranose nucleotide is an [0012] in some embodiments, the hexopyranose nucleotide is an [0013] In some embodiments, the altritol nucleotide is present in the antisense strand. Generally, the altritol nucleotide can be present anywhere in the antisense strand. For example, the altritol nucleotide can be present within the seed region (i.e., at position 3-8, of the 5’-end of the antisense strand, counting from the 5′-end). [0014] In some embodiments, the altritol nucleotide is present in the sense strand. As with antisense strand, the altritol nucleotide can be present anywhere in the sense strand.
• the altritol nucleotide can be present within a 5’-region (i.e., at position 2-8, of the 5’- end of the sense strand, counting from the 5′-end).
• the sense strand comprises an altritol nucleotide in a centrafsl region of the sense strand.
• the dsRNA molecule comprises at least one 2’-fluoro nucleotide and/or at least one 2’-OMe nucleotide.
• the dsRNA molecule comprises at least one, two, three four or more phosphorothioate internucleotide linkages.
• the dsRNA molecule further comprises a ligand conjugated to the sense strand or the antisense strand.
• the dsRNA molecule further comprises a ASGPR ligand conjugated to the sense strand or the antisnese strand.
• the ligand is conjugated at the 3’-end of the sense strand.
• the disclosure provides a method for inhibiting the expression of a target gene sequence. Generally, the method comprises administering a dsRNA molecule described herein to a cell in an amount sufficient to inhibit expression of the target gene.
• the cell can be in vitro or in vivo.
• the disclosure provides a pharmaceutical composition comprising a dsRNA molecule described herein.
• the disclosure provides a method for treating a subject using a dsRNA molecule described herein.
• the method for treatment comprises administering a therapeutically effective amount of a dsRNA molecule described herein to a subject in need thereof.
• Fig.1A depicts sense and antisense strand sequences for an exemplary dsRNA.
• Fig.1A depicts sense and antisense strand sequences for an exemplary dsRNA.
• FIG. 1B depicts strucutres of 2′-OMe RNA, 2′-F RNA and altritol nucleic acid (ANA) nucleotides.
• Fig. 2 is a bar graph showing the in vitro RNAi activity of duplexes with ANA in the antisense strand. The nucleotide at the indicated position of the antisense, also called the guide strand, was substituted with the corresponding ANA nucleotide.
• Fig. 3 is a bar graph showing the in vitro RNAi activity of duplexes with ANA in the sense strand. The nucleotide at the indicated position of the sense strand, also called the passenger strand, was substituted with the corresponding ANA nucleotide.
• Fig. 4 are line graphs showing IC50 values of selected exemplary siRNAs comprising ANA modifications. The indicated position of the antisense or sense strand carries the corresponding ANA nucleotide.
• Figs. 5A and 5B are line graphs showing on-target (Fig. 5A) and off-target (Fig. 5B) inhibitory effect of exemplary siRNAs in a luciferase reporter assay. Luciferase reporter plasmids were co-transfected with indicated siRNAs into COS-7 cells. The cells were harvested at 48 h after transfection for the dual luciferase assay.
• Figs. 6A and 6B show in vivo activity of subcutaneously dosed ANA-containing siRNAs in C57BL/6 mice.
• Fig. 6A is a bar graph showing the Ttr protein levels in circulation determined via ELISA (Mean ⁇ SD).
• Fig. 6B is a bar graph showing Ttr’s transcript levels in the liver at the end of the study (Day 14; Mean ⁇ SD).
• Fig. 7 is a schematic model of the siRNA guide strand with ANA-G at position AS7 bound to Ago2.
• Figs. 8A and 8B are line graphs showing stability of oligonucleotides carrying ANA modification against degradation.
• Fig.8A shows nuclease stability of oligonucleotides carrying a single or two ANA nucleotides at the 3′-end of a poly dT against degradation by snake venom phosphodiesterase (SVPD).
• Fig. 8B shows stability of oligonucleotides carrying a single or two ANA nucleotides at the 5′-end of a poly dT against degradation by phosphodiesterase II (PDEII).
• PDEII phosphodiesterase II
• Fig. 9 is an active site view of Xrn1 5′-exoribonuclease with bound 5′P-dTdTdT-3′ (phosphorus and carbon atoms colored in orange and yellow, respectively) as observed in the crystal structure of the complex [ref Jinek et al. Mol. Cell 2011].
• Fig. 10A is a line graph showing the ANA 3’-exonuclease stability. (Fig. 10A). Calculated t1/2 are UU-3’: ⁇ 1h, (Uan)(Uan)-3’: 4.7h, UsU-3’: 10.2, Us(Uan)-3’: 8.0h and (Uans)(Uan)-3’: 16.3h.
• Fig. 10B is a line graph showing the ANA 5’-exonuclease stability. Calculated t1/2 are 5’-UU: ⁇ 1.5h, 5’-(Uan)U: 11.5, 5’-UsU: 26.9, 5’-(Uans)U: 113h and 5’-(Uans(Uan): 458.5.
• Fig. 11 is a schematic representation showing the crystal strcutre of an ANA:RNA duplex; PDB ID 3ok2. Phosphate spacing in ANA (5.5 ⁇ ) is smaller than RNA (6 ⁇ ). Adapted from Ovaere et al. Nucleic Acid Res., 40:7573-7583 (2012).
• Fig.12 shows some exemplary hexopyranose nucleoside phosphoramidites.
• Figs.13 and 14 show some exemplary hexopyranose nucleosides and nucleotides.
• DETAILED DESCRIPTION [0036]
• the invention provides a double-stranded RNA (dsRNA) molecule, where the dsRNA is capable of inhibiting the expression of a target gene, where the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand has sufficient complementarity to the target sequence to mediate RNA interference and the dsRNA molecule comprises at least one hexopyranose nucleotide cyclohexene nucleotide, e.g., an altritol nucleotide.
• dsRNA double-stranded RNA
• the hexopyranose nucleotide or the cyclohexene nucleotide can be present any wherein in the dsRNA.
• the hexopyranose nucleotide or the cyclohexene nucleotide can be present in the sense strand of an siRNA molecule. It is noted that the hexopyranose nucleotide or the cyclohexene nucleotide can be present in the sense strand.
• the hexopyranose nucleotide or the cyclohexene nucleotide can be at the 5’-end of the sense strand, 3’-end of the sense strand, and/or at an internal position of the sense strand. [0038] In some embodiments, the hexopyranose nucleotide or the cyclohexene nucleotide is present at the 5’-end of the sense strand. In some embodiments, the hexopyranose nucleotide or the cyclohexene nucleotide is present at the 3’-end of the sense strand.
• the hexopyranose nucleotide or the cyclohexene nucleotide can be present at an internal position of the sense strand.
• the hexopyranose nucleotide or the cyclohexene nucleotide can be present at position 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 of the sense strand.
• the hexopyranose nucleotide or the cyclohexene nucleotide can be present within a 5’-region (i.e., at position 2-8, of the 5’-end of the sense strand, counting from the 5′-end).
• the hexopyranose nucleotide or the cyclohexene nucleotide can be present in a central region of the sense strand. [0040] In some embodiments, the hexopyranose nucleotide or the cyclohexene nucleotide can be present in the sense region of the sense strand at a positon opposite to a seed region of the antisense strand (i.e., position 3-8, of the 5’-end of the antisense strand, counting from the 5′- end).
• the sense strand comprises at least one, e.g., 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 more hexopyranose nucleotides and/or cyclohexene nucleotides.
• the sense strand comprises hexopyranose nucleotide and/or the cyclohexene nucleotide at least at one of positions 3 and 12.
• the sense strand comprises at least 2 or more hexopyranose nucleotide and/or the cyclohexene nucleotides.
• the sense strand comprises at least 2, e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more hexopyranose nucleotide and/or the cyclohexene nucleotides next to each other.
• the sense comprises a stretch of two or more independently selected hexopyranose nucleotides and/or cyclohexene nucleotides.
• the sense strand comprises three hexopyranose nucleotides and/or the cyclohexene nucleotides next to each other, i.e., the sense strand comprises a stretch of three independently selected hexopyranose nucleotides and/or the cyclohexene nucleotides.
• the hexopyranose nucleotide or the cyclohexene nucleotide is present in the antisense strand.
• the hexopyranose nucleotide and/or the cyclohexene nucleotide can be present anywhere in the antisense strand.
• the hexopyranose nucleotide or the cyclohexene nucleotide can be at the 5’-end of the antisense strand, 3’-end of the antisense strand, and/or at an internal position of the antisense strand.
• the hexopyranose nucleotide or the cyclohexene nucleotide is present at the 5’-end of the antisense strand.
• the hexopyranose nucleotide or the cyclohexene nucleotide is present at the 3’-end of the antisense strand.
• the hexopyranose nucleotide or the cyclohexene nucleotide can be present at an internal position of the antisense strand.
• the hexopyranose nucleotide or the cyclohexene nucleotide can be present at position 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 of the antisense strand.
• the hexopyranose nucleotide or the cyclohexene nucleotide can be present within a seed region (i.e., at position 2-8, of the 5’-end of the antisense strand, counting from the 5′-end).
• the antisense strand comprises a hexopyranose nucleotide and/or a cyclohexene nucleotide at least at one of positions 3-8, counting from 5’-end of the antisense strand.
• the hexopyranose nucleotide or the cyclohexene nucleotide can be present in a central region of the antisense strand.
• the antisense strand comprises at least one, e.g., 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 more hexopyranose nucleotides and/or cyclohexene nucleotides.
• the antisense strand comprises a hexopyranose nucleotides and/or a cyclohexene nucleotide at least at one of positions 6, 7, 9, 12, 16, 21 and 22, counting from the 5′-end of the antisense strand.
• the antisense strand comprises a hexopyranose nucleotides and/or a cyclohexene nucleotide at least at one of positions 6, 7 and 16, counting from the 5′-end of the antisense strand.
• the antisense strand comprises a hexopyranose nucleotides and/or a cyclohexene nucleotide at least at one of positions 6 and 7, counting from the 5′-end of the antisense strand.
• the antisense comprises a hexopyranose nucleotides or a cyclohexene nucleotide at position 7, counting from the 5′-end of the antisense strand.
• the antisense strand comprises at least 2 or more hexopyranose nucleotide and/or the cyclohexene nucleotides.
• the antisense strand comprises at least two, e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more hexopyranose nucleotides and/or cyclohexene nucleotides next to each other.
• the antisense comprises a stretch of two or more independently selected hexopyranose nucleotides and/or cyclohexene nucleotides.
• the antisense strand comprises three hexopyranose nucleotides and/or the cyclohexene nucleotides next to each other, i.e., the antisense strand comprises a stretch of three independently selected hexopyranose nucleotides and/or the cyclohexene nucleotides.
• the hexopyranose nucleotide is an altriol nucleotide.
• the hexopyranose nucleotide is a glucopyranose nucleotide. [0052] In some embodiments, the hexopyranose nucleotide is a mannopyranose nucleotide. [0053] In some embodiments, the hexopyranose nucleotide is a galactopyranose nucleotide. [0054] In some embodiments, the hexopyranose nucleotide is a fucopyranose nucleotide.
• the sense strand and/or the antisense strand can comprise a nucleotide containing a 5’-vinylphosphonate (VP) moiety.
• the sense strand comprises a nucleotide containing a 5’-vinylphosphonate (VP) moiety.
• the antisense strand comprises a nucleotide containing a 5’-vinylphosphonate (VP) moiety.
• the dsRNA comprises at least one altritol nucleotide.
• the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen or more altritol nucleotides. Without limitations, the altritol nucleotides all can be present in one strand. In some embodiments, the dsRNA molecule comprises one or two altritol nucleotides. In some preferred embodiments, the dsRNA molecule comprises one altritol nucleotide. [0057] In some embodiments, the antisense strand comprises at least one, e.g., two, three, four, five or more altritol nucleotides.
• an altritol nucleotide in the antisense strand can be present at any position.
• the antisense strand comprises at least one altritol nucleotide within the seed region (i.e., at position 3-8, of the 5’-end of the antisense strand, counting from the 5′-end).
• the antisense strand comprises an altritol nucleotide at least at one of positions 6, 7, 9, 12, 16, 21 and 22, counting from the 5′-end.
• the antisense strand comprises an altritol nucleotide at least at one of positions 6, 7 and 16.
• the antisense strand comprises an altritol nucleotide at least at position 6, counting froim the 5’-end.
• the antisense strand comprises an altritol nucleotide at least at position 7, counting froim the 5’-end.
• the antisense strand comprises an altritol nucleotide at least at position 16, counting froim the 5’-end.
• the antisense strand does not comprise an altritol nucleotide at position 1 and/or 2, counting from the 5’-end.
• the altritol nucleotide is present in the sense strand.
• the antisense strand comprises at least one, e.g., two, three, four, five or more altritol nucleotides.
• the altritol nucleotide can be present anywhere in the sense strand.
• the sense strand can comprise at least one altritol nucleotide at positions opposite or complimentary to the seed region (i.e., at position 3-8, of the 5’-end of the antisense strand, counting from the 5′-end.
• the sense strand can comprise an altritol nucleotide at least at one of positions 3 and 21 of the sense strand, counting from the 5’-end.
• the sense strand comprises an altritol nucleotide at position 1, counting from the 5’-end.
• the sense strand does not comprise an altritol nucleotide.
• the altritol nucleotide is a modified altritol nucleotide having the structure: where: B is a modified or unmodified nucleobase; R 1 , R 2 , R 3 , R 4 , R 5 and R 6 independently are H, halogen, OH, NH2, NHMe, NMe2, OR 9 , or C1- C 6 alkyl (e.g., methyl, ethyl, propyl, etc...); R 7 and R 8 independently are H, C 1 -C 6 alkyl (e.g., methyl, ethyl, propyl, etc...), or OR 9 ; and R 9 is C 1 -C 6 alkyl (e.g., methyl, ethyl, propyl, etc.), cycloalkyl, aryl, aralkyl, heteroaryl or sugar.
• B is a modified or unmodified nucleobase
• dsRNA molecules [0061] Aspects of the invention include double-stranded RNA molecules.
• the dsRNA molecule comprises a sense strand (also referred to as passenger strand) and an antisense strand (also referred to as guide strand).
• Each strand of the dsRNA molecule independently can range from 12-40 nucleotides in length.
• each strand independently can be between 14-40 nucleotides in length, 17-37 nucleotides in length, 25-37 nucleotides in length, 27-30 nucleotides in length, 17-23 nucleotides in length, 17-21 nucleotides in length, 17-19 nucleotides in length, 19-25 nucleotides in length, 19-23 nucleotides in length, 19-21 nucleotides in length, 21-25 nucleotides in length, or 21-23 nucleotides in length.
• the sense and antisense strands can be equal length or unequal length.
• the antisense strand is longer, e.g., by 1, 2, 3, 4, or 5 nucleotides than the sense strand.
• the antisense strand is of length 18 to 35 nucleotides. In some embodiments, the antisense strand is 21-25, 19-25, 19-21 or 21-23 nucleotides in length. In some particular embodiments, the antisense strand is 23 nucleotides in length.
• the sense strand can be, in some embodiments, 18-35 nucleotides in length. In some embodiments, the sense strand is 21-25, 19-25, 19-21 or 21-23 nucleotides in length.
• the antisense strand is 21 nucleotides in length.
• sense strand is 21 nucleotides in length and the antisense strand is 23 nucleotides in length.
• the double-stranded RNA molecule has a double-stranded or duplex region.
• the duplex region double-stranded region
• the dsRNA has a duplex region of 12-25 nucleotide pairs in length.
• the dsRNA has a duplex region of 18, 19, 20, 21, 22, 22, 23, 24, or 25 nucleotide base pairs in length.
• the dsRNA has a duplex region of 19, 20, 21 or 22 nucleotide base pairs in length.
• the dsRNA molecule described herein can comprise one or more nucleic acid modifications. It is noted that the one or more nucleic acid modifications are in addition to the altritol nucleotide(s) present in the dsRNA.
• the dsRNA molecule can comprise 2’-fluoro nucleotides, i.e., 2’-fluoro modifications.
• the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen or more 2’- fluoro nucleotides.
• the 2’-fluoro nucleotides all can be present in one strand.
• both the sense and the antisense strands comprise at least two 2’-fluoro nucleotides.
• the 2’-fluoro modification can occur on any nucleotide of the sense strand or antisense strand.
• the 2’-fluoro modification can occur on every nucleotide on the sense strand and/or antisense strand; each 2’-fluoro modification can occur in an alternating pattern on the sense strand or antisense strand; or the sense strand and antisense strand both comprise 2’-fluoro modifications in an alternating pattern.
• the alternating pattern of the 2’- fluoro modifications on the sense strand can be the same or different from the antisense strand, and the alternating pattern of the 2’-fluoro modifications on the sense strand can have a shift relative to the alternating pattern of the 2’-fluoro modifications on the antisense strand.
• the antisense strand of the dsRNA molecule can comprise at least two (e.g., two, three, four, five, six, seven, eight, nine, ten or more) 2’-fluoro nucleotides.
• the antisense strand comprises two, three, four, five or six 2’-fluoro nucleotides.
• a 2’-fluoro modification in the antisense strand can be present at any position.
• the antisense strand comprises at least three 2’-fluoro nucleotides.
• the antisense strand comprises 2’-fluoro nucleotides at least at positions 2, 14 and 16 from the 5’-end.
• the antisense comprises at least four 2’-fluoro nucleotides.
• the antisense comprises 2’-fluoro nucleotides at least at positions 2, 6, 14 and 16 from the 5’-end.
• the antisense strand comprises at least five 2’-fluoro nucleotides.
• the antisense strand comprises 2’-fluoro nucleotides at least at positions 2, 6, 9, 14 and 16 from the 5’-end.
• the antisense strand comprises at least six 2’-fluoro nucleotides.
• the antisense strand comprises 2’-fluoro nucleotides at least at positions 2, 6, 8, 9, 14 and 16 from the 5’-end.
• the sense strand of the dsRNA molecule can comprise at least two (e.g., two, three, four, five, six, seven, eight, nine, ten or more) 2’-fluoro nucleotides.
• the sense strand comprises two, three, four, or five 2’-fluoro nucleotides.
• the sense strand comprises three or four 2’-fluoro nucleotides.
• a 2’-fluoro modification in the sense strand can be present at any positions.
• the sense strand comprises at least three 2’-fluoro nucleotides.
• the sense comprises 2’-fluoro nucleotides at least at positions 7, 10 and 11 from the 5’-end.
• the sense strand comprises at least four 2’-fluoro nucleotides.
• the sense comprises 2’- fluoro nucleotides at least at positions 7, 9, 10 and 11 from the 5’-end.
• the sense strand comprises 2’-fluoro nucleotides at positions opposite or complimentary to positions 11, 12 and 15 of the antisense strand, counting from the 5’-end of the antisense strand.
• the sense strand comprises 2’-fluoro nucleotides at positions opposite or complimentary to positions 11, 12, 13 and 15 of the antisense strand, counting from the 5’-end of the antisense strand. In some embodiments, the sense strand comprises a block of two, three or four 2’-fluoro nucleotides. [0071] In some embodiments, the sense strand comprises 2’-fluoro nucleotides at least at positions 7, 9, and 11 from the 5’-end, and the antisense strand comprises 2’-fluoro nucleotides at least at positions 2, 14 and 16 from the 5’-end.
• the sense strand comprises 2’-fluoro nucleotides at least at positions 7, 9, and 11 from the 5’-end
• the antisense strand comprises 2’-fluoro nucleotides at least at positions 2, 6, 9, 14 and 16 from the 5’-end.
• the sense strand comprises 2’-fluoro nucleotides at least at positions 7, 9, and 11 from the 5’-end
• the antisense strand comprises 2’-fluoro nucleotides at least at positions 2, 6, 8, 9, 14 and 16 from the 5’-end.
• the sense strand comprises 2’-fluoro nucleotides at least at positions 7, 9, 10, and 11 from the 5’-end
• the antisense strand comprises 2’-fluoro nucleotides at least at positions 2, 14 and 16 from the 5’-end.
• the sense strand comprises 2’-fluoro nucleotides at least at positions 7, 9, 10, and 11 from the 5’-end
• the antisense strand comprises 2’-fluoro nucleotides at least at positions 2, 6, 9, 14 and 16 from the 5’-end.
• the sense strand comprises 2’-fluoro nucleotides at least at positions 7, 9, 10, and 11 from the 5’-end
• the antisense strand comprises 2’-fluoro nucleotides at least at positions 2, 6, 8, 9, 14 and 16 from the 5’-end.
• the antisense strand does not comprise a 2’-fluoro nucleotide at positions 3-9, counting from 5’-end.
• the dsRNA molecule can comprise at least one, e.g., one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty or more 2’-OMe nucleotides.
• the 2’-OMe nucleotides all can be present in one strand.
• both the sense and the antisense strands comprise at least one 2’-OMe nucleotide.
• the 2’-OMe modification can occur on any nucleotide of the sense strand or antisense strand.
• the 2’-OMe modification can occur on every nucleotide on the sense strand and/or antisense strand; each thermally stabilizing modification can occur in an alternating pattern on the sense strand or antisense strand; or the sense strand and antisense strand both comprise 2’-OMe modifications in an alternating pattern.
• the alternating pattern of the thermally stabilizing modifications on the sense strand can be the same or different from the antisense strand, and the alternating pattern of the thermally stabilizing modifications on the sense strand can have a shift relative to the alternating pattern of the 2’-OMe modifications on the antisense strand.
• the antisense strand of the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen or more 2’-OMe modifications.
• a thermally stabilizing modification in the antisense strand can be present at any position.
• the antisense strand comprises at least three thermally stabilizing modifications.
• the antisense strand does not comprise 2’-OMe modifications at least at positions 2, 14 and 16 from the 5’-end. In some other embodiments, the antisense does not comprise 2’-OMe modifications at least at positions 2, 6, 14 and 16 from the 5’-end.
• the antisense strand does not comprise 2’-OMe modifications at least at positions 2, 6, 9, 14 and 16 from the 5’-end. In still some further embodiments, the antisense strand does not comprise 2’-OMe modifications at least at positions 2, 6, 8, 9, 14 and 16 from the 5’-end.
• the sense strand of the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen or more 2’-OMe modifications. Without limitations, a 2’-OMe modification in the sense strand can be present at any positions.
• the dsRNA molecule can comprise locked nucleic acid (LNA).
• LNA locked nucleic acid
• the dsRNA molecule can comprise can comprise at least one, e.g., one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty or more LNA modifications.
• the LNA nucleotides all can be present in one strand.
• both the sense and the antisense strands comprise at least LNA modifications.
• the LNA modification can occur on any nucleotide of the sense strand or antisense strand.
• the LNA modification can occur on every nucleotide on the sense strand and/or antisense strand; each LNA modification can occur in an alternating pattern on the sense strand or antisense strand; or the sense strand and antisense strand both comprise LNA modifications in an alternating pattern.
• the alternating pattern of the LNA modifications on the sense strand can be the same or different from the antisense strand, and the alternating pattern of the LNA modifications on the sense strand can have a shift relative to the alternating pattern of the 2’-fluoro modifications on the antisense strand.
• the antisense strand of the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more LNA modifications. Without limitations, a LNA modification in the antisense strand can be present at any position.
• the sense strand of the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more LNA modifications. Without limitations, a LNA modification in the sense strand can be present at any position. In some embodiments, the sense strand comprises at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more LNA modifications and the antisense strand does not comprise a 2’-fluoro nucleotide at positions 3-9, counting from 5’-end. [0081] The dsRNA molecule can comprise bridged nucleic acid (BNA).
• BNA bridged nucleic acid
• the dsRNA molecule can comprise can comprise at least one, e.g., one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty or more BNA modifications.
• the BNA nucleotides all can be present in one strand.
• both the sense and the antisense strands comprise at least BNA modifications.
• the BNA modification can occur on any nucleotide of the sense strand or antisense strand.
• the BNA modification can occur on every nucleotide on the sense strand and/or antisense strand; each BNA modification can occur in an alternating pattern on the sense strand or antisense strand; or the sense strand and antisense strand both comprise BNA modifications in an alternating pattern.
• the alternating pattern of the BNA modifications on the sense strand can be the same or different from the antisense strand, and the alternating pattern of the BNA modifications on the sense strand can have a shift relative to the alternating pattern of the 2’-fluoro modifications on the antisense strand.
• the antisense strand of the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more BNA modifications. Without limitations, a BNA modification in the antisense strand can be present at any position.
• the sense strand of the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more BNA modifications. Without limitations, a BNA modification in the sense strand can be present at any position.
• the sense strand comprises at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more BNA modifications and the antisense strand does not comprise a 2’-fluoro nucleotide at positions 3-9, counting from 5’-end.
• the dsRNA molecule can comprise cyclohexene nucleic acid (CeNA).
• the dsRNA molecule can comprise can comprise at least one, e.g., one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty or more CeNA modifications.
• both the sense and the antisense strands comprise at least CeNA modifications.
• the CeNA modification can occur on any nucleotide of the sense strand or antisense strand.
• the CeNA modification can occur on every nucleotide on the sense strand and/or antisense strand; each CeNA modification can occur in an alternating pattern on the sense strand or antisense strand; or the sense strand and antisense strand both comprise ceNA modifications in an alternating pattern.
• the alternating pattern of the CeNA modifications on the sense strand can be the same or different from the antisense strand, and the alternating pattern of the ceNA modifications on the sense strand can have a shift relative to the alternating pattern of the 2’-fluoro modifications on the antisense strand.
• the antisense strand of the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more ceNA modifications. Without limitations, a ceNA modification in the antisense strand can be present at any position.
• the sense strand of the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more ceNA modifications. Without limitations, a ceNA modification in the sense strand can be present at any position. In some embodiments, the sense strand comprises at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more ceNA modifications and the antisense strand does not comprise a 2’-fluoro nucleotide at positions 3-9, counting from 5’-end. [0087] In some embodiments, the dsRNA molecule can comprise thermally stabilizing modifications.
• the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen or more thermally stabilizing modifications.
• the thermally stabilizing modifications all can be present in one strand.
• both the sense and the antisense strands comprise at least one, e.g., two, three, four or more thermally stabilizing modifications.
• the thermally stabilizing modification can occur on any nucleotide of the sense strand or antisense strand.
• the thermally stabilizing modification can occur on every nucleotide on the sense strand and/or antisense strand; each thermally stabilizing modification can occur in an alternating pattern on the sense strand or antisense strand; or the sense strand and antisense strand both comprise thermally stabilizing modifications in an alternating pattern.
• the alternating pattern of the thermally stabilizing modifications on the sense strand can be the same or different from the antisense strand, and the alternating pattern of the thermally stabilizing modifications on the sense strand can have a shift relative to the alternating pattern of the thermally stabilizing modifications on the antisense strand.
• the antisense strand of the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more thermally stabilizing modifications.
• the antisense strand comprises two, three, four, five or six thermally stabilizing modifications.
• a thermally stabilizing modification in the antisense strand can be present at any position.
• the antisense strand comprises at least three thermally stabilizing modifications.
• the antisense strand comprises thermally stabilizing modifications at least at one of, e.g, two or three of positions 2, 14 and 16 from the 5’- end.
• the antisense comprises at least four thermally stabilizing modifications.
• the antisense comprises thermally stabilizing modifications at least at positions 2, 6, 14 and 16 from the 5’-end.
• the antisense strand comprises at least five thermally stabilizing modifications.
• the antisense strand comprises thermally stabilizing modifications at least at positions 2, 6, 9, 14 and 16 from the 5’- end.
• the antisense strand comprises at least six thermally stabilizing modifications.
• the antisense strand comprises thermally stabilizing modifications at least at positions 2, 6, 8, 9, 14 and 16 from the 5’-end.
• the sense strand of the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more thermally stabilizing modifications.
• the sense strand comprises two, three, four, or five thermally stabilizing modifications.
• the sense strand comprises three or four thermally stabilizing modifications.
• a thermally stabilizing modification in the sense strand can be present at any positions.
• the sense strand comprises at least three thermally stabilizing modifications.
• the sense comprises thermally stabilizing modification at least at positions 7, 10 and 11 from the 5’-end.
• the sense strand comprises at least four thermally stabilizing modifications.
• the sense comprises thermally stabilizing modification at least at positions 7, 9, 10 and 11 from the 5’-end.
• the sense strand comprises thermally stabilizing modifications at positions opposite or complimentary to positions 11, 12 and 15 of the antisense strand, counting from the 5’-end of the antisense strand.
• the sense strand comprises thermally stabilizing modifications at positions opposite or complimentary to positions 11, 12, 13 and 15 of the antisense strand, counting from the 5’-end of the antisense strand.
• the sense strand comprises a block of two, three or four thermally stabilizing modification.
• the sense strand comprises thermally stabilizing modifications at least at positions 7, 9, and 11 from the 5’-end
• the antisense strand comprises thermally stabilizing modifications at least at positions 2, 14 and 16 from the 5’-end.
• the sense strand comprises thermally stabilizing modifications at least at positions 7, 9, and 11 from the 5’-end
• the antisense strand comprises thermally stabilizing modifications at least at positions 2, 6, 9, 14 and 16 from the 5’-end.
• the sense strand comprises thermally stabilizing modifications at least at positions 7, 9, and 11 from the 5’-end
• the antisense strand comprises thermally stabilizing modifications at least at positions 2, 6, 8, 9, 14 and 16 from the 5’-end.
• the sense strand comprises thermally stabilizing modifications at least at positions 7, 9, 10, and 11 from the 5’-end
• the antisense strand comprises thermally stabilizing modifications at least at positions 2, 14 and 16 from the 5’-end.
• the sense strand comprises thermally stabilizing modifications at least at positions 7, 9, 10, and 11 from the 5’-end
• the antisense strand comprises thermally stabilizing modifications at least at positions 2, 6, 9, 14 and 16 from the 5’-end.
• the sense strand comprises thermally stabilizing modifications at least at positions 7, 9, 10, and 11 from the 5’-end
• the antisense strand comprises thermally stabilizing modifications at least at positions 2, 6, 8, 9, 14 and 16 from the 5’-end.
• the sense strand does not comprise a thermally stabilizing modification in position opposite or complimentary to the thermally destabilizing modification of the duplex in the antisense strand.
• thermally stabilizing modifications include, but are not limited to 2’- fluoro modifications, locked nucleic acid (LNA), abasic modifications; mismatch with the opposing nucleotide in the opposing strand; and sugar modification such as 2’-deoxy modification or acyclic nucleotide, e.g., unlocked nucleic acids (UNA) or glycol nucleic acid (GNA).
• the destabilizing modification is selected from the group consisting of GNA-isoC, GNA-isoG, 5’-mUNA, 4’-mUNA, 3’-mUNA, and 2’-mUNA.
• the dsRNA molecule comprises one or more overhang regions (i.e., single-stranded region) and/or capping groups of dsRNA molecule at the 3’-end, or 5’-end or both ends of a strand.
• the overhang can be 1-10 nucleotides in length, 1-6 nucleotides in length, 1-5 nucleotides in length, 1-4 nucleotides in length, 1-3 nucleotides in length, 2-6 nucleotides in length, 2-5 nucleotides in length 2-4 nucleotides in length, 2-3 nucleotides in length, or 1-2 nucleotides in length.
• the overhangs can be the result of one strand being longer than the other, or the result of two strands of the same length being staggered.
• the overhang can form a mismatch with the sequence being targeted or it can be complementary to the sequence being targeted or can be other sequence.
• the first and second strands can also be joined, e.g., by additional bases to form a hairpin, or by other non-base linkers.
• the overhang can be present at the 3’-end of the sense strand, antisense strand or both strands.
• the dsRNA molecule comprises a single overhang.
• the dsRNA molecule has a single overhang and the overhang is at least two, three, four, five, six, seven, eight, nine, or ten nucleotides in length.
• the overhang is present at the 3’-end of the antisense strand.
• the dsRNA comprises a two nucleotide overhang at the 3’-end of the antisense strand.
• the dsRNA can also have a blunt end.
• one end of the dsRNA is a blunt end and the other end has an overhang.
• the blunt end can be located at the 5’-end of the antisense strand (or the 3’-end of the sense strand) or vice versa.
• the antisense strand of the dsRNA has a nucleotide overhang at the 3’-end, and the 5’-end is blunt.
• the asymmetric blunt end at the 5’-end of the antisense strand and 3’- end overhang of the antisense strand favor the guide strand loading into RISC process.
• the dsRNA has a 2 nucleotide overhang on the 3’-end of the antisense strand and a blunt end at the 5’-end of the antisense strand.
• the dsRNA molecule has two blunt ends, i.e., at both ends of the dsRNA.
• the nucleotides in the overhang region of the dsRNA molecule can each independently be a modified or unmodified nucleotide including, but not limited to 2’-sugar modified, such as, 2’-Fluoro, 2’-O-methyl, thymidine (T), 2’-O-methoxyethyl-5-methyluridine, 2’-O-methoxyethyladenosine, 2’-O-methoxyethyl-5-methylcytidine, GNA, SNA, hGNA, hhGNA, mGNA, TNA, h’GNA, and any combinations thereof.
• 2’-sugar modified such as, 2’-Fluoro, 2’-O-methyl, thymidine (T), 2’-O-methoxyethyl-5-methyluridine, 2’-O-methoxyethyladenosine, 2’-O-methoxyethyl-5-methylcyt
• TT can be an overhang sequence for either end on either strand.
• the 5’- or 3’- overhangs at the sense strand, antisense strand or both strands of the dsRNA molecule can be phosphorylated.
• the overhang region contains two nucleotides having a phosphorothioate internucleotide linkage between the two nucleotides, where the two nucleotides in the overhang region can be the same or different.
• the dsRNA molecule can comprise at least one, e.g., two, three, four, five, six, seven, eight, nine, ten or more phosphorothioate or methylphosphonate internucleotide linkage.
• the phosphorothioate or methylphosphonate internucleotide linkage modification can occur on any nucleotide of the sense strand or antisense strand or both in any position of the strand.
• the internucleotide linkage modification can occur on every nucleotide on the sense strand and/or antisense strand; each internucleotide linkage modification can occur in an alternating pattern on the sense strand or antisense strand; or the sense strand or antisense strand comprises both internucleotide linkage modifications in an alternating pattern.
• the alternating pattern of the internucleotide linkage modification on the sense strand can be the same or different from the antisense strand, and the alternating pattern of the internucleotide linkage modification on the sense strand can have a shift relative to the alternating pattern of the internucleotide linkage modification on the antisense strand.
• the dsRNA molecule comprises the phosphorothioate or methylphosphonate internucleotide linkage modification in the overhang region.
• the overhang region comprises two nucleotides having a phosphorothioate or methylphosphonate internucleotide linkage between the two nucleotides.
• Internucleotide linkage modifications also may be made to link the overhang nucleotides with the terminal paired nucleotides within duplex region.
• the overhang nucleotides can be linked through phosphorothioate or methylphosphonate internucleotide linkage, and optionally, there may be additional phosphorothioate or methylphosphonate internucleotide linkages linking the overhang nucleotide with a paired nucleotide that is next to the overhang nucleotide.
• the sense strand of the dsRNA molecule comprises 1-10 blocks of two to ten phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 phosphate internucleotide linkages, wherein one of the phosphorothioate or methylphosphonate internucleotide linkages is placed at any position in the oligonucleotide sequence and the said sense strand is paired with an antisense strand comprising any combination of phosphorothioate, methylphosphonate and phosphate internucleotide linkages or an antisense strand comprising either phosphorothioate or methylphosphonate or phosphate linkage.
• the antisense strand of the dsRNA molecule comprises two blocks of two phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 phosphate internucleotide linkages, wherein one of the phosphorothioate or methylphosphonate internucleotide linkages is placed at any position in the oligonucleotide sequence and the said antisense strand is paired with a sense strand comprising any combination of phosphorothioate, methylphosphonate and phosphate internucleotide linkages or an antisense strand comprising either phosphorothioate or methylphosphonate or phosphate linkage.
• the antisense strand of the dsRNA molecule comprises two blocks of three phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 phosphate internucleotide linkages, wherein one of the phosphorothioate or methylphosphonate internucleotide linkages is placed at any position in the oligonucleotide sequence and the said antisense strand is paired with a sense strand comprising any combination of phosphorothioate, methylphosphonate and phosphate internucleotide linkages or an antisense strand comprising either phosphorothioate or methylphosphonate or phosphate linkage.
• the antisense strand of the dsRNA molecule comprises two blocks of four phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 phosphate internucleotide linkages, wherein one of the phosphorothioate or methylphosphonate internucleotide linkages is placed at any position in the oligonucleotide sequence and the said antisense strand is paired with a sense strand comprising any combination of phosphorothioate, methylphosphonate and phosphate internucleotide linkages or an antisense strand comprising either phosphorothioate or methylphosphonate or phosphate linkage.
• the antisense strand of the dsRNA molecule comprises two blocks of five phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 phosphate internucleotide linkages, wherein one of the phosphorothioate or methylphosphonate internucleotide linkages is placed at any position in the oligonucleotide sequence and the said antisense strand is paired with a sense strand comprising any combination of phosphorothioate, methylphosphonate and phosphate internucleotide linkages or an antisense strand comprising either phosphorothioate or methylphosphonate or phosphate linkage.
• the antisense strand of the dsRNA molecule comprises two blocks of six phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 phosphate internucleotide linkages, wherein one of the phosphorothioate or methylphosphonate internucleotide linkages is placed at any position in the oligonucleotide sequence and the said antisense strand is paired with a sense strand comprising any combination of phosphorothioate, methylphosphonate and phosphate internucleotide linkages or an antisense strand comprising either phosphorothioate or methylphosphonate or phosphate linkage.
• the antisense strand of the dsRNA molecule comprises two blocks of seven phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2, 3, 4, 5, 6, 7 or 8 phosphate internucleotide linkages, wherein one of the phosphorothioate or methylphosphonate internucleotide linkages is placed at any position in the oligonucleotide sequence and the said antisense strand is paired with a sense strand comprising any combination of phosphorothioate, methylphosphonate and phosphate internucleotide linkages or an antisense strand comprising either phosphorothioate or methylphosphonate or phosphate linkage.
• the antisense strand of the dsRNA molecule comprises two blocks of eight phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2, 3, 4, 5 or 6 phosphate internucleotide linkages, wherein one of the phosphorothioate or methylphosphonate internucleotide linkages is placed at any position in the oligonucleotide sequence and the said antisense strand is paired with a sense strand comprising any combination of phosphorothioate, methylphosphonate and phosphate internucleotide linkages or an antisense strand comprising either phosphorothioate or methylphosphonate or phosphate linkage.
• the antisense strand of the dsRNA molecule comprises two blocks of nine phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2, 3 or 4 phosphate internucleotide linkages, wherein one of the phosphorothioate or methylphosphonate internucleotide linkages is placed at any position in the oligonucleotide sequence and the said antisense strand is paired with a sense strand comprising any combination of phosphorothioate, methylphosphonate and phosphate internucleotide linkages or an antisense strand comprising either phosphorothioate or methylphosphonate or phosphate linkage.
• the dsRNA molecule comprises one or more phosphorothioate or methylphosphonate internucleotide linkage modification within 1-10 of the termini position(s) of the sense and/or antisense strand.
• at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides may be linked through phosphorothioate or methylphosphonate internucleotide linkage at one end or both ends of the sense and/or antisense strand.
• the dsRNA molecule comprises one or more phosphorothioate or methylphosphonate internucleotide linkage modification within 1-10 of the internal region of the duplex of each of the sense and/or antisense strand.
• at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides may be linked through phosphorothioate methylphosphonate internucleotide linkage at position 8-16 of the duplex region counting from the 5’-end of the sense strand; the dsRNA molecule can optionally further comprise one or more phosphorothioate or methylphosphonate internucleotide linkage modification within 1-10 of the termini position(s).
• the dsRNA molecule comprises one to five phosphorothioate or methylphosphonate internucleotide linkage modification(s) within position 1-5 and one to five phosphorothioate or methylphosphonate internucleotide linkage modification(s) within position 18-23 of the sense strand (counting from the 5’-end), and one to five phosphorothioate or methylphosphonate internucleotide linkage modification at positions 1 and 2 and one to five within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises one phosphorothioate internucleotide linkage modification within position 1-5 and one phosphorothioate or methylphosphonate internucleotide linkage modification within position 18-23 of the sense strand (counting from the 5’-end), and one phosphorothioate internucleotide linkage modification at positions 1 and 2 and two phosphorothioate or methylphosphonate internucleotide linkage modifications within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises two phosphorothioate internucleotide linkage modifications within position 1-5 and one phosphorothioate internucleotide linkage modification within position 18-23 of the sense strand (counting from the 5’-end), and one phosphorothioate internucleotide linkage modification at positions 1 and 2 and two phosphorothioate internucleotide linkage modifications within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises two phosphorothioate internucleotide linkage modifications within position 1-5 and two phosphorothioate internucleotide linkage modifications within position 18-23 of the sense strand (counting from the 5’-end), and one phosphorothioate internucleotide linkage modification at positions 1 and 2 and two phosphorothioate internucleotide linkage modifications within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises two phosphorothioate internucleotide linkage modifications within position 1-5 and two phosphorothioate internucleotide linkage modifications within position 18-23 of the sense strand (counting from the 5’-end), and one phosphorothioate internucleotide linkage modification at positions 1 and 2 and one phosphorothioate internucleotide linkage modification within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises one phosphorothioate internucleotide linkage modification within position 1-5 and one phosphorothioate internucleotide linkage modification within position 18-23 of the sense strand (counting from the 5’-end), and two phosphorothioate internucleotide linkage modifications at positions 1 and 2 and two phosphorothioate internucleotide linkage modifications within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises one phosphorothioate internucleotide linkage modification within position 1-5 and one within position 18-23 of the sense strand (counting from the 5’-end), and two phosphorothioate internucleotide linkage modification at positions 1 and 2 and one phosphorothioate internucleotide linkage modification within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises one phosphorothioate internucleotide linkage modification within position 1-5 (counting from the 5’-end) of the sense strand, and two phosphorothioate internucleotide linkage modifications at positions 1 and 2 and one phosphorothioate internucleotide linkage modification within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises two phosphorothioate internucleotide linkage modifications within position 1-5 (counting from the 5’-end) of the sense strand, and one phosphorothioate internucleotide linkage modification at positions 1 and 2 and two phosphorothioate internucleotide linkage modifications within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises two phosphorothioate internucleotide linkage modifications within position 1-5 and one within position 18-23 of the sense strand (counting from the 5’-end), and two phosphorothioate internucleotide linkage modifications at positions 1 and 2 and one phosphorothioate internucleotide linkage modification within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises two phosphorothioate internucleotide linkage modifications within position 1-5 and one phosphorothioate internucleotide linkage modification within position 18-23 of the sense strand (counting from the 5’-end), and two phosphorothioate internucleotide linkage modifications at positions 1 and 2 and two phosphorothioate internucleotide linkage modifications within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises two phosphorothioate internucleotide linkage modifications within position 1-5 and one phosphorothioate internucleotide linkage modification within position 18-23 of the sense strand (counting from the 5’-end), and one phosphorothioate internucleotide linkage modification at positions 1 and 2 and two phosphorothioate internucleotide linkage modifications within positions 18-23 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises two phosphorothioate internucleotide linkage modifications at position 1 and 2, and two phosphorothioate internucleotide linkage modifications at position 20 and 21 of the sense strand (counting from the 5’-end), and one phosphorothioate internucleotide linkage modification at positions 1 and one at position 21 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises one phosphorothioate internucleotide linkage modification at position 1, and one phosphorothioate internucleotide linkage modification at position 21 of the sense strand (counting from the 5’-end), and two phosphorothioate internucleotide linkage modifications at positions 1 and 2 and two phosphorothioate internucleotide linkage modifications at positions 20 and 21 the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises two phosphorothioate internucleotide linkage modifications at position 1 and 2, and two phosphorothioate internucleotide linkage modifications at position 21 and 22 of the sense strand (counting from the 5’-end), and one phosphorothioate internucleotide linkage modification at positions 1 and one phosphorothioate internucleotide linkage modification at position 21 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises one phosphorothioate internucleotide linkage modification at position 1, and one phosphorothioate internucleotide linkage modification at position 21 of the sense strand (counting from the 5’-end), and two phosphorothioate internucleotide linkage modifications at positions 1 and 2 and two phosphorothioate internucleotide linkage modifications at positions 21 and 22 the antisense strand (counting from the 5’-end).
• the dsRNA molecule comprises two phosphorothioate internucleotide linkage modifications at position 1 and 2, and two phosphorothioate internucleotide linkage modifications at position 22 and 23 of the sense strand (counting from the 5’-end), and one phosphorothioate internucleotide linkage modification at positions 1 and one phosphorothioate internucleotide linkage modification at position 21 of the antisense strand (counting from the 5’-end).
• the dsRNA molecule one phosphorothioate internucleotide linkage modification at position 1, and one phosphorothioate internucleotide linkage modification at position 21 of the sense strand (counting from the 5’-end), and two phosphorothioate internucleotide linkage modifications at positions 1 and 2 and two phosphorothioate internucleotide linkage modifications at positions 23 and 23 the antisense strand (counting from the 5’-end).
• the sense strand can comprise 0, 1, 2, 3 or 4 phsophorothioate internucleotide linkages.
• the sense strand comprises phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3.
• the antisense strand can comprise 1, 2, 3 or 4 phsophorothioate internucleotide linkages.
• the sense strand comprises phosphorothioate internucleotide linkages between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23.
• the antisense strand comprises phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23.
• the sense strand comprises phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3, and the antisense strand comprises phosphorothioate internucleotide linkages between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23.
• the sense strand comprises phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3
• the antisense strand comprises phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23.
• 5’-modifications [00135]
• the dsRNA molecule can be 5’ phosphorylated or include a phosphoryl analog at the 5’ terminus.
• Exemplary 5'-phosphate modifications include those which are compatible with RISC mediated gene silencing.
• Suitable modifications include: 5'- monophosphate ((HO) 2 (O)P-O-5'); 5'-diphosphate ((HO) 2 (O)P-O-P(HO)(O)-O-5'); 5'- triphosphate ((HO) 2 (O)P-O-(HO)(O)P-O-P(HO)(O)-O-5'); 5'-guanosine cap (7-methylated or non-methylated) (7m-G-O-5'-(HO)(O)P-O-(HO)(O)P-O-P(HO)(O)-O-5'); 5'-adenosine cap (Appp), and any modified or unmodified nucleotide cap structure (N-O-5'-(HO)(O)P-O- (HO)(O)P-O-P(HO)(O)-O-5'); 5'-monothiophosphate (phosphorothioate; (HO)2(S)P-O-5'); 5'-
• the antisense strand can comprise a 5’-vinylphosphonate nucleotide at 5’-end.
• the antisense comprises 5’-E-vinylphosphanate.
• the antisense strand comprises 5’-E-vinylphosphanate and a nucleoside at position N-1 that reduces or inhibits activity of siRNA relative to a siRNA having the same antisense strand sequence but unmodified N-1 position and a nucleoside at position N-1 that reduces or inhibits activity of siRNA relative to a siRNA having the same antisense strand sequence but unmodified N-1 position
• the sense strand comprises a 5’-morpholino, a 5’- dimethylamino, a 5’-deoxy, an inverted abasic, or an inverted abasic locked nucleic acid modification at the 5’-end.
• the dsRNA has a melting temperature in the range from about 40°C to about 80°C.
• the dsRNA has a melting temperature with a lower end of the range from about 40°C, 45°C, 50°C, 55°C, 60°C or 65°C, and upper end of the range from about 70°C, 75°C or 80°C.
• the dsRNA has a melting temperature in the range from about 55°C to about 70°C or in the range from about 60°C to about 75°C.
• the dsRNA has a melting temperature in the range from about 57°C to about 67°C.
• the dsRNA has a melting temperature in the range from about 60°C to about 67°C. In some additional embodiments, the dsRNA has a melting temperature in the range from about 62°C to about 66°C. [00139] Without wishing to be bound by a theory, dsRNA molecules having a melting temperature of at least 60°C are more effective in vivo and in vitro. Accordingly, in some embodiments, the dsRNA has a melting temperature of at least 60°C. [00140] Without wishing to be bound by a theory, for the dsRNA molecules to be more effective in vivo, the antisense strand must have some metabolic stability.
• some amount of the antisense stand may need to be present in vivo after a period time after administration. Accordingly, in some embodiments, at least 40%, for example at least 45%, at least 50%, at least 55%, at least 60%., at least 65%, at least 70%, at least 75%, or at least 80% of the antisense strand of the dsRNA is present in vivo, for example in mounse liver, at day 5 after in vivo administration.
• At least 40%, for example at least 45%, at least 50%, at least 55%, at least 60%., at least 65%, at least 70%, at least 75%, or at least 80% of the antisense strand of the dsRNA is present in vivo, for example in mounse liver, at day 6 after in vivo administration.
• at least 40%, for example at least 45%, at least 50%, at least 55%, at least 60%., at least 65%, at least 70%, at least 75%, or at least 80% of the antisense strand of the dsRNA is present in vivo, for example in mounse liver, at day 7 after in vivo administration.
• At least 40%, for example at least 45%, at least 50%, at least 55%, at least 60%., at least 65%, at least 70%, at least 75%, or at least 80% of the antisense strand of the dsRNA is present in vivo, for example in mounse liver, at day 8 after in vivo administration.
• at least 40%, for example at least 45%, at least 50%, at least 55%, at least 60%., at least 65%, at least 70%, at least 75%, or at least 80% of the antisense strand of the dsRNA is present in vivo, for example in mounse liver, at day 9 after in vivo administration.
• At least 40%, for example at least 45%, at least 50%, at least 55%, at least 60%., at least 65%, at least 70%, at least 75%, or at least 80% of the antisense strand of the dsRNA is present in vivo, for example in mounse liver, at day 10 after in vivo administration.
• at least 40%, for example at least 45%, at least 50%, at least 55%, at least 60%., at least 65%, at least 70%, at least 75%, or at least 80% of the antisense strand of the dsRNA is present in vivo, for example in mounse liver, at day 11 after in vivo administration.
• At least 40%, for example at least 45%, at least 50%, at least 55%, at least 60%., at least 65%, at least 70%, at least 75%, or at least 80% of the antisense strand of the dsRNA is present in vivo, for example in mounse liver, at day 12 after in vivo administration.
• at least 40%, for example at least 45%, at least 50%, at least 55%, at least 60%., at least 65%, at least 70%, at least 75%, or at least 80% of the antisense strand of the dsRNA is present in vivo, for example in mounse liver, at day 13 after in vivo administration.
• At least 40%, for example at least 45%, at least 50%, at least 55%, at least 60%., at least 65%, at least 70%, at least 75%, or at least 80% of the antisense strand of the dsRNA is present in vivo, for example in mounse liver, at day 14 after in vivo administration.
• at least 40%, for example at least 45%, at least 50%, at least 55%, at least 60%., at least 65%, at least 70%, at least 75%, or at least 80% of the antisense strand of the dsRNA is present in vivo, for example in mounse liver, at day 15 after in vivo administration.
• thermally destabilizing modifications in the 5’-region of the antisense strand can reduce or inhibit off-target gene silencing.
• the antisense strand comprises at least one (e.g., one, two, three, four, five or more) thermally destabilizing modification of the duplex within the first 9 nucleotide positions of the 5’ region of the antisense strand.
• thermally destabilizing modification(s) includes modification(s) that would result with a dsRNA with a lower overall melting temperature (Tm) (preferably a Tm with one, two, three or four degrees lower than the Tm of the dsRNA without having such modification(s).
• Tm overall melting temperature
• thermally destabilizing modification is located at position 2, 3, 4, 5, 6, 7, 8 or 9, or preferably at position 4, 5, 6, 7, or 8, from the 5’-end of the antisense strand.
• the thermally destabilizing modification is located at position 2, 3, 4, 5 or 9 from the 5’-end of the antisense strand.
• the thermally destabilizing modification is located at position 6, 7 or 8 from the 5’-end of the antisense strand. In some particular embodiments, the thermally destabilizing modification is located at position 7 from the 5’-end of the antisense strand.
• the thermally destabilizing modifications can include, but are not limited to, abasic modifications; mismatch with the opposing nucleotide in the opposing strand; and sugar modification such as 2’-deoxy modification or acyclic nucleotide, e.g., unlocked nucleic acids (UNA) or glycol nucleic acid (GNA).
• Exemplary abasic modifications include, but are not limited to, the following: wherein R is H, Me, Et or OMe; R’ is H, Me, Et or OMe; R” is H, Me, Et or OMe; and * represents either R, S or racemic.
• Exemplary destabilizing sugar modifications include, but are not limited to the following: wherein B is a modified or unmodified nucleobase.
• Additional sugar modifications include, but are not limited to the following: wherein B is a modified or unmodified nucleobase.
• the thermally destabilizing modification is selected from the group consisting of: wherein B is a modified or unmodified nucleobase and the asterisk on each structure represents either R, S or racemic.
• acyclic nucleotide refers to any nucleotide having an acyclic ribose sugar, for example, where any of bonds between the ribose carbons (e.g., C1’-C2’, C2’-C3’, C3’-C4’, C4’-O4’, or C1’-O4’) is absent and/or at least one of ribose carbons or oxygen (e.g., C1’, C2’, C3’, C4’ or O4’) are independently or in combination absent from the nucleotide.
• R 1 and R 2 independently are H, halogen, OR3, or alkyl; and R3 is H, alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar).
• the term “UNA” refers to unlocked acyclic nucleic acid, wherein any of the bonds of the sugar has been removed, forming an unlocked “sugar” residue.
• UNA also encompasses monomers with bonds between C1'-C4' being removed (i.e. the covalent carbon-oxygen-carbon bond between the C1' and C4' carbons).
• the C2'-C3' bond i.e. the covalent carbon-carbon bond between the C2' and C3' carbons
• the acyclic derivative provides greater backbone flexibility without affecting the Watson-Crick pairings.
• the acyclic nucleotide can be linked via 2’-5’ or 3’-5’ linkage.
• glycol nucleic acid refers to glycol nucleic acid which is a polymer similar to DNA or RNA but differing in the composition of its “backbone” in that is composed of repeating glycerol units linked by phosphodiester bonds:
• the thermally destabilizing modification of the duplex can be mismatches (i.e., noncomplementary base pairs) between the thermally destabilizing nucleotide and the opposing nucleotide in the opposite strand within the dsRNA duplex.
• exemplary mismatch base pairs include G:G, G:A, G:U, G:T, A:A, A:C, C:C, C:U, C:T, U:U, T:T, U:T, or a combination thereof.
• Other mismatch base pairings known in the art are also amenable to the present invention.
• a mismatch can occur between nucleotides that are either naturally occurring nucleotides or modified nucleotides, i.e., the mismatch base pairing can occur between the nucleobases from respective nucleotides independent of the modifications on the ribose sugars of the nucleotides.
• the dsRNA molecule comprises at least one nucleobase in the mismatch pairing that is a 2’-deoxy nucleobase; e.g., the 2’-deoxy nucleobase is in the sense strand.
• the thermally destabilizing modification in the seed region of the antisense strand includes nucleotides with impaired W-C H-bonding to complementary base on the target mRNA.
• nucleotides with impaired W-C H-bonding to complementary base on the target mRNA include, but are not limited to, nucleotides comprising a nucleobase independently selected from the following: .
• nucleobase independently selected from the following: .
• Additional examples of abasic nucleotide, acyclic nucleotide modifications (including UNA and GNA), and mismatch modifications have been described in detail in WO 2011/133876, which is herein incorporated by reference in its entirety.
• the thermally destabilizing modifications can also include a universal nucleobase with reduced or abolished capability to form hydrogen bonds with the opposing bases, and phosphate modifications.
• the thermally destabilizing modification includes nucleotides with non-canonical bases such as, but not limited to, nucleobase modifications with impaired or completely abolished capability to form hydrogen bonds with bases in the opposite strand. These nucleobase modifications have been evaluated for destabilization of the central region of the dsRNA duplex as described in WO 2010/0011895, which is herein incorporated by reference in its entirety.
• the thermally destabilizing modification includes one or more ⁇ -nucleotide complementary to the base on the target mRNA, such as: wherein R is H, OH, OCH3, F, NH2, NHMe, NMe2 or O-alkyl
• R is H, OH, OCH3, F, NH2, NHMe, NMe2 or O-alkyl
• Exemplary phosphate modifications known to decrease the thermal stability of dsRNA duplexes compared to natural phosphodiester linkages include, but are not limited to, the following:
• the alkyl for the R group can be a C 1 -C 6 alkyl.
• the destabilizing modification is selected from the following: [00159]
• the antisense strand comprises at least one stabilizing modification adjacent to the destabilizing modification.
• the stabilizing modification can be the nucleotide at the 5’-end or the 3’-end of the destabilizing modification, i.e., at position -1 or +1 from the position of the destabilizing modification.
• the antisense strand comprises a stabilizing modification at each of the 5’-end and the 3’-end of the destabilizing modification, i.e., positions -1 and +1 from the position of the destabilizing modification.
• the antisense strand comprises at least two stabilizing modifications at the 3’-end of the destabilizing modification, i.e., at positions +1 and +2 from the position of the destabilizing modification.
• the sense strand does not comprise a thermally stabilizing modification in position opposite or complimentary to the thermally destabilizing modification of the duplex in the antisense strand.
• the antisense strand comprises at least one 2’-fluoro nucleotide adjacent to the destabilizing modification.
• the 2’-fluoro nucleotide can be the nucleotide at the 5’-end or the 3’-end of the destabilizing modification, i.e., at position -1 or +1 from the position of the destabilizing modification.
• the antisense strand comprises a 2’-fluoro nucleotide at each of the 5’-end and the 3’-end of the destabilizing modification, i.e., positions -1 and +1 from the position of the destabilizing modification.
• the antisense strand comprises at least two 2’-fluoro nucleotides at the 3’-end of the destabilizing modification, i.e., at positions +1 and +2 from the position of the destabilizing modification.
• the sense strand does not comprise a 2’-fluoro nucleotide in position opposite or complimentary to the thermally destabilizing modification of the duplex in the antisense strand.
• every nucleotide in the sense strand and/or the antisense strand of the dsRNA molecule can be modified.
• Each nucleotide can be modified with the same or different modification which can include one or more alteration of one or both of the non-linking phosphate oxygens and/or of one or more of the linking phosphate oxygens; alteration of a constituent of the ribose sugar, e.g., of the 2 ⁇ hydroxyl on the ribose sugar; wholesale replacement of the phosphate moiety with “dephospho” linkers; modification or replacement of a naturally occurring base; and replacement or modification of the ribose-phosphate backbone.
• nucleic acids are polymers of monomers
• many of the modifications occur at a position which is repeated within a nucleic acid, e.g., a modification of a base, or a phosphate moiety, or a non-linking O of a phosphate moiety.
• the modification will occur at all of the subject positions in the nucleic acid but in many cases it will not.
• a modification may only occur at a 3’ or 5’ terminal position, may only occur in a terminal region, e.g., at a position on a terminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand.
• a modification may occur in a double strand region, a single strand region, or in both.
• a modification may occur only in the double strand region of a RNA or may only occur in a single strand region of a RNA.
• a phosphorothioate modification at a non-linking O position may only occur at one or both termini, may only occur in a terminal region, e.g., at a position on a terminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand, or may occur in double strand and single strand regions, particularly at termini.
• the 5’ end or ends can be phosphorylated.
• Modifications can include, e.g., the use of modifications at the 2’ position of the ribose sugar with modifications that are known in the art, e.g., the use of deoxyribonucleotides, 2’-deoxy-2’-fluoro (2’-F) or 2’-O-methyl modified instead of the ribosugar of the nucleobase, and modifications in the phosphate group, e.g., phosphorothioate modifications. Overhangs need not be homologous with the target sequence.
• each residue of the sense strand and antisense strand is independently modified with LNA, HNA, CeNA, 2’-methoxyethyl, 2’- O-methyl, 2’-O-allyl, 2’- C- allyl, 2’-deoxy, or 2’-fluoro.
• the strands can contain more than one modification.
• each residue of the sense strand and antisense strand is independently modified with 2’-O-methyl or 2’-fluoro.
• the sense strand and antisense strand each comprises two differently modified nucleotides selected from 2’-O-methyl, 2’-fluoro and/or 2’-deoxy.
• each residue of the sense strand and antisense strand is independently modified with 2'-O-methyl nucleotide, 2’-deoxy nucleotide, 2 ⁇ -deoxy-2’-fluoro nucleotide, 2'-O-N- methylacetamido (2'-O-NMA) nucleotide, a 2'-O-dimethylaminoethoxyethyl (2'-O-DMAEOE) nucleotide, 2'-O-aminopropyl (2'-O-AP) nucleotide, or 2'-ara-F nucleotide.
• the dsRNA molecule comprises modifications of an alternating pattern, particular in the B1, B2, B3, B1’, B2’, B3’, B4’ regions.
• alternating motif or “alternative pattern” as used herein refers to a motif having one or more modifications, each modification occurring on alternating nucleotides of one strand.
• the alternating nucleotide may refer to one per every other nucleotide or one per every three nucleotides, or a similar pattern.
• the alternating motif can be “ABABABABABAB...,” “AABBAABBAABB...,” “AABAABAABAAB...,” “AAABAAABAAAB...,” “AAABBBAAABBB...,” or “ABCABCABCABC...,” etc.
• the type of modifications contained in the alternating motif may be the same or different.
• the alternating pattern i.e., modifications on every other nucleotide
• the alternating pattern may be the same, but each of the sense strand or antisense strand can be selected from several possibilities of modifications within the alternating motif such as “ABABAB...”, “ACACAC...” “BDBDBD...” or “CDCDCD...,” etc.
• the dsRNA molecule comprises the modification pattern for the alternating motif on the sense strand relative to the modification pattern for the alternating motif on the antisense strand is shifted.
• the shift may be such that the modified group of nucleotides of the sense strand corresponds to a differently modified group of nucleotides of the antisense strand and vice versa.
• the sense strand when paired with the antisense strand in the dsRNA duplex the alternating motif in the sense strand may start with “ABABAB” from 5’-3’ of the strand and the alternating motif in the antisense strand may start with “BABABA” from 3’-5’of the strand within the duplex region.
• the alternating motif in the sense strand may start with “AABBAABB” from 5’-3’ of the strand and the alternating motif in the antisense strand may start with “BBAABBAA” from 3’-5’of the strand within the duplex region, so that there is a complete or partial shift of the modification patterns between the sense strand and the antisense strand.
• the dsRNA molecule comprises mismatch(es) with the target, within the duplex, or combinations thereof. The mismatch can occur in the overhang region or the duplex region.
• the base pair can be ranked on the basis of their propensity to promote dissociation or melting (e.g., on the free energy of association or dissociation of a particular pairing, the simplest approach is to examine the pairs on an individual pair basis, though next neighbor or similar analysis can also be used).
• A:U is preferred over G:C
• G:U is preferred over G:C
• Mismatches e.g., non-canonical or other than canonical pairings (as described elsewhere herein) are preferred over canonical (A:T, A:U, G:C) pairings; and pairings which include a universal base are preferred over canonical pairings.
• the dsRNA molecule comprises at least one of the first 1, 2, 3, 4, or 5 base pairs within the duplex regions from the 5’- end of the antisense strand can be chosen independently from the group of: A:U, G:U, I:C, and mismatched pairs, e.g., non-canonical or other than canonical pairings or pairings which include a universal base, to promote the dissociation of the antisense strand at the 5’-end of the duplex.
• the nucleotide at the 1 position within the duplex region from the 5’-end in the antisense strand is selected from the group consisting of A, dA, dU, U, and dT.
• At least one of the first 1, 2 or 3 base pair within the duplex region from the 5’- end of the antisense strand is an AU base pair.
• the first base pair within the duplex region from the 5’- end of the antisense strand is an AU base pair.
• introducing 4’-modified and/or 5’-modified nucleotides to the 3’-end of a phosphodiester (PO), phosphorothioate (PS), and/or phosphorodithioate (PS2) linkage of a dinucleotide at any position of single stranded or double stranded oligonucleotide can exert steric effect to the internucleotide linkage and, hence, protecting or stabilizing it against nucleases.
• 5’-modified nucleoside is introduced at the 3’-end of a dinucleotide at any position of the dsRNA molecule.
• a 5’-alkylated nucleoside can be introduced at the 3’-end of a dinucleotide at any position of the dsRNA.
• the alkyl group at the 5’ position of the ribose sugar can be racemic or chirally pure R or S isomer.
• An exemplary 5’-alkylated nucleoside is 5’-methyl nucleoside.
• the 5’-methyl can be either racemic or chirally pure R or S isomer.
• a 4’-modified nucleoside is introduced at the 3’-end of a dinucleotide at any position of the dsRNA.
• a 4’-alkylated nucleoside may be introduced at the 3’-end of a dinucleotide at any position of dsRNA.
• the alkyl group at the 4’ position of the ribose sugar can be racemic or chirally pure R or S isomer.
• An exemplary 4’- alkylated nucleoside is 4’-methyl nucleoside.
• the 4’-methyl can be either racemic or chirally pure R or S isomer.
• a 4’-O-alkylated nucleoside may be introduced at the 3’-end of a dinucleotide at any position of single stranded or double stranded siRNA.
• the 4’-O-alkyl of the ribose sugar can be racemic or chirally pure R or S isomer.
• An exemplary 4’-O-alkylated nucleoside is 4’-O-methyl nucleoside.
• the 4’-O-methyl can be either racemic or chirally pure R or S isomer.
• a 5’-alkylated nucleoside is introduced at any position on the sense strand or antisense strand of the dsRNA, and such modification maintains or improves potency of the dsRNA.
• the 5’-alkyl can be either racemic or chirally pure R or S isomer.
• An exemplary 5’-alkylated nucleoside is 5’-methyl nucleoside.
• the 5’-methyl can be either racemic or chirally pure R or S isomer.
• a 4’-alkylated nucleoside is introduced at any position on the sense strand or antisense strand of the dsRNA, and such modification maintains or improves potency of the dsRNA.
• the 4’-alkyl can be either racemic or chirally pure R or S isomer.
• An exemplary 4’-alkylated nucleoside is 4’-methyl nucleoside.
• the 4’-methyl can be either racemic or chirally pure R or S isomer.
• a 4’-O-alkylated nucleoside is introduced at any position on the sense strand or antisense strand of the dsRNA, and such modification maintains or improves potency of the dsRNA.
• the 5’-alkyl can be either racemic or chirally pure R or S isomer.
• An exemplary 4’-O-alkylated nucleoside is 4’-O-methyl nucleoside.
• the 4’-O-methyl can be either racemic or chirally pure R or S isomer.
• the 2’-5’ linkages modifications can be used to promote nuclease resistance or to inhibit binding of the sense to the antisense strand, or can be used at the 5’ end of the sense strand to avoid sense strand activation by RISC.
• the sense strand comprises a 2’-5’-linkage between positions N-1 and N-2, counting from 5’-end.
• the dsRNA molecule can comprise L sugars (e.g., L ribose, L- arabinose with 2’-H, 2’-OH and 2’-OMe).
• these L sugars modifications can be used to promote nuclease resistance or to inhibit binding of the sense to the antisense strand, or can be used at the 5’ end of the sense strand to avoid sense strand activation by RISC.
• the sense strand comprises a L sugar nucleotide at the 5’-end.
• At least one of the sense stand and the antisense can comprise at least one, e.g., at least two, at least three, at least four, at least five, at least six, at least seven or more, 2’-deoxy modification in positions 5-17, e.g., positions 6-16, positions 6-15, positions 6-14, positions 6-13, positions 6-12, positions 7-15, positions 7-14, positions 7-13, positions, 7-12, positions 8-16, positions 8-15, positions 8-14, positions 8-13, positions 8-12, positions 9-16, positions 9-15, positions 9-14, positions 9-13, positions 9-12, positions 10-16, positions 10-15, positions 10-14, positions 10-13 or positions 10-12, counting from the 5’-end of the sense strand or the antisense strand.
• the dsRNA comprises at least three 2’-deoxy modifications, wherein the 2’-deoxy modifications are at positions 2 and 14 of the antisense strand, counting from 5’-end of the antisense strand, and at position 11 of the sense strand, counting from 5’-end of the sense strand.
• the dsRNA comprises at least five 2’-deoxy modifications, wherein the 2’-deoxy modifications are at positions 2, 12 and 14 of the antisense strand, counting from 5’-end of the antisense strand, and at positions 9 and 11 of the sense strand, counting from 5’-end of the sense strand.
• the dsRNA comprises at least seven 2’-deoxy modifications, wherein the 2’-deoxy modifications are at positions 2, 5, 7, 12 and 14 of the antisense strand, counting from 5’-end of the antisense strand, and at positions 9 and 11 of the sense strand, counting from 5’-end of the sense strand.
• the antisense strand comprises at least five 2’-deoxy modifications at positions 2, 5, 7, 12 and 14, counting from 5’-end of the antisense strand.
• the antisense strand has a length of 18-25 nucleotides, preferably, a length of 18-23 nucleotides.
• the dsRNA agent can comprise one or more non-natural nucleotides.
• the dsRNA agent can comprise less than 20%, e.g., less than 15%, less than 10%, or less than 5% non-natural nucleotides, or the dsRNA comprises no non-natural nucleotides.
• the dsRNA agent comprises all natural nucleotides.
• Some exemplary non-natural nucleotides include, but are not limited to, acyclic nucleotides, locked nucleic acid (LNA), HNA, CeNA, 2’-methoxyethyl, 2’-O-allyl, 2’-C-allyl, 2’-fluoro, 2'-O-N-methylacetamido (2'-O-NMA), a 2'-O-dimethylaminoethoxyethyl (2'-O-DMAEOE), 2'-O-aminopropyl (2'-O-AP), and 2'-ara-F.
• LNA locked nucleic acid
• HNA locked nucleic acid
• CeNA 2’-methoxyethyl
• 2’-C-allyl 2’-fluoro
• 2'-O-NMA 2'-O-N-methylacetamido
• Preferred moieties are ligands, which are coupled, preferably covalently, either directly or indirectly via an intervening tether.
• a ligand alters the distribution, targeting or lifetime of the molecule into which it is incorporated.
• a ligand provides an enhanced affinity for a selected target, e.g., molecule, cell or cell type, compartment, receptor e.g., a cellular or organ compartment, tissue, organ or region of the body, as, e.g., compared to a species absent such a ligand.
• Ligands providing enhanced affinity for a selected target are also termed targeting ligands.
• Some ligands can have endosomolytic properties.
• the endosomolytic ligands promote the lysis of the endosome and/or transport of the composition of the invention, or its components, from the endosome to the cytoplasm of the cell.
• the endosomolytic ligand may be a polyanionic peptide or peptidomimetic which shows pH-dependent membrane activity and fusogenicity.
• the endosomolytic ligand assumes its active conformation at endosomal pH.
• the “active” conformation is that conformation in which the endosomolytic ligand promotes lysis of the endosome and/or transport of the composition of the invention, or its components, from the endosome to the cytoplasm of the cell.
• Exemplary endosomolytic ligands include the GALA peptide (Subbarao et al., Biochemistry, 1987, 26: 2964-2972, which is incorporated by reference in its entirety), the EALA peptide (Vogel et al., J. Am. Chem. Soc., 1996, 118: 1581-1586, which is incorporated by reference in its entirety), and their derivatives (Turk et al., Biochem. Biophys. Acta, 2002, 1559: 56-68, which is incorporated by reference in its entirety).
• the endosomolytic component may contain a chemical group (e.g., an amino acid) which will undergo a change in charge or protonation in response to a change in pH.
• the endosomolytic component may be linear or branched.
• Ligands can improve transport, hybridization, and specificity properties and may also improve nuclease resistance of the resultant natural or modified oligoribonucleotide, or a polymeric molecule comprising any combination of monomers described herein and/or natural or modified ribonucleotides.
• Ligands in general can include therapeutic modifiers, e.g., for enhancing uptake; diagnostic compounds or reporter groups e.g., for monitoring distribution; cross-linking agents; and nuclease-resistance conferring moieties.
• General examples include lipids, steroids, vitamins, sugars, proteins, peptides, polyamines, and peptide mimics.
• Ligands can include a naturally occurring substance, such as a protein (e.g., human serum albumin (HSA), low-density lipoprotein (LDL), high-density lipoprotein (HDL), or globulin); a carbohydrate (e.g., a dextran, pullulan, chitin, chitosan, inulin, cyclodextrin or hyaluronic acid); or a lipid.
• the ligand may also be a recombinant or synthetic molecule, such as a synthetic polymer, e.g., a synthetic polyamino acid, an oligonucleotide (e.g. an aptamer).
• polyamino acids examples include polyamino acid is a polylysine (PLL), poly L-aspartic acid, poly L-glutamic acid, styrene-maleic acid anhydride copolymer, poly(L-lactide-co-glycolide) copolymer, divinyl ether-maleic anhydride copolymer, N-(2-hydroxypropyl)methacrylamide copolymer (HMPA), polyethylene glycol (PEG), polyvinyl alcohol (PVA), polyurethane, poly(2- ethylacryllic acid), N-isopropylacrylamide polymers, or polyphosphazine.
• PLL polylysine
• poly L-aspartic acid poly L-glutamic acid
• styrene-maleic acid anhydride copolymer poly(L-lactide-co-glycolide) copolymer
• divinyl ether-maleic anhydride copolymer divinyl ether
• polyamines include: polyethylenimine, polylysine (PLL), spermine, spermidine, polyamine, pseudopeptide-polyamine, peptidomimetic polyamine, dendrimer polyamine, arginine, amidine, protamine, cationic lipid, cationic porphyrin, quaternary salt of a polyamine, or an alpha helical peptide.
• Ligands can also include targeting groups, e.g., a cell or tissue targeting agent, e.g., a lectin, glycoprotein, lipid or protein, e.g., an antibody, that binds to a specified cell type such as a kidney cell.
• a targeting group can be a thyrotropin, melanotropin, lectin, glycoprotein, surfactant protein A, Mucin carbohydrate, multivalent lactose, multivalent galactose, N-acetyl- galactosamine, N-acetyl-glucosamine multivalent mannose, multivalent fucose, glycosylated polyamino acids, multivalent galactose, transferrin, bisphosphonate, polyglutamate, polyaspartate, a lipid, cholesterol, a steroid, bile acid, folate, vitamin B12, biotin, an RGD peptide, an RGD peptide mimetic or an aptamer.
• ligands include dyes, intercalating agents (e.g. acridines), cross- linkers (e.g. psoralen, mitomycin C), porphyrins (TPPC4, texaphyrin, Sapphyrin), polycyclic aromatic hydrocarbons (e.g., phenazine, dihydrophenazine), artificial endonucleases or a chelating agent (e.g.
• intercalating agents e.g. acridines
• cross- linkers e.g. psoralen, mitomycin C
• porphyrins TPPC4, texaphyrin, Sapphyrin
• polycyclic aromatic hydrocarbons e.g., phenazine, dihydrophenazine
• artificial endonucleases e.g.
• EDTA lipophilic molecules, e.g., cholesterol, cholic acid, adamantane acetic acid, 1-pyrene butyric acid, dihydrotestosterone, 1,3-Bis-O(hexadecyl)glycerol, geranyloxyhexyl group, hexadecylglycerol, borneol, menthol, 1,3-propanediol, heptadecyl group, palmitic acid, myristic acid,O3-(oleoyl)lithocholic acid, O3-(oleoyl)cholenic acid, dimethoxytrityl, or phenoxazine)and peptide conjugates (e.g., antennapedia peptide, Tat peptide), alkylating agents, phosphate, amino, mercapto, PEG (e.g., PEG-40K), MPEG, [MPEG]2, polyamino, alkyl, substituted
• biotin e.g., aspirin, vitamin E, folic acid
• transport/absorption facilitators e.g., aspirin, vitamin E, folic acid
• synthetic ribonucleases e.g., imidazole, bisimidazole, histamine, imidazole clusters, acridine-imidazole conjugates, Eu3+ complexes of tetraazamacrocycles), dinitrophenyl, HRP, or AP.
• Ligands can be proteins, e.g., glycoproteins, or peptides, e.g., molecules having a specific affinity for a co-ligand, or antibodies e.g., an antibody, that binds to a specified cell type such as a cancer cell, endothelial cell, or bone cell.
• Ligands may also include hormones and hormone receptors. They can also include non-peptide species, such as lipids, lectins, carbohydrates, vitamins, cofactors, multivalent lactose, multivalent galactose, N-acetyl- galactosamine, N-acetyl-glucosamine multivalent mannose, multivalent fucose, or aptamers.
• the ligand can be, for example, a lipopolysaccharide, an activator of p38 MAP kinase, or an activator of NF- ⁇ B.
• the ligand can be a substance, e.g., a drug, which can increase the uptake of the iRNA agent into the cell, for example, by disrupting the cell’s cytoskeleton, e.g., by disrupting the cell’s microtubules, microfilaments, and/or intermediate filaments.
• the drug can be, for example, taxon, vincristine, vinblastine, cytochalasin, nocodazole, japlakinolide, latrunculin A, phalloidin, swinholide A, indanocine, or myoservin.
• the ligand can increase the uptake of the oligonucleotide into the cell by activating an inflammatory response, for example.
• Exemplary ligands that would have such an effect include tumor necrosis factor alpha (TNF-alpha), interleukin-1 beta, or gamma interferon.
• TNF-alpha tumor necrosis factor alpha
• interleukin-1 beta interleukin-1 beta
• gamma interferon gamma interferon.
• the ligand is a lipid or lipid-based molecule.
• Such a lipid or lipid- based molecule preferably binds a serum protein, e.g., human serum albumin (HSA).
• HSA binding ligand allows for distribution of the conjugate to a target tissue, e.g., a non-kidney target tissue of the body.
• the target tissue can be the liver, including parenchymal cells of the liver.
• Other molecules that can bind HSA can also be used as ligands. For example, naproxen or aspirin can be used.
• a lipid or lipid-based ligand can (a) increase resistance to degradation of the conjugate, (b) increase targeting or transport into a target cell or cell membrane, and/or (c) can be used to adjust binding to a serum protein, e.g., HSA.
• a lipid based ligand can be used to modulate, e.g., control the binding of the conjugate to a target tissue. For example, a lipid or lipid-based ligand that binds to HSA more strongly will be less likely to be targeted to the kidney and therefore less likely to be cleared from the body. A lipid or lipid-based ligand that binds to HSA less strongly can be used to target the conjugate to the kidney.
• the lipid based ligand binds HSA. Preferably, it binds HSA with a sufficient affinity such that the conjugate will be preferably distributed to a non- kidney tissue. However, it is preferred that the affinity not be so strong that the HSA-ligand binding cannot be reversed. [00204] In another preferred embodiment, the lipid based ligand binds HSA weakly or not at all, such that the conjugate will be preferably distributed to the kidney. Other moieties that target to kidney cells can also be used in place of or in addition to the lipid based ligand.
• the ligand is a moiety, e.g., a vitamin, which is taken up by a target cell, e.g., a proliferating cell.
• a target cell e.g., a proliferating cell.
• vitamins include vitamin A, E, and K.
• B vitamins e.g., folic acid, B12, riboflavin, biotin, pyridoxal or other vitamins or nutrients taken up by cancer cells.
• HAS low density lipoprotein
• HDL high-density lipoprotein
• the ligand is a cell-permeation agent, preferably a helical cell- permeation agent.
• the agent is amphipathic.
• An exemplary agent is a peptide such as tat or antennapedia. If the agent is a peptide, it can be modified, including a peptidylmimetic, invertomers, non-peptide or pseudo-peptide linkages, and use of D-amino acids.
• the helical agent is preferably an alpha-helical agent, which preferably has a lipophilic and a lipophobic phase.
• the ligand can be a peptide or peptidomimetic.
• a peptidomimetic (also referred to herein as an oligopeptidomimetic) is a molecule capable of folding into a defined three- dimensional structure similar to a natural peptide.
• the peptide or peptidomimetic moiety can be about 5-50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids long.
• a peptide or peptidomimetic can be, for example, a cell permeation peptide, cationic peptide, amphipathic peptide, or hydrophobic peptide (e.g., consisting primarily of Tyr, Trp or Phe).
• the peptide moiety can be a dendrimer peptide, constrained peptide or cross-linked peptide.
• the peptide moiety can include a hydrophobic membrane translocation sequence (MTS).
• An exemplary hydrophobic MTS-containing peptide is RFGF having the amino acid sequence AAVALLPAVLLALLAP.
• An RFGF analogue e.g., amino acid sequence AALLPVLLAAP
• the peptide moiety can be a “delivery” peptide, which can carry large polar molecules including peptides, oligonucleotides, and protein across cell membranes.
• sequences from the HIV Tat protein (GRKKRRQRRRPPQ) and the Drosophila Antennapedia protein (RQIKIWFQNRRMKWKK) have been found to be capable of functioning as delivery peptides.
• a peptide or peptidomimetic can be encoded by a random sequence of DNA, such as a peptide identified from a phage-display library, or one-bead-one-compound (OBOC) combinatorial library (Lam et al., Nature, 354:82-94, 1991, which is incorporated by reference in its entirety).
• the peptide or peptidomimetic tethered to an iRNA agent via an incorporated monomer unit is a cell targeting peptide such as an arginine-glycine-aspartic acid (RGD)-peptide, or RGD mimic.
• RGD arginine-glycine-aspartic acid
• a peptide moiety can range in length from about 5 amino acids to about 40 amino acids.
• the peptide moieties can have a structural modification, such as to increase stability or direct conformational properties. Any of the structural modifications described below can be utilized.
• An RGD peptide moiety can be used to target a tumor cell, such as an endothelial tumor cell or a breast cancer tumor cell (Zitzmann et al., Cancer Res., 62:5139-43, 2002, which is incorporated by reference in its entirety).
• An RGD peptide can facilitate targeting of an iRNA agent to tumors of a variety of other tissues, including the lung, kidney, spleen, or liver (Aoki et al., Cancer Gene Therapy 8:783-787, 2001, which is incorporated by reference in its entirety).
• the RGD peptide will facilitate targeting of an iRNA agent to the kidney.
• the RGD peptide can be linear or cyclic, and can be modified, e.g., glycosylated or methylated to facilitate targeting to specific tissues.
• a glycosylated RGD peptide can deliver an iRNA agent to a tumor cell expressing ⁇ V ß 3 (Haubner et al., Jour. Nucl. Med., 42:326-336, 2001, which is incorporated by reference in its entirety).
• Peptides that target markers enriched in proliferating cells can be used.
• RGD containing peptides and peptidomimetics can target cancer cells, in particular cells that exhibit an integrin.
• RGD peptides cyclic peptides containing RGD, RGD peptides that include D-amino acids, as well as synthetic RGD mimics.
• RGD one can use other moieties that target the integrin ligand.
• such ligands can be used to control proliferating cells and angiogenesis.
• a “cell permeation peptide” is capable of permeating a cell, e.g., a microbial cell, such as a bacterial or fungal cell, or a mammalian cell, such as a human cell.
• a microbial cell- permeating peptide can be, for example, an ⁇ -helical linear peptide (e.g., LL-37 or Ceropin P1), a disulfide bond-containing peptide (e.g., ⁇ -defensin, ⁇ -defensin or bactenecin), or a peptide containing only one or two dominating amino acids (e.g., PR-39 or indolicidin).
• a cell permeation peptide can also include a nuclear localization signal (NLS).
• a cell permeation peptide can be a bipartite amphipathic peptide, such as MPG, which is derived from the fusion peptide domain of HIV-1 gp41 and the NLS of SV40 large T antigen (Simeoni et al., Nucl. Acids Res.31:2717-2724, 2003, which is incorporated by reference in its entirety).
• a targeting peptide can be an amphipathic ⁇ -helical peptide.
• amphipathic ⁇ -helical peptides include, but are not limited to, cecropins, lycotoxins, paradaxins, buforin, CPF, bombinin-like peptide (BLP), cathelicidins, ceratotoxins, S. clava peptides, hagfish intestinal antimicrobial peptides (HFIAPs), magainines, brevinins-2, dermaseptins, melittins, pleurocidin, H 2 A peptides, Xenopus peptides, esculentinis-1, and caerins. A number of factors will preferably be considered to maintain the integrity of helix stability.
• helix stabilization residues e.g., leu, ala, or lys
• a minimum number of helix destabilization residues will be utilized (e.g., proline, or cyclic monomeric units.
• the capping residue will be considered (for example Gly is an exemplary N- capping residue and/or C-terminal amidation can be used to provide an extra H-bond to stabilize the helix. Formation of salt bridges between residues with opposite charges, separated by i ⁇ 3, or i ⁇ 4 positions can provide stability.
• Peptide and peptidomimetic ligands include those having naturally occurring or modified peptides, e.g., D or L peptides; ⁇ , ⁇ , or ⁇ peptides; N-methyl peptides; azapeptides; peptides having one or more amide, i.e., peptide, linkages replaced with one or more urea, thiourea, carbamate, or sulfonyl urea linkages; or cyclic peptides.
• the targeting ligand can be any ligand that is capable of targeting a specific receptor. Examples are: folate, GalNAc, galactose, mannose, mannose-6P, clusters of sugars such as GalNAc cluster, mannose cluster, galactose cluster, or an aptamer. A cluster is a combination of two or more sugar units.
• the targeting ligands also include integrin receptor ligands, Chemokine receptor ligands, transferrin, biotin, serotonin receptor ligands, PSMA, endothelin, GCPII, somatostatin, LDL and HDL ligands.
• the ligands can also be based on nucleic acid, e.g., an aptamer.
• the aptamer can be unmodified or have any combination of modifications disclosed herein.
• Endosomal release agents include imidazoles, poly or oligoimidazoles, PEIs, peptides, fusogenic peptides, polycarboxylates, polycations, masked oligo or poly cations or anions, acetals, polyacetals, ketals/polyketals, orthoesters, polymers with masked or unmasked cationic or anionic charges, dendrimers with masked or unmasked cationic or anionic charges.
• PK modulator stands for pharmacokinetic modulator.
• PK modulator include lipophiles, bile acids, steroids, phospholipid analogues, peptides, protein binding agents, PEG, vitamins etc.
• Exemplary PK modulator include, but are not limited to, cholesterol, fatty acids, cholic acid, lithocholic acid, dialkylglycerides, diacylglyceride, phospholipids, sphingolipids, naproxen, ibuprofen, vitamin E, biotin etc.
• Oligonucleotides that comprise a number of phosphorothioate linkages are also known to bind to serum protein, thus short oligonucleotides, e.g.
• oligonucleotides of about 5 bases, 10 bases, 15 bases or 20 bases, comprising multiple of phosphorothioate linkages in the backbone are also amenable to the present invention as ligands (e.g. as PK modulating ligands).
• ligands e.g. as PK modulating ligands.
• aptamers that bind serum components e.g. serum proteins
• PK modulating ligands are also amenable to the present invention as PK modulating ligands.
• Other ligand conjugates amenable to the invention are described in U.S.
• ligands can all have same properties, all have different properties or some ligands have the same properties while others have different properties.
• a ligand can have targeting properties, have endosomolytic activity or have PK modulating properties.
• all the ligands have different properties.
• Ligands can be coupled to the oligonucleotides at various places, for example, 3’-end, 5’-end, and/or at an internal position.
• the ligand is attached to the oligonucleotides via an intervening tether, e.g. a carrier described herein.
• the ligand or tethered ligand may be present on a monomer when said monomer is incorporated into the growing strand.
• the ligand may be incorporated via coupling to a “precursor” monomer after said “precursor” monomer has been incorporated into the growing strand.
• a monomer having, e.g., an amino-terminated tether (i.e., having no associated ligand), e.g., TAP- (CH2)nNH2 may be incorporated into a growing oligonucleotide strand.
• a ligand having an electrophilic group e.g., a pentafluorophenyl ester or aldehyde group, can subsequently be attached to the precursor monomer by coupling the electrophilic group of the ligand with the terminal nucleophilic group of the precursor monomer’s tether.
• a monomer having a chemical group suitable for taking part in Click Chemistry reaction may be incorporated e.g., an azide or alkyne terminated tether/linker.
• a ligand having complementary chemical group e.g. an alkyne or azide can be attached to the precursor monomer by coupling the alkyne and the azide together.
• ligands can be attached to one or both strands.
• a double-stranded iRNA agent contains a ligand conjugated to the sense strand.
• a double-stranded iRNA agent contains a ligand conjugated to the antisense strand.
• ligand can be conjugated to nucleobases, sugar moieties, or internucleosidic linkages of nucleic acid molecules. Conjugation to purine nucleobases or derivatives thereof can occur at any position including, endocyclic and exocyclic atoms. In some embodiments, the 2-, 6-, 7-, or 8-positions of a purine nucleobase are attached to a conjugate moiety. Conjugation to pyrimidine nucleobases or derivatives thereof can also occur at any position.
• the 2-, 5-, and 6-positions of a pyrimidine nucleobase can be substituted with a conjugate moiety.
• Conjugation to sugar moieties of nucleosides can occur at any carbon atom.
• Example carbon atoms of a sugar moiety that can be attached to a conjugate moiety include the 2', 3', and 5' carbon atoms.
• the 1' position can also be attached to a conjugate moiety, such as in an abasic residue.
• Internucleosidic linkages can also bear conjugate moieties.
• the conjugate moiety can be attached directly to the phosphorus atom or to an O, N, or S atom bound to the phosphorus atom.
• the conjugate moiety can be attached to the nitrogen atom of the amine or amide or to an adjacent carbon atom.
• the ligand is conjugated to the sense strand.
• the ligand can be conjugated at the 3’-end, 5’-end or at an internal position of the sense strand. In some embodiments, the ligand is conjugated to the 3’-end of the sense strand. Further, the ligand can be conjugated to a nucleobase, sugar moiety or internucleotide linkage of the sense strand. [00222] Any suitable ligand in the field of RNA interference may be used, although the ligand is typically a carbohydrate e.g. monosaccharide (such as GalNAc), disaccharide, trisaccharide, tetrasaccharide, polysaccharide.
• monosaccharide such as GalNAc
• Linkers that conjugate the ligand to the nucleic acid include those discussed above.
• the ligand can be one or more GalNAc (N-acetylgalactosamine) derivatives attached through a monovalent, bivalent or trivalent branched linker.
• GalNAc N-acetylgalactosamine
• the dsRNA of the invention is conjugated to a bivalent and trivalent branched linkers include the structures shown in any of formula (IV) – (VII): ; wherein: q 2A , q 2B , q 3A , q 3B , q4 A , q 4B , q 5A , q 5B and q 5C represent independently for each occurrence 0-20 and wherein the repeating unit can be the same or different; P 2A , P 2B , P 3A , P 3B , P 4A , P 4B , P 5A , P 5B , P 5C , T 2A , T 2B , T 3A , T 3B , T 4A , T 4B , T 5A , T 5B , T 5C are each independently for each occurrence absent, CO, NH, O, S, OC(O), NHC(O), CH2, CH2NH or CH2O
• Trivalent conjugating GalNAc derivatives are particularly useful for use with RNAi agents for inhibiting the expression of a target gene, such as those of formula (VII): , wherein L 5A , L 5B and L 5C represent a monosaccharide, such as GalNAc derivative.
• Examples of suitable bivalent and trivalent branched linker groups conjugating GalNAc derivatives include, but are not limited to, the following compounds: Ligand 2 Ligand 8.
• a dsRNA described herein comprises Ligand 1, i.e., a ligand having the following structure: [00228] In some embodiments, a dsRNA described herein comprises a ligand described in US Patent No.5,994,517 or US Patent No.6,906,182, content of each of which is incorporated herein by reference in its entirety. [00229] In some embodiments, the ligand can be a tri-antennary ligand described in Figure 3 of US Patent No. 6,906,182. For example, a dsRNA described herein can comprise a ligand selected from the following tri-antennary ligands:
• the ligand is a multivalent ligand, e.g., a ligand of Formula (VII).
• the ligand is a GalNAc derivative, e.g., a ligand selected from the Ligands 1-8 disclosed herein.
• the ligand may be attached to the dsRNA via a carrier.
• the carriers include (i) at least one “backbone attachment point,” preferably two “backbone attachment points” and (ii) at least one “tethering attachment point.”
• a “backbone attachment point” as used herein refers to a functional group, e.g.
• a “tethering attachment point” in some embodiments refers to a constituent ring atom of the cyclic carrier, e.g., a carbon atom or a heteroatom (distinct from an atom which provides a backbone attachment point), that connects a selected moiety.
• the moiety can be, e.g., a carbohydrate, e.g.
• the selected moiety is connected by an intervening tether to the cyclic carrier.
• the cyclic carrier will often include a functional group, e.g., an amino group, or generally, provide a bond, that is suitable for incorporation or tethering of another chemical entity, e.g., a ligand to the constituent ring.
• the dsRNA molecule of the invention is conjugated to a ligand via a carrier, wherein the carrier can be cyclic group or acyclic group; preferably, the cyclic group is selected from pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, [1,3]dioxolane, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuryl and decalin; preferably, the acyclic group is selected from serinol backbone or diethanolamine backbone.
• the ligand can be attached to the sense strand, antisense strand or both strands, at the 3’-end, 5’-end or both ends.
• the ligand can be conjugated to the sense strand, in particular, the 3’-end of the sense strand.
• the dsRNA molecule comprises at least one ASGPR ligand.
• the ASGPR ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker, such as: [00235]
• the ASGPR ligand is attached to the 3’ end of the sense strand.
• Linkers [00236] Aspects of the conjugates disclosed herein include linkers, which can comprise one or more linker components.
• linker means an organic moiety that connects two parts of a compound, e.g., a DVD immunoglobulin to a dsRNA.
• Linkers typically comprise a direct bond or an atom such as oxygen or sulfur, a unit such as NR 1 , C(O), C(O)O, C(O)NR 1 , SO, SO 2 , SO 2 NH or a chain of atoms, such as substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, arylalkyl, arylalkenyl, arylalkynyl, heteroarylalkyl, heteroarylalkenyl, heteroarylalkynyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, aryl, heteroaryl, heterocyclyl, cycloalkyl, cycloalkenyl, alkylarylalkyl, alkylarylalkenyl, alkylarylalkynyl, alkenylarylalkyl, alkenylarylal
• linker functionality can be included in the subject dsRNAs, including but not limited to cleavable linkers, and non-cleavable linkers, as well as reversible linkers and irreversible linkers.
• the linker is a cleavable linker.
• Cleavable linkers are those that rely on processes inside a target cell to liberate the two parts the linker is holding together, as reduction in the cytoplasm, exposure to acidic conditions in a lysosome or endosome, or cleavage by specific enzymes (e.g. proteases) within the cell.
• cleavable linkers allow the two parts to be released in their original form after internalization and processing inside a target cell.
• Cleavable linkers include, but are not limited to, those whose bonds can be cleaved by enzymes (e.g., peptide linkers); reducing conditions (e.g., disulfide linkers); or acidic conditions (e.g., hydrazones and carbonates).
• the cleavable linker comprises at least one cleavable linking group.
• a cleavable linking group is one which is sufficiently stable outside the cell, but which upon entry into a target cell is cleaved to release the two parts the linker is holding together.
• the cleavable linking group is cleaved at least 10 times or more, preferably at least 100 times faster in the target cell or under a first reference condition (which can, e.g., be selected to mimic or represent intracellular conditions) than in the blood or serum of a subject, or under a second reference condition (which can, e.g., be selected to mimic or represent conditions found in the blood or serum).
• Cleavable linking groups are susceptible to cleavage agents, e.g., pH, redox potential or the presence of degradative molecules. Generally, cleavage agents are more prevalent or found at higher levels or activities inside cells than in serum or blood.
• degradative agents include: redox agents which are selected for particular substrates or which have no substrate specificity, including, e.g., oxidative or reductive enzymes or reductive agents such as mercaptans, present in cells, that can degrade a redox cleavable linking group by reduction; esterases; endosomes or agents that can create an acidic environment, e.g., those that result in a pH of five or lower; enzymes that can hydrolyze or degrade an acid cleavable linking group by acting as a general acid, peptidases (which can be substrate specific), and phosphatases.
• a cleavable linkage group, such as a disulfide bond can be susceptible to pH.
• a linker can include a cleavable linking group that is cleavable by a particular enzyme. The type of cleavable linking group incorporated into a linker can depend on the cell to be targeted.
• liver targeting ligands can be linked to the cationic lipids through a linker that includes an ester group.
• Liver cells are rich in esterases, and therefore the linker will be cleaved more efficiently in liver cells than in cell types that are not esterase-rich.
• Other cell- types rich in esterases include cells of the lung, renal cortex, and testis.
• Linkers that contain peptide bonds can be used when targeting cell types rich in peptidases, such as liver cells and synoviocytes.
• the suitability of a candidate cleavable linking group can be evaluated by testing the ability of a degradative agent (or condition) to cleave the candidate linking group.
• the candidate cleavable linking group for the ability to resist cleavage in the blood or when in contact with other non-target tissue.
• the evaluations can be carried out in cell free systems, in cells, in cell culture, in organ or tissue culture, or in whole animals. It may be useful to make initial evaluations in cell-free or culture conditions and to confirm by further evaluations in whole animals.
• useful candidate compounds are cleaved at least 2, 4, 10 or 100 times faster in the cell (or under in vitro conditions selected to mimic intracellular conditions) as compared to blood or serum (or under in vitro conditions selected to mimic extracellular conditions).
• cleavable linking groups is redox cleavable linking groups, which may be used in the dsRNA molecule according to the present invention that are cleaved upon reduction or oxidation.
• reductively cleavable linking group is a disulfide linking group (-S-S-).
• a candidate cleavable linking group is a suitable “reductively cleavable linking group,” or for example is suitable for use with a particular iRNA moiety and particular targeting agent one can look to methods described herein.
• a candidate can be evaluated by incubation with dithiothreitol (DTT), or other reducing agent using reagents know in the art, which mimic the rate of cleavage which would be observed in a cell, e.g., a target cell.
• DTT dithiothreitol
• the candidates can also be evaluated under conditions which are selected to mimic blood or serum conditions.
• candidate compounds are cleaved by at most 10% in the blood.
• useful candidate compounds are degraded at least 2, 4, 10 or 100 times faster in the cell (or under in vitro conditions selected to mimic intracellular conditions) as compared to blood (or under in vitro conditions selected to mimic extracellular conditions).
• the rate of cleavage of candidate compounds can be determined using standard enzyme kinetics assays under conditions chosen to mimic intracellular media and compared to conditions chosen to mimic extracellular media.
• Phosphate-based cleavable linking groups which may be used in the dsRNA molecule according to the present invention, are cleaved by agents that degrade or hydrolyze the phosphate group.
• An example of an agent that cleaves phosphate groups in cells are enzymes such as phosphatases in cells.
• phosphate-based linking groups are -O-P(O)(ORk)- O-, -O-P(S)(ORk)-O-, -O-P(S)(SRk)-O-, -S-P(O)(ORk)-O-, -O-P(O)(ORk)-S-, -O-P(O)(ORk)-S-, -O-P(S)(ORk)-S-, -S-P(S)(ORk)-O-, -O-P(S)(ORk)-O-, -O-P(O)(Rk)-O-, -O-P(S)(Rk)-O-, -S-P(O)(Rk)-O-, -S- P(S)(Rk)-O-, -S-P(O)(Rk)-S-, -O-P(S)( Rk)-S-.
• Preferred embodiments are -O-P(O)(OH)-O-, -O- P(S)(OH)-O-, -O-P(S)(SH)-O-, -S-P(O)(OH)-O-, -O-P(O)(OH)-S-, -S-P(O)(OH)-S-, -O- P(S)(OH)-S-, -S-P(S)(OH)-O-, -O-P(O)(H)-O-, -O-P(S)(H)-O-, -S-P(O)(H)-O-, -S-P(O)(H)-O-, -S-P(S)(H)-O-, -S-P(S)(H)-O-, - S-P(O)(H)-S-, -O-P(S)(H)-S-.
• Acid cleavable linking groups which may be used in the dsRNA molecule according to the present invention, are linking groups that are cleaved under acidic conditions.
• acid cleavable linking groups are cleaved in an acidic environment with a pH of about 6.5 or lower (e.g., about 6.0, 5.5, 5.0, or lower), or by agents such as enzymes that can act as a general acid.
• specific low pH organelles such as endosomes and lysosomes can provide a cleaving environment for acid cleavable linking groups.
• Acid cleavable linking groups include but are not limited to hydrazones, esters, and esters of amino acids.
• a preferred embodiment is when the carbon attached to the oxygen of the ester (the alkoxy group) is an aryl group, substituted alkyl group, or tertiary alkyl group such as dimethyl pentyl or t-butyl.
• Ester-based cleavable linking groups which may be used in the dsRNA molecule according to the present invention, are cleaved by enzymes such as esterases and amidases in cells.
• ester-based cleavable linking groups include but are not limited to esters of alkylene, alkenylene and alkynylene groups.
• Ester cleavable linking groups have the general formula -C(O)O-, or -OC(O)-. These candidates can be evaluated using methods analogous to those described above.
• Peptide-based cleavable linking groups which may be used in the dsRNA molecule according to the present invention, are cleaved by enzymes such as peptidases and proteases in cells.
• Peptide-based cleavable linking groups are peptide bonds formed between amino acids to yield oligopeptides (e.g., dipeptides, tripeptides etc.) and polypeptides.
• Peptide-based cleavable groups do not include the amide group (-C(O)NH-).
• the amide group can be formed between any alkylene, alkenylene or alkynylene.
• a peptide bond is a special type of amide bond formed between amino acids to yield peptides and proteins.
• the peptide based cleavage group is generally limited to the peptide bond (i.e., the amide bond) formed between amino acids yielding peptides and proteins and does not include the entire amide functional group.
• Peptide-based cleavable linking groups have the general formula – NHCHR A C(O)NHCHR B C(O)-, where R A and R B are the R groups of the two adjacent amino acids. These candidates can be evaluated using methods analogous to those described above.
• Uses of the dsRNAs [00249]
• the dsRNAs described herein can be used for inhibiting the expression of a target gene. Accordingly, in another aspect, provided herein is a method for inhibiting the expression of a target gene.
• the method comprises the step of administering a dsRNA described herein to a cell in an amount sufficient to inhibit expression of the target gene.
• the present invention further relates to a use of a dsRNA described herein for inhibiting expression of a target gene in a target cell in vitro.
• Exemplary target genes include, but are not limited to, ⁇ -catenin (CTNNB1), IRF4, Factor VII, Eg5, PCSK9, TPX2, apoB, SAA, TTR, RSV, PDGF beta gene, Erb-B gene, Src gene, CRK gene, GRB2 gene, RAS gene, MEKK gene, JNK gene, RAF gene, Erk1/2 gene, PCNA(p21) gene, MYB gene, JUN gene, FOS gene, BCL-2 gene, hepcidin, Activated Protein C, Cyclin D gene, VEGF gene, EGFR gene, Cyclin A gene, Cyclin E gene, WNT-1 gene, beta- catenin gene, c-MET gene, PKC gene, NFKB gene, STAT3 gene, survivin gene, Her2/Neu gene, topoisomerase I gene, topoisomerase II alpha gene, p73 gene, mutations in the p21(WAF1/CIP1) gene, mutations in the
• a dsRNA described herein can be used for treatment of a subject or mammal.
• Pharmaceutical compositions [00252] For therapeutic uses, dsNRAs described herein can be formulated into pharmaceutical compositions. Accordingly, in another aspect, the invention provides a pharmaceutical composition comprising a dsRNA as defined herein.
• Pharmaceutically acceptable compositions comprise a therapeutically-effective amount of one or more of the dsRNAs described herein, taken alone or formulated together with one or more pharmaceutically acceptable carriers (additives), excipient and/or diluents.
• compositions can be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; (2) parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained- release formulation; (3) topical application, for example, as a cream, ointment, or a controlled- release patch or spray applied to the skin; (4) intravaginally or intrarectally, for example, as a pessary, cream or foam; (5) sublingually; (6) ocularly; (7) transdermally; or (8) nasally.
• oral administration for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.
• the phrase “therapeutically-effective amount” as used herein means that amount of a compound, material, or composition comprising a conjugate described herein which is effective for producing some desired therapeutic effect in at least a sub-population of cells in an animal at a reasonable benefit/risk ratio applicable to any medical treatment.
• pharmaceutically acceptable is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
• phrases “pharmaceutically acceptable carrier” as used herein means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body.
• manufacturing aid e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid
• solvent encapsulating material involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body.
• Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient.
• materials which can serve as pharmaceutically acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such as magnesium state, sodium lauryl sulfate and talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; (12) esters, such as ethyl oleate and ethyl laurate; (13)
• pharmaceutically acceptable carrier is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.
• the use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.
• Pharmaceutical carriers include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. The use of such media and agents for pharmaceutically active substances is known in the art.
• the formulations can conveniently be presented in unit dosage form and can be prepared by any methods well known in the art of pharmacy.
• the amount of active ingredient which can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated, the particular mode of administration.
• the amount of active ingredient which can be combined with a carrier material to produce a single dosage form will generally be that amount of the compound which produces a therapeutic effect. Generally, out of one hundred per cent, this amount will range from about 0.1 per cent to about ninety-nine percent of active ingredient, preferably from about 5 per cent to about 70 per cent, most preferably from about 10 per cent to about 30 per cent.
• a formulation of the present invention comprises an excipient selected from the group consisting of cyclodextrins, celluloses, liposomes, micelle forming agents, e.g., bile acids, and polymeric carriers, e.g., polyesters and polyanhydrides; and a conjugate described herein.
• an aforementioned formulation renders orally bioavailable a conjugate described herein.
• the dsRNA preparation can be formulated in combination with another agent, e.g., another therapeutic agent or an agent that stabilizes the dsRNA.
• Still other agents include chelating agents, e.g., EDTA (e.g., to remove divalent cations such as Mg 2+ ), salts, RNAse inhibitors (e.g., a broad specificity RNAse inhibitor such as RNAsin) and so forth.
• chelating agents e.g., EDTA (e.g., to remove divalent cations such as Mg 2+ )
• salts e.g., to remove divalent cations such as Mg 2+
• RNAse inhibitors e.g., a broad specificity RNAse inhibitor such as RNAsin
• Methods of preparing these formulations or compositions include the step of bringing into association a dsRNA of the present invention with the carrier and, optionally, one or more accessory ingredients.
• the formulations are prepared by uniformly and intimately bringing into association a dsRNA of the present invention with liquid carriers, or finely divided solid carriers, or both, and then,
• dsRNAs according to the invention can be formulated for administration in any convenient way for use in human or veterinary medicine, by analogy with other pharmaceuticals.
• compositions can also contain adjuvants such as preservatives, wetting agents, emulsifying agents and/or dispersing agents. Prevention of the presence of microorganisms can be ensured both by sterilization procedures and by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol, sorbic acid, and the like. It can also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form can be brought about by the inclusion of agents that delay absorption, such as aluminum monostearate and gelatin.
• a composition must be sterile and fluid to the extent that the composition is deliverable by syringe.
• the carrier preferably is an isotonic buffered saline solution.
• Routes of administration [00266]
• the dsRNAs described herein or a pharmaceutical composition comprising same can be administered by a variety of methods known in the art. As will be appreciated by the skilled artisan, the route and/or mode of administration will vary depending upon the target disease or condition and the desired results. To administer a dsRNA described herein by certain routes of administration, it can be necessary to coat the dsRNA with, or co-administer the dsRNA with, a material to prevent its inactivation.
• a dsRNA can be administered to a subject in an appropriate carrier, for example, liposomes, or a diluent.
• Pharmaceutically acceptable diluents include saline and aqueous buffer solutions.
• Exemplary routes for administration include, but are not limited to, intravenous, subcutaneous, intratumoral, topical, rectal, anal, vaginal, nasal, pulmonary, and ocular.
• the compositions of the present invention can be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration can be topical (including ophthalmic, vaginal, rectal, intranasal, transdermal), oral or parenteral.
• Parenteral administration includes intravenous drip, subcutaneous, intraperitoneal or intramuscular injection, or intrathecal or intraventricular administration.
• the route and site of administration can be chosen to enhance targeting. For example, to target muscle cells, intramuscular injection into the muscles of interest would be a logical choice. Lung cells might be targeted by administering the dsRNA in aerosol form. The vascular endothelial cells could be targeted by coating a balloon catheter with the dsRNA and mechanically introducing the dsRNA.
• Dosage [00270] Actual dosage levels of the active ingredients, e.g., the dsRNA described herein, in the pharmaceutical compositions of the present invention can be varied so as to obtain an amount of the active ingredient which is effective to achieve the desired therapeutic response for a particular patient, composition, and mode of administration, without being toxic to the patient.
• a selected dosage level will depend upon a variety of pharmacokinetic factors including the activity of the particular compositions of the present invention employed, the route of administration, the time of administration, the rate of excretion of the particular compound being employed, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compositions employed, the age, sex, weight, condition, general health and prior medical history of the patient being treated, and like factors well known in the medical arts.
• the unit dose is less than 10 mg per kg of bodyweight, or less than 10, 5, 2, 1, 0.5, 0.1, 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, 0.00005 or 0.00001 mg per kg of bodyweight, and less than 200 nmole of dsRNA molecule (e.g., about 4.4 x 10 16 copies) per kg of bodyweight, or less than 1500, 750, 300, 150, 75, 15, 7.5, 1.5, 0.75, 0.15, 0.075, 0.015, 0.0075, 0.0015, 0.00075, 0.00015 nmole of dsRNA molecule per kg of bodyweight.
• dsRNA molecule e.g., about 4.4 x 10 16 copies
• the defined amount can be an amount effective to treat or prevent a disease or disorder, e.g., a disease or disorder associated with the target gene.
• the unit dose for example, can be administered by injection (e.g., intravenous, subcutaneous or intramuscular), an inhaled dose, or a topical application. In some embodiments dosages may be less than 10, 5, 2, 1, or 0.1 mg/kg of body weight. [00273] In some embodiments, the unit dose is administered less frequently than once a day, e.g., less than every 2, 4, 8 or 30 days. In another embodiment, the unit dose is not administered with a frequency (e.g., not a regular frequency). For example, the unit dose may be administered a single time.
• the effective dose is administered with other traditional therapeutic modalities.
• a subject is administered an initial dose and one or more maintenance doses.
• the maintenance dose or doses can be the same or lower than the initial dose, e.g., one-half less of the initial dose.
• a maintenance regimen can include treating the subject with a dose or doses ranging from 0.01 ⁇ g to 15 mg/kg of body weight per day, e.g., 10, 1, 0.1, 0.01, 0.001, or 0.00001 mg per kg of bodyweight per day.
• the maintenance doses are, for example, administered no more than once every 2, 5, 10, or 30 days.
• the treatment regimen may last for a period of time which will vary depending upon the nature of the particular disease, its severity and the overall condition of the patient.
• the dosage may be delivered no more than once per day, e.g., no more than once per 24, 36, 48, or more hours, e.g., no more than once for every 5 or 8 days.
• the patient can be monitored for changes in his condition and for alleviation of the symptoms of the disease state.
• the dosage of the compound may either be increased in the event the patient does not respond significantly to current dosage levels, or the dose may be decreased if an alleviation of the symptoms of the disease state is observed, if the disease state has been ablated, or if undesired side-effects are observed.
• the effective dose can be administered in a single dose or in two or more doses, as desired or considered appropriate under the specific circumstances. If desired to facilitate repeated or frequent infusions, implantation of a delivery device, e.g., a pump, semi-permanent stent (e.g., intravenous, intraperitoneal, intracisternal or intracapsular), or reservoir may be advisable.
• a delivery device e.g., a pump, semi-permanent stent (e.g., intravenous, intraperitoneal, intracisternal or intracapsular), or reservoir may be advisable.
• the composition includes a plurality of dsRNA molecule species.
• the dsRNA molecule species has sequences that are non- overlapping and non-adjacent to another species with respect to a naturally occurring target sequence.
• the plurality of dsRNA molecule species is specific for different naturally occurring target genes.
• the dsRNA molecule is allele specific.
• the dsRNAs described herein can be administered to mammals, particularly large mammals such as nonhuman primates or humans in a number of ways.
• the administration of the dsRNA is parenteral, e.g., intravenous (e.g., as a bolus or as a diffusible infusion), intradermal, intraperitoneal, intramuscular, intrathecal, intraventricular, intracranial, subcutaneous, transmucosal, buccal, sublingual, endoscopic, rectal, oral, vaginal, topical, pulmonary, intranasal, urethral or ocular.
• Administration can be provided by the subject or by another person, e.g., a health care provider.
• the medication can be provided in measured doses or in a dispenser which delivers a metered dose.
• Liposomes and lipid formulations [00280]
• the dsRNAs described herein can be formulated for delivery in a membranous molecular assembly, e.g., a liposome or a micelle.
• liposome refers to a vesicle composed of amphiphilic lipids arranged in at least one bilayer, e.g., one bilayer or a plurality of bilayers. Liposomes include unilamellar and multilamellar vesicles that have a membrane formed from a lipophilic material and an aqueous interior. The aqueous portion contains the siRNA composition.
• the lipophilic material isolates the aqueous interior from an aqueous exterior, which typically does not include the dsRNA composition, although in some examples, it may.
• Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomal bilayer fuses with bilayer of the cellular membranes. As the merging of the liposome and cell progresses, the internal aqueous contents that include a dsRNA described herien are delivered into the cell where the dsRNA can specifically bind to a target RNA and can mediate RNAi.
• a liposome containing a dsRNA described herein can be prepared by a variety of methods.
• the lipid component of a liposome is dissolved in a detergent so that micelles are formed with the lipid component.
• the lipid component can be an amphipathic cationic lipid or lipid conjugate.
• the detergent can have a high critical micelle concentration and may be nonionic.
• Exemplary detergents include cholate, CHAPS, octylglucoside, deoxycholate, and lauroyl sarcosine.
• the dsRNA preparation is then added to the micelles that include the lipid component.
• the cationic groups on the lipid interact with the dsRNA and condense around the dsRNA to form a liposome.
• the detergent is removed, e.g., by dialysis, to yield a liposomal preparation of dsRNA.
• a carrier compound that assists in condensation can be added during the condensation reaction, e.g., by controlled addition.
• the carrier compound can be a polymer other than a nucleic acid (e.g., spermine or spermidine). pH can also be adjusted to favor condensation.
• Liposome formation can also include one or more aspects of exemplary methods described in Felgner, P. L. et al., Proc. Natl. Acad. Sci., USA 8:7413-7417, 1987; U.S. Pat. No. 4,897,355; U.S. Pat. No. 5,171,678; Bangham, et al. M. Mol. Biol. 23:238, 1965; Olson, et al. Biochim. Biophys.
• Microfluidization can be used when consistently small (50 to 200 nm) and relatively uniform aggregates are desired (Mayhew, et al. Biochim. Biophys. Acta 775:169, 1984, which is incorporated by reference in its entirety). These methods are readily adapted to packaging siRNA preparations into liposomes. [00284] Liposomes that are pH-sensitive or negatively-charged entrap nucleic acid molecules rather than complex with them. Since both the nucleic acid molecules and the lipid are similarly charged, repulsion rather than complex formation occurs. Nevertheless, some nucleic acid molecules are entrapped within the aqueous interior of these liposomes.
• pH-sensitive liposomes have been used to deliver DNA encoding the thymidine kinase gene to cell monolayers in culture. Expression of the exogenous gene was detected in the target cells (Zhou et al., Journal of Controlled Release, 19, (1992) 269-274, which is incorporated by reference in its entirety).
• One major type of liposomal composition includes phospholipids other than naturally-derived phosphatidylcholine.
• Neutral liposome compositions for example, can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl phosphatidylcholine (DPPC).
• Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic liposomes are formed primarily from dioleoyl phosphatidylethanolamine (DOPE).
• DOPE dioleoyl phosphatidylethanolamine
• Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC, and egg PC.
• PC phosphatidylcholine
• Another type is formed from mixtures of phospholipid and/or phosphatidylcholine and/or cholesterol.
• cationic liposomes are used. Cationic liposomes possess the advantage of being able to fuse to the cell membrane.
• Non-cationic liposomes although not able to fuse as efficiently with the plasma membrane, are taken up by macrophages in vivo and can be used to deliver siRNAs to macrophages.
• Further advantages of liposomes include: liposomes obtained from natural phospholipids are biocompatible and biodegradable; liposomes can incorporate a wide range of water and lipid soluble drugs; liposomes can protect encapsulated siRNAs in their internal compartments from metabolism and degradation (Rosoff, in “Pharmaceutical Dosage Forms,” Lieberman, Rieger and Banker (Eds.), 1988, volume 1, p. 245).
• a positively charged synthetic cationic lipid, N-[1-(2,3-dioleyloxy)propyl]-N,N,N- trimethylammonium chloride can be used to form small liposomes that interact spontaneously with nucleic acid to form lipid-nucleic acid complexes which are capable of fusing with the negatively charged lipids of the cell membranes of tissue culture cells, resulting in delivery of siRNA (see, e.g., Felgner, P. L. et al., Proc. Natl. Acad.
• a DOTMA analogue, 1,2-bis(oleoyloxy)-3-(trimethylammonia)propane (DOTAP) can be used in combination with a phospholipid to form DNA-complexing vesicles.
• DOTAP 1,2-bis(oleoyloxy)-3-(trimethylammonia)propane
• LipofectinTM Bethesda Research Laboratories, Gaithersburg, Md. is an effective agent for the delivery of highly anionic nucleic acids into living tissue culture cells that comprise positively charged DOTMA liposomes which interact spontaneously with negatively charged polynucleotides to form complexes.
• DOTAP 1,2-bis(oleoyloxy)-3,3-(trimethylammonia)propane
• cationic lipid compounds include those that have been conjugated to a variety of moieties including, for example, carboxyspermine which has been conjugated to one of two types of lipids and includes compounds such as 5-carboxyspermylglycine dioctaoleoylamide (“DOGS”) (TransfectamTM, Promega, Madison, Wisconsin) and dipalmitoylphosphatidylethanolamine 5-carboxyspermyl-amide (“DPPES”) (see, e.g., U.S. Pat. No.5,171,678).
• DOGS 5-carboxyspermylglycine dioctaoleoylamide
• DPES dipalmitoylphosphatidylethanolamine 5-carboxyspermyl-amide
• Another cationic lipid conjugate includes derivatization of the lipid with cholesterol (“DC-Chol”) which has been formulated into liposomes in combination with DOPE (See, Gao, X. and Huang, L., Biochim. Biophys. Res. Commun. 179:280, 1991). Lipopolylysine, made by conjugating polylysine to DOPE, has been reported to be effective for transfection in the presence of serum (Zhou, X. et al., Biochim. Biophys. Acta 1065:8, 1991, which is incorporated by reference in its entirety).
• these liposomes containing conjugated cationic lipids are said to exhibit lower toxicity and provide more efficient transfection than the DOTMA- containing compositions.
• Other commercially available cationic lipid products include DMRIE and DMRIE-HP (Vical, La Jolla, California) and Lipofectamine (DOSPA) (Life Technology, Inc., Gaithersburg, Maryland).
• DOSPA Lipofectamine
• Other cationic lipids suitable for the delivery of oligonucleotides are described in WO 98/39359 and WO 96/37194.
• Liposomal formulations are particularly suited for topical administration. Liposomes present several advantages over other formulations.
• liposomes are used for delivering siRNA to epidermal cells and also to enhance the penetration of siRNA into dermal tissues, e.g., into skin.
• the liposomes can be applied topically. Topical delivery of drugs formulated as liposomes to the skin has been documented (see, e.g., Weiner et al., Journal of Drug Targeting, 1992, vol. 2,405-410 and du Plessis et al., Antiviral Research, 18, 1992, 259-265; Mannino, R. J.
• Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol.
• Non-ionic liposomal formulations comprising Novasome I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome II (glyceryl distearate/ cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver a drug into the dermis of mouse skin. Such formulations with siRNA are useful for treating a dermatological disorder.
• Liposomes that include a conjugate described herein can be made highly deformable.
• transfersomes are a type of deformable liposomes.
• Transfersomes can be made by adding surface edge activators, usually surfactants, to a standard liposomal composition.
• Transfersomes that include siRNA can be delivered, for example, subcutaneously by infection in order to deliver siRNA to keratinocytes in the skin.
• lipid vesicles In order to cross intact mammalian skin, lipid vesicles must pass through a series of fine pores, each with a diameter less than 50 nm, under the influence of a suitable transdermal gradient.
• these transfersomes can be self-optimizing (adaptive to the shape of pores, e.g., in the skin), self-repairing, and can frequently reach their targets without fragmenting, and often self-loading.
• Other formulations amenable to the present invention are described in United States provisional application serial nos. 61/018,616, filed January 2, 2008; 61/018,611, filed January 2, 2008; 61/039,748, filed March 26, 2008; 61/047,087, filed April 22, 2008 and 61/051,528, filed May 8, 2008.
• PCT application no PCT/US2007/080331, filed October 3, 2007 also describes formulations that are amenable to the present invention.
• Surfactants are described in United States provisional application serial nos. 61/018,616, filed January 2, 2008; 61/018,611, filed January 2, 2008; 61/039,748, filed March 26, 2008; 61/047,087, filed April 22, 2008 and 61/051,528, filed May 8, 2008.
• a conjugate formulation can include a surfactant.
• a conjugate described herein is formulated as an emulsion that includes a surfactant.
• HLB hydrophile/lipophile balance
• Nonionic surfactants find wide application in pharmaceutical products and are usable over a wide range of pH values. In general, their HLB values range from 2 to about 18 depending on their structure.
• Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters.
• Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and ethoxylated/propoxylated block polymers are also included in this class.
• the polyoxyethylene surfactants are the most popular members of the nonionic surfactant class. [00299] If the surfactant molecule carries a negative charge when it is dissolved or dispersed in water, the surfactant is classified as anionic.
• Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates.
• the most important members of the anionic surfactant class are the alkyl sulfates and the soaps. [00300] If the surfactant molecule carries a positive charge when it is dissolved or dispersed in water, the surfactant is classified as cationic.
• Cationic surfactants include quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are the most used members of this class. [00301] If the surfactant molecule has the ability to carry either a positive or negative charge, the surfactant is classified as amphoteric. Amphoteric surfactants include acrylic acid derivatives, substituted alkylamides, N-alkylbetaines and phosphatides. [00302] The use of surfactants in drug products, formulations and in emulsions has been reviewed (Rieger, in “Pharmaceutical Dosage Forms,” Marcel Dekker, Inc., New York, NY, 1988, p.285).
• micellar formulation comprising a conjugate described herein can be provided as a micellar formulation.
• “Micelles” are defined herein as a particular type of molecular assembly in which amphipathic molecules are arranged in a spherical structure such that all the hydrophobic portions of the molecules are directed inward, leaving the hydrophilic portions in contact with the surrounding aqueous phase. The converse arrangement exists if the environment is hydrophobic.
• a mixed micellar formulation suitable for delivery through transdermal membranes may be prepared by mixing an aqueous solution of the siRNA composition, an alkali metal C 8 to C22 alkyl sulphate, and a micelle forming compounds.
• Exemplary micelle forming compounds include lecithin, hyaluronic acid, pharmaceutically acceptable salts of hyaluronic acid, glycolic acid, lactic acid, chamomile extract, cucumber extract, oleic acid, linoleic acid, linolenic acid, monoolein, monooleates, monolaurates, borage oil, evening of primrose oil, menthol, trihydroxy oxo cholanyl glycine and pharmaceutically acceptable salts thereof, glycerin, polyglycerin, lysine, polylysine, triolein, polyoxyethylene ethers and analogues thereof, polidocanol alkyl ethers and analogues thereof, chenodeoxycholate, deoxycholate, and mixtures thereof.
• the micelle forming compounds may be added at the same time or after addition of the alkali metal alkyl sulphate. Mixed micelles will form with substantially any kind of mixing of the ingredients but vigorous mixing in order to provide smaller size micelles.
• a first micellar composition is prepared which contains conjugate described herein and at least the alkali metal alkyl sulphate. The first micellar composition is then mixed with at least three micelle forming compounds to form a mixed micellar composition.
• the micellar composition is prepared by mixing conjugate described herein, the alkali metal alkyl sulphate and at least one of the micelle forming compounds, followed by addition of the remaining micelle forming compounds, with vigorous mixing.
• Phenol and/or m-cresol may be added to the mixed micellar composition to stabilize the formulation and protect against bacterial growth.
• phenol and/or m-cresol may be added with the micelle forming ingredients.
• An isotonic agent such as glycerin may also be added after formation of the mixed micellar composition.
• the formulation can be put into an aerosol dispenser and the dispenser is charged with a propellant.
• the propellant which is under pressure, is in liquid form in the dispenser.
• the ratios of the ingredients are adjusted so that the aqueous and propellant phases become one, i.e., there is one phase.
• Propellants may include hydrogen-containing chlorofluorocarbons, hydrogen- containing fluorocarbons, dimethyl ether and diethyl ether. In certain embodiments, HFA 134a (1,1,1,2 tetrafluoroethane) may be used. [00309] The specific concentrations of the essential ingredients can be determined by relatively straightforward experimentation.
• kits for absorption through the oral cavities, it is often desirable to increase, e.g., at least double or triple, the dosage for through injection or administration through the gastrointestinal tract.
• conjugate described herein can be incorporated into a particle, e.g., a microparticle.
• Microparticles can be produced by spray-drying, but may also be produced by other methods including lyophilization, evaporation, fluid bed drying, vacuum drying, or a combination of these techniques.
• Kits [00311] The invention also provides kits comprising the dsRNA described herein.
• Embodiment 1 A double-stranded RNA (dsRNA) molecule capable of inhibiting the expression of a target gene, comprising a sense strand and an antisense strand, each strand having 14 to 40 nucleotides, wherein the antisense strand has sufficient complementarity to the target sequence to mediate RNA interference, wherein the dsRNA molecule comprises an hexopyranose nucleoside and wherein the dsRNA comprises a ligand.
• dsRNA double-stranded RNA
• Embodiment 2 A double-stranded RNA molecule capable of inhibiting the expression of a target gene, comprising a sense strand and an antisense strand, each strand having 14 to 40 nucleotides, wherein the antisense strand has sufficient complementarity to the target sequence to mediate RNA interference, wherein the antisense strand comprises at least one hexopyranose nucleoside in a seed region of the antisense strand or the sense strand comprises at least one altritol nucleotide in a central region of the sense strand.
• Embodiment 3 A double-stranded RNA molecule capable of inhibiting the expression of a target gene, comprising a sense strand and an antisense strand, each strand having 14 to 40 nucleotides, wherein the antisense strand has sufficient complementarity to the target sequence to mediate RNA interference, wherein the dsRNA comprises at least one hexopyranose nucleoside, at least one 2’-fluoro nucleotide and at least one 2’-OMe nucleotide.
• Embodiment 4 A double-stranded RNA molecule capable of inhibiting the expression of a target gene, comprising a sense strand and an antisense strand, each strand having 14 to 40 nucleotides, wherein the antisense strand has sufficient complementarity to the target sequence to mediate RNA interference, wherein the dsRNA comprises at least one hexopyranose nucleoside and the dsRNA comprises at least four phosphorothioate internucleotide linkages.
• Embodiment 5 The double-stranded RNA molecule of any one of embodiments 1-4, wherein the antisense strand comprises a hexopyranose nucleoside in the seed region of the antisense strand.
• Embodiment 6 The double-stranded RNA molecule of any one of embodiments 1-5, wherein the antisense strand comprises a hexopyranose nucleoside at least at one of positions 3-8, counting from 5’-end of the antisense strand.
• Embodiment 7 The double-stranded RNA molecule of any one of embodiments 1-6, wherein the antisense strand comprises a hexopyranose nucleoside at least at one of positions 6, 7, 9, 12, 16, 21 and 22, counting from the 5′-end of the antisense strand.
• Embodiment 8 The double-stranded RNA molecule of embodiment 7, wherein the antisense strand comprises a hexopyranose nucleoside at least at one of positions 6, 7 and 16.
• Embodiment 9 The double-stranded RNA molecule of embodiment 8, wherein the antisense strand comprises a hexopyranose nucleoside at least at one of positions 6 and 7.
• Embodiment 10 The double-stranded RNA molecule of embodiment 9, wherein the antisense strand comprises a hexopyranose nucleoside at position 7.
• Embodiment 11 The double-stranded RNA molecule of any one of embodiments 1- 10, wherein the sense strand comprises at least two or more consecutive independently selected hexopyranose nucleosides.
• Embodiment 12 The double-stranded RNA molecule of any one of embodiments 1- 11, wherein the sense strand comprises at least three or more consecutive independently selected hexopyranose nucleosides.
• Embodiment 13 The double-stranded RNA molecule of any one of embodiments 1- 12, wherein the sense strand comprises a hexopyranose nucleoside in the central region of the sense strand.
• Embodiment 14 The double-stranded RNA molecule of any one of embodiments 1- 13, wherein the sense strand comprises a hexopyranose nucleoside at least at one of positions 3 and 12.
• Embodiment 15 The double-stranded RNA molecule of any one of embodiments 1- 14, wherein the antisense strand comprises at least two or more consecutive independently selected hexopyranose nucleosides.
• Embodiment 16 The double-stranded RNA molecule of any one of embodiments 1- 15, wherein the antisense strand comprises at least three or more consecutive independently selected hexopyranose nucleosides.
• Embodiment 17 The double-stranded RNA molecule of any one of embodiments 1- 16, wherein the sense strand comprises a hexopyranose nucleoside at 5’-end of the sense strand.
• Embodiment 18 The double-stranded RNA molecule of any one of embodiments 1- 17, wherein the sense strand comprises a hexopyranose nucleoside at 5’-end of the sense strand.
• Embodiment 19 The double-stranded RNA molecule of any one of embodiments 1- 18, wherein sense strand comprises a 5’-vinylphosphonate (VP) group.
• Embodiment 20 The double-stranded RNA molecule of any one of embodiments 1- 19, wherein the hexopyranose nucleotide is selected from the group consisting of allopyranose nucleotide, altriol nucleotide, glucopyranose nucleotide, mannopyranose nucleotide, gulopyranose nucleotide, idopyranose nucleotide, galactopyranose nucleotide, talopyranose nucleotide, fucopyranose nucleotide, rhamopyranose nucleotide, quinovopyranose nucleotide, pneumopyranose nucleotide, and any combinations thereof.
• Embodiment 21 The double-stranded RNA molecule of any one of embodiments 1- 20, wherein the hexopyranose nucleotide is selected from the group consisting of altriol nucleotide, glucopyranose nucleotide, mannopyranose nucleotide, galactopyranose nucleotide, fucopyranose nucleotide, and any combinations thereof.
• Embodiment 22 The double-stranded RNA molecule of any one of embodiments 2- 21, wherein the dsRNA comprises a ligand.
• Embodiment 23 The double-stranded RNA molecule of embodiment 1 or 22, wherein the ligand is an ASGPR ligand.
• Embodiment 24 The double-stranded RNA molecule of embodiment 23, wherein the ASGPR ligand is: [00337]
• Embodiment 25 The double-stranded RNA molecule of any one of embodiments 1- 24, wherein the sense strand comprises 1, 2, 3 or 4 phosphorothioate internucleotide linkages.
• Embodiment 26 The double-stranded RNA molecule of any one of embodiments 1- 25, wherein the sense strand comprises phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between positons 2 and 3 (counting from the 5’ end).
• Embodiment 27 The double-stranded RNA molecule of any one of embodiments 1- 26, wherein the antisense strand comprises 1, 2, 3 or 4 phosphorothioate internucleotide linkages.
• Embodiment 28 The double-stranded RNA molecule of any one of embodiments 1- 27, wherein the antisense strand comprises phosphorothioate internucleotide linkages between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end).
• Embodiment 29 The double-stranded RNA molecule of any one of embodiments 1- 28, wherein the antisense strand comprises phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end).
• Embodiment 30 The double-stranded RNA molecule of any one of embodiments 1- 29, wherein the sense strand and the antisense strand are independently 19-25 nucleotides in length.
• Embodiment 31 The double-stranded RNA molecule of any one of embodiments 1- 30, wherein the sense strand is 21 nucleotides in length.
• Embodiment 32 The double-stranded RNA molecule of any one of embodiments 1- 31, wherein the antisense strand is 23 nucleotides in length.
• Embodiment 33 The double-stranded RNA molecule of any one of embodiments 1- 32, wherein the sense strand is 21 nucleotides in length and the antisense strand is 23 nucleotides in length.
• Embodiment 34 The double-stranded RNA molecule of any one of embodiments 1- 33, wherein the dsRNA comprises a single stranded overhang at 3’-end of the antisense strand.
• Embodiment 35 The double-stranded RNA molecule of any one of embodiments 1- 34, wherein the dsRNA comprises a blunt end at the 5’-end of the antisense strand.
• Embodiment 36 The double-stranded RNA molecule of any one of embodiments 1- 35, wherein the dsRNA comprises a 2’-fluoro or 2’-OMe nucleotide in positions complimentary to the hexopyranose nucleotide.
• Embodiment 37 The double-stranded RNA molecule of any one of embodiments 1- 36, wherein the dsRNA does not comprise nucleotides other than hexopyranose, 2’-fluoro and 2- OMe nucleotides.
• Embodiment 38 The double-stranded RNA molecule of any one of embodiments 1- 36, wherein the dsRNA comprises a nucleotide selected from the group consisting of acyclic nucleotides, locked nucleic acid (LNA), HNA, CeNA, 2’-methoxyethyl, 2’-O-allyl, 2’-C-allyl, 2'- O-N-methylacetamido (2'-O-NMA), a 2'-O-dimethylaminoethoxyethyl (2'-O-DMAEOE), 2'-O- aminopropyl (2'-O-AP), 2'-ara-F, and 2’-deoxy.
• LNA locked nucleic acid
• HNA locked nucleic acid
• CeNA CeNA
• 2’-methoxyethyl 2’-O-allyl
• 2’-C-allyl 2'- O-N-methylacetamido
• 2'-O-NMA 2'
• Embodiment 39 The double-stranded RNA molecule of any one of embodiments 1- 38, wherein the sense strand comprises a 5’-morpholino, a 5’-dimethylamino, a 5’-deoxy, an inverted abasic, or an inverted abasic locked nucleic acid modification at the 5’-end.
• Embodiment 40 The double-stranded RNA molecule of any one of embodiments 1- 39, wherein the dsRNA has a melting temperature in the range from about 40°C to about 80°C.
• Embodiment 41 A pharmaceutical composition comprising the dsRNA agent according to any one of embodiments 1-40 alone or in combination with a pharmaceutically acceptable carrier or excipient.
• Embodiment 42 A gene silencing kit containing the dsRNA molecule of any one of any one embodiments 1-40.
• Embodiment 43 A method for silencing a target gene in a cell, the method comprising a step of introducing the dsRNA molecule of any one of embodiments 1-40 into the cell.
• Embodiment 44 The method of embodiment 43, wherein the dsRNA agent is administered through subcutaneous or intravenous administration.
• Embodiment 45 A method for silencing a target gene in a cell, the method comprising a step of expressing the dsRNA molecule of any one of embodiments 1-40 into the cell.
• the near or approximating unrecited number may be a number which, in the context in which it is presented, provides the substantial equivalent of the specifically recited number.
• the term “comprising” or “comprises” is used in reference to compositions, methods, and respective component(s) thereof, that are essential to the invention, yet open to the inclusion of unspecified elements, whether essential or not.
• the singular terms “a,” “an,” and “the” include plural referents unless context clearly indicates otherwise.
• the word “or” is intended to include “and” unless the context clearly indicates otherwise.
• dsRNA RNA
• siRNA agent agents that can mediate silencing of a target RNA, e.g., mRNA, e.g., a transcript of a gene that encodes a protein.
• mRNA e.g., a transcript of a gene that encodes a protein.
• mRNA e.g., a transcript of a gene that encodes a protein.
• mRNA e.g., a transcript of a gene that encodes a protein.
• mRNA e.g., a transcript of a gene that encodes a protein.
• mRNA e.g., a transcript of a gene that encodes a protein.
• mRNA e.g., a transcript of a gene that encodes a protein.
• mRNA e.g., a transcript of a gene that encodes a protein.
• mRNA e.g., a transcript of a gene that encodes
• RNA to be silenced is an endogenous gene, exogenous gene or a pathogen gene.
• RNAs other than mRNA e.g., tRNAs, and viral RNAs, can also be targeted.
• the phrase “mediates RNAi” refers to the ability to silence, in a sequence specific manner, a target gene, e.g., mRNA. While not wishing to be bound by theory, it is believed that silencing uses the RNAi machinery or process and a guide RNA, e.g., antisense strand of a dsRNA, where the antisense strand is 21 to 23 nucleotides in length.
• “specifically hybridizable” and “complementary” are terms which are used to indicate a sufficient degree of complementarity such that stable and specific binding occurs between a compound of the invention and a target RNA molecule. Specific binding requires a sufficient degree of complementarity to avoid non-specific binding of the oligomeric compound to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of assays or therapeutic treatment, or in the case of in vitro assays, under conditions in which the assays are performed.
• the non-target sequences typically differ by at least 5 nucleotides.
• a dsRNA molecule is “sufficiently complementary” to a target RNA, e.g., a target mRNA, such that the dsRNA molecule silences production of protein encoded by the target mRNA.
• the dsRNA molecule is “exactly complementary” to a target RNA, e.g., the target RNA and the dsRNA duplex agent anneal, for example to form a hybrid made exclusively of Watson-Crick base pairs in the region of exact complementarity.
• a “sufficiently complementary” target RNA can include an internal region (e.g., of at least 10 nucleotides) that is exactly complementary to a target RNA.
• the dsRNA molecule specifically discriminates a single-nucleotide difference.
• the dsRNA molecule only mediates RNAi if exact complementary is found in the region (e.g., within 7 nucleotides of) the single-nucleotide difference.
• oligonucleotide refers to a nucleic acid molecule (RNA or DNA) for example of length less than 100, 200, 300, or 400 nucleotides.
• BNA refers to bridged nucleic acid, and is often referred as constrained or inaccessible RNA.
• BNA can contain a 5-, 6- membered, or even a 7-membered bridged structure with a “fixed” C3’-endo sugar puckering.
• the bridge is typically incorporated at the 2’-, 4’- position of the ribose to afford a 2’, 4’-BNA nucleotide (e.g., LNA, or ENA).
• BNA nucleotides include the following nucleosides: [00371]
• LNA refers to locked nucleic acid, and is often referred as constrained or inaccessible RNA.
• LNA is a modified RNA nucleotide.
• the ribose moiety of an LNA nucleotide is modified with an extra bridge (e.g., a methylene bridge or an ethylene bridge) connecting the 2′ hydroxyl to the 4′ carbon of the same ribose sugar.
• the bridge can “lock” the ribose in the 3′-endo North) conformation: .
• ENA refers to ethylene-bridged nucleic acid, and is often referred as constrained or inaccessible RNA.
• the “cleavage site” herein means the backbone linkage in the target gene or the sense strand that is cleaved by the RISC mechanism by utilizing the iRNA agent.
• the target cleavage site region comprises at least one or at least two nucleotides on both side of the cleavage site.
• the cleavage site is the backbone linkage in the sense strand that would get cleaved if the sense strand itself was the target to be cleaved by the RNAi mechanism.
• the cleavage site can be determined using methods known in the art, for example the 5’-RACE assay as detailed in Soutschek et al., Nature (2004) 432, 173-178, which is incorporated by reference in its entirety.
• the cleavage site region for a conical double stranded RNAi agent comprising two 21-nucleotides long strands (wherein the strands form a double stranded region of 19 consecutive base pairs having 2-nucleotide single stranded overhangs at the 3’-ends), the cleavage site region corresponds to positions 9-12 from the 5’-end of the sense strand.
• the terms “decrease”, “reduced”, “reduction”, or “inhibit” are all used herein to mean a decrease by a statistically significant amount.
• “reduce,” “reduction” or “decrease” or “inhibit” typically means a decrease by at least 10% as compared to a reference level (e.g. the absence of a given treatment) and can include, for example, a decrease by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, at least about 99% , or more.
• a “central region” of a strand refers to positions 8-16, e.g., positions 8-15, positions 8-14, positions 8-13, positions 8-12, positions 9-16, positions 9-15, positions 9- 14, positions 9-13, positions 9-12, positions 10-16, positions 10-15, positions 10-14, positions 10- 13 or positions 10-12, counting from the 5’-end of the strand.
• the central region of a strand means positions 8, 9, 10, 11, 12, 13, 14, 15 and 16 of the strand.
• a preferred central region for the sense strand is positions 8, 9, 10, 11, 12, 13, and 14, counting from the 5’-end of the sense strand.
• a more preferred central region for the sense strand is positions 10, 11, 12 and 13, counting from the 5’-end of the sense strand.
• a preferred central region for the antisense strand is positions 9, 10, 11, 12, 13, 14, 15, and 16, counting from 5’-end of the antisense strand.
• a more preferred central region for the antisense strand is positions 10, 11, 12, 13, 14 and 15 and, counting from 5’-end of the antisense strand.
• binding refers to the binding of a binding moiety to a binding target, such as the binding of an immunoglobulin to a target antigen, e.g., an epitope on a particular polypeptide, peptide, or other target (e.g. a glycoprotein target), and means binding that is measurably different from a non-specific interaction (e.g., a non-specific interaction can be binding to bovine serum albumin or casein).
• target antigen e.g., an epitope on a particular polypeptide, peptide, or other target (e.g. a glycoprotein target)
• target antigen e.g., an epitope on a particular polypeptide, peptide, or other target (e.g. a glycoprotein target)
• target antigen e.g., an epitope on a particular polypeptide, peptide, or other target (e.g. a glycoprotein target)
• target antigen e.g., an epitope on a
• specific binding can be determined by competition with a control molecule that is similar to the target, for example, an excess of non-labeled target. In this case, specific binding is indicated if the binding of the labeled target to a probe is competitively inhibited by excess unlabeled target.
• telomere binding or “specifically binds to” or is “specific for” as used herein can be exhibited, for example, by a molecule having a Kd for the target of at least about 200 nM, alternatively at least about 150 nM, alternatively at least about 100 nM, alternatively at least about 60 nM, alternatively at least about 50 nM, alternatively at least about 40 nM, alternatively at least about 30 nM, alternatively at least about 20 nM, alternatively at least about 10 nM, alternatively at least about 8 nM, alternatively at least about 6 nM, alternatively at least about 4 nM, alternatively at least about 2 nM, alternatively at least about 1 nM, or greater.
• binding affinity refers to the strength of the sum total of noncovalent interactions between a single binding site of a molecule (e.g., an immunoglobulin) and its binding partner (e.g., an antigen).
• binding affinity refers to intrinsic binding affinity which reflects a 1:1 interaction between members of a binding pair (e.g., immunoglobulin and antigen).
• the affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (K d ).
• the K d can be about 200 nM, 150 nM, 100 nM, 60 nM, 50 nM, 40 nM, 30 nM, 20 nM, 10 nM, 8 nM, 6 nM, 4 nM, 2 nM, 1 nM, or stronger.
• Affinity can be measured by common methods known in the art, including those described herein. Low-affinity antibodies generally bind antigen slowly and tend to dissociate readily, whereas high-affinity antibodies generally bind antigen faster and tend to remain bound longer. A variety of methods of measuring binding affinity are known in the art.
• the “Kd” or “Kd value” refers to a dissociation constant measured by a technique appropriate for the immunoglobulin and target pair, for example using surface plasmon resonance assays, for example, using a Biacore X100 or a Biacore T200 (GE Healthcare, Piscataway, N.J.) at 25°C with immobilized antigen CM5 chips.
• “Treating” or “treatment” refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) a targeted pathologic condition or disorder.
• a subject or mammal is successfully “treated” for cancer, if, after receiving a therapeutic amount of a conjugate described herein, the subject shows observable and/or measurable reduction in or absence of one or more of the following: reduction in the number of cancer cells or absence of the cancer cells; reduction in the tumor size; inhibition (i.e., slowing to some extent and preferably stopping) of cancer cell infiltration into peripheral organs, including the spread of cancer into soft tissue and bone; inhibition (i.e., slowing to some extent and preferably stopping) of tumor metastasis; inhibition, to some extent, of tumor growth; and/or relief to some extent of one or more of the symptoms associated with the specific cancer; reduced morbidity and/or mortality, and improvement in quality of life.
• “treating” or “treatment” refers to therapeutic treatment.
• a “subject” means a human or animal. Usually the animal is a vertebrate such as a primate, rodent, domestic animal or game animal. Primates include chimpanzees, cynomologous monkeys, spider monkeys, and macaques, e.g., Rhesus. Rodents include mice, rats, woodchucks, ferrets, rabbits and hamsters.
• domestic and game animals include cows, horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, canine species, e.g., dog, fox, wolf, avian species, e.g., chicken, emu, ostrich, and fish, e.g., trout, catfish and salmon.
• the subject is a mammal, e.g., a primate, e.g., a human.
• the terms, “individual,” “patient” and “subject” are used interchangeably herein. [00381]
• the subject is a mammal.
• the mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but is not limited to these examples. Mammals other than humans can be advantageously used as subjects that represent animal models of cancer.
• a subject can be male or female.
• a subject can be one who has been previously diagnosed with or identified as suffering from or having a condition in need of treatment (e.g. cancer) or one or more complications related to such a condition, and optionally, have already undergone treatment for cancer or the one or more complications related to cancer.
• a subject can also be one who has not been previously diagnosed as having cancer or one or more complications related to cancer.
• a subject can be one who exhibits one or more risk factors for cancer or one or more complications related to cancer or a subject who does not exhibit risk factors.
• a “subject in need” of treatment for a particular condition can be a subject having that condition, diagnosed as having that condition, or at risk of developing that condition.
• each of the individual aspects described and illustrated herein has discrete components and features which can be readily separated from or combined with the features of any of the other several aspects without departing from the scope or spirit of the present invention. Any recited method can be carried out in the order of events recited or in any other order which is logically possible.
• RNA nucleotides contain a ribose sugar that adopts a C3′-endo conformation and form an A-type duplex.
• ANA is considered an RNA analog and may find useful applications in cases where the RNA geometry needs to be preserved.
• siRNA small interfering RNA
• the siRNAs were designed to silence the expression of the transthyretin (Ttr) gene and were conjugated to N-acetylgalactosamine (GalNAc) for targeted delivery to hepatocytes.
• Ttr transthyretin
• GalNAc N-acetylgalactosamine
• a single nucleotide positional walk of ANA modification was performed along the sense and antisense strands of the parent duplex, and the resulting modified duplexes were screened for their potential to target Ttr mRNA in vitro. This analysis unexpectedly and surprisingly revealed that ANA is well accommodated in the seed region, especially at positions 6 and 7 of the antisense strand.
• the corresponding duplexes also showed good on- and off-target activity in a luciferase reporter assay.
• siRNAs small interfering RNAs
• siRNAs take advantage of a natural gene regulatory mechanism called RNA interference (RNAi) for silencing the expression of a given gene of interest.
• RNAi RNA interference
• 3,4 siRNAs composed of natural RNA nucleotides are susceptible to fast enzymatic degradation and do not readily reach their target organ when administered systemically. Thus, it is necessary to use chemically modified siRNAs for therapeutic applications.
• 5 . 2′-Deoxy-2′-fluoro-(2′-F RNA, Figure 1b) 6,7 and 2′-O-methyl- (2′-OMe RNA, Figure 1b) RNA modifications are compatible with natural RNA induced silencing complex (RISC) and are widely used to stabilize siRNAs.
• RISC RNA induced silencing complex
• siRNAs composed of 2′-F and 2′-OMe RNA with strategic placement of phosphorothioate linkages and conjugated to the N- acetylgalactosamine (GalNAc) ligand, are being studied in the clinic. 8
• GalNAc N- acetylgalactosamine
• ANA has a preorganized structure mimicking an N-type furanose sugar, while the presence of the hydroxyl group at the 3'- position contributes to duplex stabilization via hydration.
• the RNA-like (A-type geometry of ANA renders it a suitable candidate for incorporation into siRNAs, where maintaining RNA-like structure is advantageous.
• ANA-modified siRNAs have evaluated and showed better RNAi activity compared to unmodified siRNAs. 16-19 However, it remains to be seen how ANA would behave when used in synergy with other modified nucleotides/ligands.
• oligonucleotides were prepared on an ABI 394 or MerMade 192 synthesizer on a 1 ⁇ mole scale using universal or custom supports.
• ABI all phosphoramidites were dissolved at a concentration of 0.15M in 100% acetonitrile or 9:1 acetonitrile:DMF (2′- OMe-C, 2′-OMe-U).
• DMF acetonitrile
• Mermade 192 a concentration of 0.10M was used.
• ETT was used as an activator and 3% trichloroacetic acid in dichloromethane for detritylation.
• MerMade 192 Workup: After the trityl-off synthesis using the MerMade 192, columns were incubated with 150 ⁇ L of 40% aqueous methylamine for 30 min at room temperature and the solution was drained via vacuum into a 96-well plate. After repeating the incubation and draining with a fresh portion of aqueous methylamine, the plate containing the crude oligonucleotides was sealed and shaken at room temperature for an additional 60 min to completely remove all protecting groups.
• Precipitation of the crude oligonucleotides was accomplished via the addition of 1.2 mL of 9:1 acetonitrile:EtOH to each well, followed by incubation at ⁇ 20 °C overnight. The plate was then centrifuged at 3000 rpm for 45 min at 4 °C, the supernatant removed from each well, and the pellets resuspended in 950 ⁇ L of 20 mM aqueous NaOAc. Each crude solution was finally desalted over a GE Hi-Trap desalting column (Sephadex G25 Superfine) using water to elute the final oligonucleotide products.
• GE Hi-Trap desalting column Sephadex G25 Superfine
• siRNA knockdown 5 ⁇ L of siRNA was placed in a 384-well collagen- coated plate, followed by addition of 4.90 ⁇ L of Opti-MEM and 0.1 ⁇ L of Lipofectamine RNAiMax (Invitrogen) to each well. The final siRNA concentrations were 0.1 or 10 nM. Plates were incubated at room temperature for 15 min. Primary mouse hepatocytes cells were suspended in media Invitrogro CP rodent medium (#Z990028 BioIVT) and 40 ⁇ L of this suspension (containing approximately 5000 cells) was added to each well. Each siRNA was assessed in quadruplicate.
• COS-7 cells were cultured at 37°C, 5% CO 2 in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Cells were co-transfected in 96-well plates (15,000 cells / well) with 10 ng luciferase reporter plasmid and 0.64 pM to 50 nM siRNA in 5-fold dilutions using 2 ⁇ g/mL Lipofectamine 2000 (Thermo Fisher Scientific) according to the manufacturer’s instructions. Cells were harvested at 48 h after transfection for the dual luciferase assay (Promega) according to the manufacturer’s instructions.
• DMEM Modified Eagle Medium
• FBS fetal bovine serum
• the on-target reporter plasmid contained a single perfectly-complementary site to the antisense strand in the 3′-untranslated (3’ UTR) of Renilla luciferase.
• the off-target reporter plasmid contained four tandem seed-complementary sites separated by a 19-nucleotide spacer (TAATATTACATAAATAAAA) in the 3′-UTR of Renilla luciferase. Both plasmids co- expressed Firefly luciferase as a transfection control.
• RNA from liver was done with the PerkinElmer Chemagic system (Waltham, MA), according to the supplier’s guidelines, followed by cDNA preparation and multiplexed RT-qPCR analysis to assess the Ttr transcript levels (Taqman probe Mm00443267_m1; mouse Gapdh 4351309 from ABI). Quantification of the Ttr protein levels in serum was done spectrophotometrically with a mouse pre-albumin/Ttr ELISA kit (41-PALMS- E01), in accordance to the manufacturer’s protocol (ALPCO, Salem, NH).
• Nuclease stability assay Modified oligonucleotides were prepared in a final concentration of 0.1 mg/mL in either 50 mM Tris (pH 7.2) with 10 mM MgCl 2 or 50 mM sodium acetate (pH 6.5) with 10 mM MgCl 2 for assessing the stability towards 3′- or 5′-specific exonucleases, respectively.
• exonuclease 150 mU/mL SVPDE or 500 mU/mL phosphodiesterase II
• IEX HPLC dionex DNAPac PA200,4x250 mm
• mobile phase 1 M NaBr, 20 mM sodium phosphate, pH 11, 15% MeCN
• stationary phase 20 mM sodium phosphate, 15% MeCN, pH 11
• Samples were injected at the given timepoints and monitored for up to 24 h. The quantity of full-length ON was determined as the area under the curve at A260.
• the activity of enzyme was verified for each experiment by including a oligo-2′-deoxythymidylate with a terminal phosphorothioate linkage (5′-T19•T or 5′- T•T 19 for 3′- or 5′-exonuclease activity, respectively). Each aliquot of enzyme was thawed just prior to the experiment. The half-life was determined by fitting to first order kinetics. [00396] X-ray crystallography: Two ANA-modified oligonucleotides were subjected to crystallization trials.
• the glycosidic torsion angle of the ANA purine residue adjusted slightly to restore stacking on the adjacent residue C8 as seen in the crystal structure of the Ago2 complex with native RNA.
• the crystal structure of the complex between the Xrn1 5′-exoribonuclease and 5′P-dTdTdT-3′ with PDB ID 2Y35 21 was retrieved from the Protein Data Bank.
• the dimer 5′P-aC9aC10-3′P was excised from strand A of the crystal structure of the ANA:RNA hybrid duplex and the bases converted to U using the program UCSF Chimera.
• the 5′-Monophosphate plays an important role in RISC loading by interacting with the Ago2 MID domain and therefore, the lack of a 5′-monophosphate is known to impair RNAi activity. 25-28 Presence of ANA modification at position AS2 was detrimental to RNAi activity. [00400] Unexpectedly, ANA modification in the seed (nucleotides 3-8) was better accommodated, and two modified duplexes with an ANA nucleotide at position AS6 or AS7 showed RNAi activity comparable to the parent duplex at 10 nM ( Figure 2). In addition, ANA at position AS16 also maintained the RNAi activity. However, none of the modified duplexes showed higher activity compared to the parent siRNA.
• On-target and off-target activity in the luciferase reporter assay Seed-mediated off-target activity has been reported to contribute to rat hepatoxicity of siRNAs. 10 To reduce such off-target effects, thermally destabilizing modifications such as GNA have been incorporated into the seed region of siRNA duplexes. 10 GNA can efficiently mitigate seed-mediated off-target effects while maintaining on-target potency. ANA is well tolerated in the seed region at positions 6 or 7 in the antisense strand.
• the same duplex showed RNAi activity comparable to the parent duplex during in vitro screening, which may suggest intrinsic intracellular differences between the in vitro and in vivo models.
• the duplex with ANA modification at S12 was slightly less active than the parent one, but maintained its activity until day 14.
• the duplex modified with ANA at the 5′-end of the antisense stand (AS1) was not effective, most likely because ANA cannot be phosphorylated by endogenous intracellular kinases.
• the animals were sacrificed at day 14 and RNA from liver was extracted, followed by cDNA preparation and multiplexed RT-qPCR analysis to assess the Ttr transcript levels (Figure 6B). The results were well aligned with those obtained from serum samples at day 14.
• An ANA residue can thus perfectly mimic a ribonucleotide at position AS7 where a kink in the siRNA guide strand results in locally contracted phosphate-phosphate distances.
• ONs with ANA at the 5’-end were more resistant to nuclease degradation than natural RNA counterparts. However, this gain in stability was not found in assays testing resistance against degradation by SVPD, a 3′-exonuclease.
• a model of an ON with two ANA-uridines at the 5′-end bound to a 5′- exoribonuclease indicates that steric bulk and altered phosphate-phosphate spacing relative to DNA and RNA are the main reasons for the increased protection against nuclease degradation.

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