US20040014956A1 - Double-stranded oligonucleotides - Google Patents

Double-stranded oligonucleotides Download PDF

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US20040014956A1
US20040014956A1 US10/357,529 US35752903A US2004014956A1 US 20040014956 A1 US20040014956 A1 US 20040014956A1 US 35752903 A US35752903 A US 35752903A US 2004014956 A1 US2004014956 A1 US 2004014956A1
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Prior art keywords
nucleomonomers
oligonucleotide
sequence
composition
double
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Tod Woolf
Kristin Wiederholt
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Life Technologies Corp
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Sequitur Inc
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First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=41112152&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=US20040014956(A1) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Priority to US10/357,529 priority Critical patent/US20040014956A1/en
Assigned to SEQUITUR, INC. reassignment SEQUITUR, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: WIEDERHOLT, KRISTIN A., WOOLF, TOD M.
Application filed by Sequitur Inc filed Critical Sequitur Inc
Publication of US20040014956A1 publication Critical patent/US20040014956A1/en
Priority to US11/049,636 priority patent/US20060009409A1/en
Priority to US11/776,313 priority patent/US20090023216A1/en
Priority to US12/062,380 priority patent/US20100136695A1/en
Priority to US13/211,250 priority patent/US20120107897A1/en
Priority to US13/277,957 priority patent/US8815821B2/en
Assigned to SEQUITUR, INC. reassignment SEQUITUR, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: TAYLOR, MARGARET F., WOOLF, TOD M.
Assigned to SEQUITUR, INC. reassignment SEQUITUR, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: WOOLF, TOD M.
Priority to US14/446,022 priority patent/US9592250B2/en
Priority to US15/418,653 priority patent/US10106793B2/en
Priority to US16/131,512 priority patent/US20190002880A1/en
Abandoned legal-status Critical Current

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Definitions

  • oligonucleotide sequences are promising therapeutic agents and useful research tools in elucidating gene function.
  • oligonucleotide molecules of the prior art are often subject to nuclease degradation when applied to biological systems. Therefore, it is often difficult to achieve efficient inhibition of gene expression (including protein synthesis) using such compositions.
  • the instant invention is based, at least in part, on the discovery that double-stranded oligonucleotides comprising an antisense oligonucleotide and a protector oligonucleotide, are capable of inhibiting gene function.
  • the invention improves the prior art antisense sequences, inter alia, by providing oligonucleotides which are resistant to degradation by cellular nucleases.
  • the invention provides optimized oligonucleotide compositions and methods for making and using both in in vitro, and in vivo systems, e.g., therapeutically.
  • the invention pertains to a double-stranded oligonucleotide composition having the structure:
  • N is a nucleomonomer in complementary oligonucleotide strands of equal length and where the sequence of Ns corresponds to a target gene sequence and
  • X and Y are each independently selected from a group consisting of nothing; from about 1 to about 20 nucleotides of 5′ overhang; from about 1 to about 20 nucleotides of 3′ overhang; and a loop structure consisting from about 4 to about 20 nucleomonomers, where the nucleomonomers are selected from the group consisting of G and A.
  • An “overhang” is a relatively short single-stranded nucleotide sequence on the 5′- or 3′-hydroxyl end of a double-stranded oligonucleotide molecule (also referred to as an “extension,” “protruding end,” or “sticky end”).
  • the number of Ns in each strand of the duplex is between about 12 and about 50 (i.e., in the figure above, oligo(N) has between about 12 and about 50 nucleomonomers). In other embodiments, the number of Ns in each strand of the duplex is between about 12 and about 40; or between about 15 and about 35; or more particularly between about 20 and about 30; or even between about 21 and about 25.
  • X is a sequence of about 4 to about 20 nucleomonomers which form a loop, wherein the nucleomonomers are selected from the group consisting of G and A.
  • two of the Ns are unlinked, i.e., there is no phosphodiester bond between the two nucleomonomers.
  • the unlinked Ns are not in the antisense sequence.
  • the nucleotide sequence of the loop is GAAA.
  • the invention pertains to a double-stranded oligonucleotide composition having the structure:
  • N is a nucleomonomer in complementary oligonucleotide strands of equal length where the sequence of Ns corresponds to a target gene sequence; and (2) Z is a nucleomonomer in complementary oligonucleotide strands of between about 2 and about 8 nucleomonomers in length and where the sequence of Zs optionally corresponds to the target sequence; and (3) where M is a nucleomonomer in complementary oligonucleotide strands of between about 2 and about 8 nucleomonomers in length and where the sequence of Ms optionally corresponds to the target sequence.
  • the sequences of N nucleomonomers should be of the same length, the sequences of Z and M nucleomonomers may optionally be of the same length.
  • Z and M are nucleomonomers selected from the group consisting of C and G.
  • the sequence of Zs or Ms is CC, GG, CG, GC, CCC, GGG, CGG, GCC, GCG, CGC, CGGG, GCCC, CCCC, GGGG, GCGC, CGCG, GGGC, CCCG, CGGG, GCCC, GGCC, or CCGG.
  • the invention pertains to a double-stranded oligonucleotide composition having the structure:
  • N is a nucleomonomer in complementary oligonucleotide strands of equal length and where the sequence of Ns corresponds to a target gene sequence and (2) X is selected from the group consisting of nothing; 1-20 nucleotides of 5′ overhang; 1-20 nucleotides of 3′ overhang.
  • X is a loop structure consisting of from about 4 to about 20 nucleomonomers, where the nucleomonomers are selected from the group consisting of G and A.
  • M is a nucleomonomer in complementary oligonucleotide strands of between about 2 and about 8 nucleomonomers in length which optionally correspond to the target sequence.
  • M is a nucleomonomer selected from the group consisting of contain C and G.
  • the sequence of M is CC, GG, CG, GC, CCC, GGG, CGG, GCC, GCG, CGC, CGGG, GCCC, CCCC, GGGG, GCGC, CGCG, GGGC, CCCG, CGGG, GCCC, GGCC, or CCGG.
  • the invention pertains to a double-stranded oligonucleotide composition having the structure:
  • N is a nucleomonomer in complementary oligonucleotide strands of equal length and which correspond to a target gene sequence and (2) Y is selected from the group consisting of nothing; 1-20 nucleotides of 5′ overhang; 1-20 nucleotides of 3′ overhang; a loop consisting of a sequence of from about 4 to about 20 nucleomonomers, where the nucleomonomers are all either Gs or A's and (3) where Z is a nucleomonomer in complementary oligonucleotide strands of between about 2 and about 8 nucleomonomers in length and which comprise a sequence which can optionally correspond to the target sequence.
  • Zs are nucleomonomers selected from the group consisting of C and G.
  • the sequence of Zs is CC, GG, CG, GC, CCC, GGG, CGG, GCC, GCG, CGC, CGGG, GCCC, CCCC, GGGG, GCGC, CGCG, GGGC, CCCG, CGGG, GCCC, GGCC, or CCGG.
  • the invention pertains to a method of regulating gene expression in a cell, comprising forming a double-stranded oligonucleotide composition as described herein and contacting a cell with the double-stranded duplex, to thereby regulate gene expression in a cell.
  • the invention pertains to a method of increasing the nuclease resistance of an antisense sequence, comprising forming a double-stranded oligonucleotide composition as described herein, such that a double-stranded duplex is formed, wherein the nuclease resistance of the antisense sequence is increased compared to a double-stranded, unmodified RNA molecule.
  • FIG. 1 shows that the length of double-stranded oligonucleotides and the presence or absence of overhangs has no effect on function.
  • FIG. 1B shows the effect of structural changes on the efficacy of siRNAs targeting ⁇ -3-Integrin.
  • FIG. 2 shows that there is no correlation was observed between the length of the double-stranded oligonucleotide and the level of PKR induction for the given sequences.
  • FIG. 2B shows effect of ⁇ -3-integrin targeted 21-mer and 27-mers on PKR expression in HMVEC Cells.
  • FIG. 3 shows the effect of 5′ or 3′ modification on activity of double-stranded RNA duplexes.
  • FIG. 4 shows the effect of the size of the modifying group on activity of the double-stranded RNA duplex.
  • FIG. 5 shows the results of 2′-O-Me modifications on the activity of double-stranded RNA duplexes.
  • FIG. 6 shows the inhibition of p53 by 32- and 37-mer blunt-end siRNAs.
  • the instant invention advances the prior art by providing double-stranded oligonucleotide compositions for use, both in vitro and in vivo, e.g., therapeutically, and by providing methods of making and using the double-stranded antisense oligomer compositions.
  • Double-stranded oligonucleotides of the invention are capable of inhibiting the synthesis of a target protein, which is encoded by a target gene.
  • the target gene can be endogenous or exogenous (e.g., introduced into a cell by a virus or using recombinant DNA technology) to a cell.
  • target gene includes polynucleotides comprising a region that encodes a polypeptide or polynucleotide region that regulates replication, transcription, translation, or other process important in expression of the target protein; or a polynucleotide comprising a region that encodes the target polypeptide and a region that regulates expression of the target polypeptide; or non-coding regions such as the 5′ or 3′ UTR or introns. Accordingly, the term “target gene” as used herein may refer to, for example, an mRNA molecule produced by transcription a gene of interest.
  • oligomer corresponds to a target gene sequence
  • two sequences are complementary or homologous or bear such other biologically rational relationship to each other (e.g., based on the sequence of nucleomonomers and their base-pairing properties).
  • the “target gene” to which an RNA molecule of the invention is directed may be associated with a pathological condition.
  • the gene may be a pathogen-associated gene, e.g., a viral gene, a tumor-associated gene, or an autoimmune disease-associated gene.
  • the target gene may also be a heterologous gene expressed in a recombinant cell or a genetically altered organism. By determining or modulating (e.g., inhibiting) the function of such a gene, valuable information and therapeutic benefits in medicine, veterinary medicine, and biology may be obtained.
  • oligonucleotide includes two or more nucleomonomers covalently coupled to each other by linkages (e.g., phosphodiesters) or substitute linkages.
  • linkages e.g., phosphodiesters
  • substitute linkages e.g., phosphodiesters
  • the oligonucleotide can include a nick in either the sense of the antisense sequence.
  • antisense refers to a nucleotide sequence that is inverted relative to its normal orientation for transcription and so expresses an RNA transcript that is complementary to a target gene mRNA molecule expressed within the host cell (e.g., it can hybridize to the target gene mRNA molecule through Watson-Crick base pairing).
  • An antisense strand may be constructed in a number of different ways, provided that it is capable of interfering with the expression of a target gene.
  • the antisense strand can be constructed by inverting the coding region (or a portion thereof) of the target gene relative to its normal orientation for transcription to allow the transcription of its complement, (e.g., RNAs encoded by the antisense and sense gene may be complementary).
  • the antisense oligonucleotide strand need not have the same intron or exon pattern as the target gene, and noncoding segments of the target gene may be equally effective in achieving antisense suppression of target gene expression as coding segments.
  • one aspect of the invention is a method of inhibiting the activity of a target gene by introducing an RNAi agent into a cell, such that the dsRNA component of the RNAi agent is targeted to the gene.
  • an RNA oligonucleotide molecule may contain at least one nucleomonomer that is a modified nucleotide analogue.
  • the nucleotide analogues may be located at positions where the target-specific activity, e.g., the RNAi mediating activity is not substantially effected, e.g., in a region at the 5′-end or the 3′-end of the double-stranded molecule, where the overhangs may be stabilized by incorporating modified nucleotide analogues.
  • double-stranded RNA molecules known in the art can be used in the methods of the present invention.
  • Double-stranded RNA molecules known in the art may also be modified according to the teachings herein in conjunction with such methods, e.g., by using modified nucleomonomers.
  • modified nucleomonomers see U.S. Pat. No. 6,506,559; U.S. Pat. No. 2002/0,173,478 A1; U.S. Pat. No. 2002/0,086,356 A1; Shuey, et al., “RNAi: gene-silencing in therapeutic intervention.” Drug Discov. Today 2002 Oct 15;7(20):1040-6; Aoki, et al., “Clin. Exp.
  • RNA interference is a functional pathway with therapeutic potential in human myeloid leukemia cell lines. Cancer Gene Ther. 2003 Feb;10(2):125-33.
  • RNA molecules include those disclosed in the following references: Kawasaki, et al., “Short hairpin type of dsRNAs that are controlled by tRNA(Val) promoter significantly induce RNAi-mediated gene silencing in the cytoplasm of human cells.” Nucleic Acids Res. 2003 Jan 15;31(2):700-7; Cottrell, et al., “Silence of the strands: RNA interference in eukaryotic pathogens.” Trends Microbiol. 2003 Jan; 11(1):37-43; Links, “Mammalian RNAi for the masses.” Trends Genet.
  • a nick is two non-linked nucleomonomers in an oligonucleotide.
  • a nick can be included at any point along the sense or antisense nucleotide sequence.
  • a nick is in the sense sequence.
  • the nick is at least about four nucleomonomers in from an end of the duplexed region of the oligonucleotide (e.g., is at least about four nucleomonomers away from the 5′ or 3′ end of the oligonucleotide or away from a loop structure.
  • the nick is present in the middle of the sense strand of the duplex molecule (e.g., if the sense sequence of the duplex is 30 nucleomonomers in length, nucleomonomers 14 and 15 or 15 and 16 are unlinked).
  • a nick may optionally be ligated to form a circular nucleic acid molecule.
  • the indicated U nucleomonomer is not bonded to the neighboring nucleomonomer, e.g., by a phosphodiester bond.
  • the 5′ OH of the nick may optionally be phosphorylated to allow enzymatic ligation of the oligonucleotide into a circle.
  • nucleotide includes any monomeric unit of DNA or RNA containing a sugar moiety (pentose), a phosphate, and a nitrogenous heterocyclic base.
  • the base is usually linked to the sugar moiety via the glycosidic carbon (at the 1′ carbon of pentose) and that combination of base and sugar is called a “nucleoside.”
  • the base characterizes the nucleotide with the four customary bases of DNA being adenine (A), guanine (G), cytosine (C) and thymine (T).
  • Inosine (I) is an example of a synthetic base that can be used to substitute for any of the four, naturally-occurring bases (A, C, G, or T).
  • the four RNA bases are A, G, C, and uracil (U).
  • an oligonucleotide may be a nucleotide sequence comprising a linear array of nucleotides connected by phosphodiester bonds between the 3′ and 5′ carbons of adjacent pentoses. Other modified nucleosides/nucleotides are described herein and may also be used in the oligonucleotides of the invention.
  • Oligonucleotides may comprise, for example, oligonucleotides, oligonucleosides, polydeoxyribonucleotides (containing 2′-deoxy-D-ribose) or modified forms thereof, e.g., DNA, polyribonucleotides (containing D-ribose or modified forms thereof), RNA, or any other type of polynucleotide which is an N-glycoside or C-glycoside of a purine or pyrimidine base, or modified purine or pyrimidine base.
  • oligonucleotide includes compositions in which adjacent nucleomonomers are linked via phosphorothioate, amide or other linkages (e.g., Neilsen, P. E., et al. 1991. Science. 254:1497).
  • linkages refers to any physical connection, preferably covalent coupling, between two or more nucleic acid components, e.g., catalyzed by an enzyme such as a ligase.
  • oligonucleotide includes any structure that serves as a scaffold or support for the bases of the oligonucleotide, where the scaffold permits binding to the target nucleic acid molecule in a sequence-dependent manner.
  • Oligonucleotides of the invention are isolated.
  • isolated includes nucleic acid molecules which are synthesized (e.g., chemically, enzymatically, or recombinantly) or are naturally occurring but separated from other nucleic acid molecules which are present in a natural source of the nucleic acid.
  • a naturally occurring “isolated” nucleic acid molecule is free of sequences which naturally flank the nucleic acid molecule (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid molecule) in a nucleic acid molecule in an organism from which the nucleic acid molecule is derived.
  • nucleomonomer includes a single base covalently linked to a second moiety.
  • Nucleomonomers include, for example, nucleosides and nucleotides. Nucleomonomers can be linked to form oligonucleotides that bind to target nucleic acid sequences in a sequence specific manner.
  • modified (non-naturally occurring) nucleomonomers can be used in the oligonucleotides described herein.
  • nucleomonomers which are based on bases (purines, pyrimidines, and derivatives and analogs thereof) bound to substituted and unsubstituted cycloalkyl moieties, e.g., cyclohexyl or cyclopentyl moieties, and substituted and unsubstituted heterocyclic moieties, e.g., 6-member morpholino moieties or, preferably, sugar moieties.
  • Sugar moieties include natural, unmodified sugars, e.g., monosaccharides (such as pentoses, e.g., ribose, deoxyribose), modified sugars and sugar analogs. Possible modifications of nucleomonomers, particularly of a sugar moiety, include, for example, replacement of one or more of the hydroxyl groups with a halogen, a heteroatom, an aliphatic group, or the functionalization of the hydroxyl group as an ether, an amine, a thiol, or the like.
  • monosaccharides such as pentoses, e.g., ribose, deoxyribose
  • Possible modifications of nucleomonomers, particularly of a sugar moiety include, for example, replacement of one or more of the hydroxyl groups with a halogen, a heteroatom, an aliphatic group, or the functionalization of the hydroxyl group as an ether, an amine, a thiol, or the
  • modified nucleomonomers are 2′-O-methyl nucleotides, especially when the 2′-O-methyl nucleotides are used as nucleomonomers in the ends of the oligomers.
  • Such 2′O-methyl nucleotides may be referred to as “methylated,” and the corresponding nucleotides may be made from unmethylated nucleotides followed by alkylation or directly from methylated nucleotide reagents.
  • Modified nucleomonomers may be used in combination with unmodified nucleomonomers.
  • an oligonucleotide of the invention may contain both methylated and unmethylated nucleomonomers.
  • modified nucleomonomers include sugar-or backbone-modified ribonucleotides.
  • Modified ribonucleotides may contain a nonnaturally occurring base (instead of a naturally occurring base) such as uridines or cytidines modified at the 5-position, e.g., 5-(2-amino)propyl uridine and 5-bromo uridine; adenosines and guanosines modified at the 8-position, e.g., 8-bromo guanosine; deaza nucleotides, e.g., 7-deaza-adenosine; and N-alkylated nucleotides, e.g., N6-methyl adenosine.
  • uridines or cytidines modified at the 5-position e.g., 5-(2-amino)propyl uridine and 5-bromo uridine
  • sugar-modified ribonucleotides may have the 2′-OH group replaced by a H, alxoxy (or OR), R or alkyl, halogen, SH, SR, amino (such as NH 2 , NHR, NR 2, ), or CN group, wherein R is lower alkyl, alkenyl, or alkynyl.
  • Modified ribonucleotides may also have the phosphoester group connecting to adjacent ribonucleotides replaced by a modified group, e.g., of phosphothioate group. More generally, the various nucleotide modifications may be combined.
  • sense oligomers may have 2′ modifications on the ends (1 on each end, 2 on each end, 3 on each end, and 4 on each end, and so on; as well as 1 on one end, 2 on one end, 3 on one end, and 4 on one end, and so on; and even unbalanced combinations such as 1 on one end and 2 on the other end, and so on).
  • the antisense strand may have 2′ modifications on the ends (1 on each end, 2 on each end, 3 on each end, and 4 on each end, and so on; as well as 1 on one end, 2 on one end, 3 on one end, and 4 on one end, and so on; and even unbalanced combinations such as 1 on one end and 2 on the other end, and so on).
  • such 2′-modifications are in the sense RNA strand or the sequences other than the antisense strand.
  • composition of the invention has end-blocks on both ends of a sense oligonucleotide and only the 3′ end of an antisense oligonucleotide.
  • the inventors believe that a 2′-O-modified sense strand works less well than unmodified because it is not efficiently unwound.
  • another embodiment of the invention includes duplexes in which nucleomonomer-nucleomonomer mismatches are present in a sense 2′-O-methly strand (and are thought to be easier to unwind).
  • a number of complementary second oligonucleotide strands are permitted according to the invention.
  • a targeted and a non-targeted oligonucleotide are illustrated with several possible complementary oligonucleotides.
  • the individual nucleotides may be 2′-OH RNA nucleotides (R) or the corresponding 2′-OMe nucleotides (M), and the oligonucleotides themselves may contain mismatched nucleotides (lower case letters).
  • Targeted Oligonucleotide First CCCUUCUGUCUUGAACAUGAG (SEQ ID NO: ##) Strand: Second CTgATGTTCAAGACAGAAcGG (SEQ ID NO: ##) Strand: (methyl MMMMMMMMMMMMMMMMM groups ⁇ ) CTgATGTTCAAGACAGAAcGG (SEQ ID NO: ##) RRRRRRRRRRRRRRRDD CTCAUGUUCAAGACAGAAGGG (SEQ ID NO: ##) RRRRRRMMMMMMMMMRRRRRR CTCAUGUUCAAGACAGAAGGG (SEQ ID NO: ##) MMMMMMRRRRRRRRRMMMMMM CTCAUGUUCAAGACAGAAGGG (SEQ ID NO: ##) RMRMRMRMRMRMRMRMRMRMRMR
  • Non-Targeted Oligonucleotide First GAGTACAAGTTCTGTCTTCCC (SEQ ID NO: ##) Strand: Second GGcAAGACAGAACTTGTAgTC (SEQ ID NO: ##) Strand: (methyl MMMMMMMMMMMMMMM groups ⁇ ) GGGAAGACAGAACTTGTACTC (SEQ ID NO: ##) RRRRRRMMMMMMMRRRRRR GGGAAGACAGAACTTGTACTC (SEQ ID NO: ##) MMMMMMRRRRRRRRRMMMMMMMM GGGAAGACAGAACTTGTACTC (SEQ ID NO: ##) RMRMRMRMRMRMRMRMRMRMRMR
  • the length of the sense strand can be 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, or 18 nucleotides, with a complementary duplexed RNA strand, optionally having overhangs.
  • RNA having 2′-O-methyl nucleomonomers may not be recognized by cellular machinery that is thought to recognize unmodified RNA.
  • the use of 2′-O-methylated or partially 2′-O-methylated RNA may avoid the interferon response to double-stranded nucleic acids, while maintaining target RNA inhibition.
  • This RNAi (“stealth RNAi”) is useful for avoiding the interferon or other cellular stress responses, both in short RNAi (e.g., siRNA) sequences that induce the interferon response, and in longer RNAi sequences that may induce the interferon response.
  • An especially advantageous use of the present invention is in gene function studies in which multiple RNAi sequences are used. According to present methods known in the art, frequently there is no way of predicting which sequences might induce a stress response, including the interferon response, and in this regard the present invention significantly advances the state of the art. For example, if all of the multiple sequences are partially 2-O-methylated, the stress response, including interferon response, may be avoided, and thus avoid confounding results in which some sequences affect cellular phenotype independent of the target gene inhibition. Other chemical modifications in addition to 2′-O-methylation may also achieve this effect.
  • modified sugars include D-ribose, 2′-O-alkyl (including 2′-O-methyl and 2′-O-ethyl), i.e., 2′-alkoxy, 2′-amino, 2′-S-alkyl, 2′-halo (including 2′-fluoro), 2′-methoxyethoxy, 2′-allyloxy (—OCH 2 CH ⁇ CH 2 ), 2′-propargyl, 2′-propyl, ethynyl, ethenyl, propenyl, and cyano and the like.
  • the sugar moiety can be a hexose and incorporated into an oligonucleotide as described (Augustyns, K., et al., Nucl. Acids. Res. 1992. 18:4711).
  • Exemplary nucleomonomers can be found, e.g., in U.S. Pat. No. 5,849,902, incorporated by reference herein.
  • alkyl includes saturated aliphatic groups, including straight-chain alkyl groups (e.g., methyl, ethyl, propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, etc.), branched-chain alkyl groups (isopropyl, tert-butyl, isobutyl, etc.), cycloalkyl (alicyclic) groups (cyclopropyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl), alkyl substituted cycloalkyl groups, and cycloalkyl substituted alkyl groups.
  • straight-chain alkyl groups e.g., methyl, ethyl, propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl,
  • a straight chain or branched chain alkyl has 6 or fewer carbon atoms in its backbone (e.g., C 1 -C 6 for straight chain, C 3 -C 6 for branched chain), and more preferably 4 or fewer.
  • preferred cycloalkyls have from 3-8 carbon atoms in their ring structure, and more preferably have 5 or 6 carbons in the ring structure.
  • the term C 1 -C 6 includes alkyl groups containing 1 to 6 carbon atoms.
  • alkyl includes both “unsubstituted alkyls” and “substituted alkyls,” the latter of which refers to alkyl moieties having substituents replacing a hydrogen on one or more carbons of the hydrocarbon backbone.
  • substituents can include, for example, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sul
  • Cycloalkyls can be further substituted, e.g., with the substituents described above.
  • An “alkylaryl” or an “arylalkyl” moiety is an alkyl substituted with an aryl (e.g., phenylmethyl (benzyl)).
  • the term “alkyl” also includes the side chains of natural and unnatural amino acids.
  • n-alkyl means a straight chain (i.e., unbranched) unsubstituted alkyl group.
  • alkenyl includes unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double bond.
  • alkenyl includes straight-chain alkenyl groups (e.g., ethylenyl, propenyl, butenyl, pentenyl, hexenyl, heptenyl, octenyl, nonenyl, decenyl, etc.), branched-chain alkenyl groups, cycloalkenyl (alicyclic) groups (cyclopropenyl, cyclopentenyl, cyclohexenyl, cycloheptenyl, cyclooctenyl), alkyl or alkenyl substituted cycloalkenyl groups, and cycloalkyl or cycloalkenyl substituted alkenyl groups.
  • a straight chain or branched chain alkenyl group has 6 or fewer carbon atoms in its backbone (e.g., C 2 -C 6 for straight chain, C 3 -C 6 for branched chain).
  • cycloalkenyl groups may have from 3-8 carbon atoms in their ring structure, and more preferably have 5 or 6 carbons in the ring structure.
  • the term C 2 -C 6 includes alkenyl groups containing 2 to 6 carbon atoms.
  • alkenyl includes both “unsubstituted alkenyls” and “substituted alkenyls,” the latter of which refers to alkenyl moieties having substituents replacing a hydrogen on one or more carbons of the hydrocarbon backbone.
  • substituents can include, for example, alkyl groups, alkynyl groups, halogens, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate,
  • alkynyl includes unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but which contain at least one triple bond.
  • alkynyl includes straight-chain alkynyl groups (e.g., ethynyl, propynyl, butynyl, pentynyl, hexynyl, heptynyl, octynyl, nonynyl, decynyl, etc.), branched-chain alkynyl groups, and cycloalkyl or cycloalkenyl substituted alkynyl groups.
  • a straight chain or branched chain alkynyl group has 6 or fewer carbon atoms in its backbone (e.g., C 2 -C 6 for straight chain, C 3 -C 6 for branched chain).
  • the term C 2 -C 6 includes alkynyl groups containing 2 to 6 carbon atoms.
  • alkynyl includes both “unsubstituted alkynyls” and “substituted alkynyls,” the latter of which refers to alkynyl moieties having substituents replacing a hydrogen on one or more carbons of the hydrocarbon backbone.
  • substituents can include, for example, alkyl groups, alkynyl groups, halogens, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate,
  • lower alkyl as used herein means an alkyl group, as defined above, but having from one to five carbon atoms in its backbone structure.
  • Lower alkenyl and “lower alkynyl” have chain lengths of, for example, 2-5 carbon atoms.
  • alkoxy includes substituted and unsubstituted alkyl, alkenyl, and alkynyl groups covalently linked to an oxygen atom.
  • alkoxy groups include methoxy, ethoxy, isopropyloxy, propoxy, butoxy, and pentoxy groups.
  • substituted alkoxy groups include halogenated alkoxy groups.
  • the alkoxy groups can be substituted with groups such as alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate
  • heteroatom includes atoms of any element other than carbon or hydrogen. Preferred heteroatoms are nitrogen, oxygen, sulfur and phosphorus.
  • hydroxy or “hydroxyl” includes groups with an —OH or —O ⁇ (with an appropriate counterion).
  • halogen includes fluorine, bromine, chlorine, iodine, etc.
  • perhalogenated generally refers to a moiety wherein all hydrogens are replaced by halogen atoms.
  • substituted includes substituents which can be placed on the moiety and which allow the molecule to perform its intended function.
  • substituents include alkyl, alkenyl, alkynyl, aryl, (CR′R′′) 0-3 NR′R′′, (CR′R′′) 0-3 CN, NO 2 , halogen, (CR′R′′) O-3 C(halogen) 3 , (CR′R′′) 0-3 CH(halogen) 2 , (CR′R′′) 0-3 CH 2 (halogen), (CR′R′′) 0-3 CONR′R′′, (CR′R′′) 0-3 S(O) 1-2 NR′R′′, (CR′R′′) 0-3 CHO, (CR′R′′) 0-3 O(CR′R′′) 0-3 H, (CR′R′′) 0-3 S(O) 0-2 R′, (CR′R′′) 0-3 O(CR′R′′) 0-3 H, (CR′R′′) 0-3 S(
  • amine or “amino” includes compounds or moieties in which a nitrogen atom is covalently bonded to at least one carbon or heteroatom.
  • alkyl amino includes groups and compounds wherein the nitrogen is bound to at least one additional alkyl group.
  • dialkyl amino includes groups wherein the nitrogen atom is bound to at least two additional alkyl groups.
  • ether includes compounds or moieties which contain an oxygen bonded to two different carbon atoms or heteroatoms.
  • alkoxyalkyl refers to an alkyl, alkenyl, or alkynyl group covalently bonded to an oxygen atom which is covalently bonded to another alkyl group.
  • base includes the known purine and pyrimidine heterocyclic bases, deazapurines, and analogs (including heterocyclic substituted analogs, e.g., aminoethyoxy phenoxazine), derivatives (e.g., 1-alkyl-, 1-alkenyl-, heteroaromatic- and 1-alkynyl derivatives) and tautomers thereof.
  • purines include adenine, guanine, inosine, diaminopurine, and xanthine and analogs (e.g., 8-oxo-N 6 -methyladenine or 7-diazaxanthine) and derivatives thereof.
  • Pyrimidines include, for example, thymine, uracil, and cytosine, and their analogs (e.g., 5-methylcytosine, 5-methyluracil, 5-(1-propynyl)uracil, 5-(1-propynyl)cytosine and 4,4-ethanocytosine).
  • suitable bases include non-purinyl and non-pyrimidinyl bases such as 2-aminopyridine and triazines.
  • the nucleomonomers of an oligonucleotide of the invention are RNA nucleotides. In another preferred embodiment, the nucleomonomers of an oligonucleotide of the invention are modified RNA nucleotides.
  • nucleoside includes bases which are covalently attached to a sugar moiety, preferably ribose or deoxyribose.
  • examples of preferred nucleosides include ribonucleosides and deoxyribonucleosides.
  • Nucleosides also include bases linked to amino acids or amino acid analogs which may comprise free carboxyl groups, free amino groups, or protecting groups. Suitable protecting groups are well known in the art (see P. G. M. Wuts and T. W. Greene, “Protective Groups in Organic Synthesis”, 2 nd Ed., Wiley-Interscience, New York, 1999).
  • nucleotide includes nucleosides which further comprise a phosphate group or a phosphate analog.
  • linkage includes a naturally occurring, unmodified phosphodiester moiety (—O—(PO 2 ⁇ )—O—) that covalently couples adjacent nucleomonomers.
  • substitute linkage includes any analog or derivative of the native phosphodiester group that covalently couples adjacent nucleomonomers.
  • Substitute linkages include phosphodiester analogs, e.g., phosphorothioate, phosphorodithioate, and P-ethyoxyphosphodiester, P-ethoxyphosphodiester, P-alkyloxyphosphotriester, methylphosphonate, and nonphosphorus containing linkages, e.g., acetals and amides.
  • Such substitute linkages are known in the art (e.g., Bjergarde et al. 1991. Nucleic Acids Res. 19:5843; Caruthers et al. 1991. Nucleosides Nucleotides. 10:47).
  • oligonucleotides of the invention comprise 3′ and 5′ termini (except for circular oligonucleotides).
  • the 3′ and 5′ termini of an oligonucleotide can be substantially protected from nucleases e.g., by modifying the 3′ or 5′ linkages (e.g., U.S. Pat. No. 5,849,902 and WO 98/13526).
  • oligonucleotides can be made resistant by the inclusion of a “blocking group.”
  • blocking group refers to substituents (e.g., other than OH groups) that can be attached to oligonucleotides or nucleomonomers, either as protecting groups or coupling groups for synthesis (e.g., FITC, propyl (CH 2 -CH 2 -CH 3 ), phosphate (PO 3 2 ⁇ ), hydrogen phosphonate, or phosphoramidite).
  • Blocking groups also include “end blocking groups” or “exonuclease blocking groups” which protect the 5′ and 3′ termini of the oligonucleotide, including modified nucleotides and non-nucleotide exonuclease resistant structures.
  • Exemplary end-blocking groups include cap structures (e.g., a 7-methylguanosine cap), inverted nucleomonomers, e.g., with 3′-3′ or 5′-5′ end inversions (see, e.g., Ortiagao et al. 1992. Antisense Res. Dev. 2:129), methylphosphonate, phosphoramidite, non-nucleotide groups (e.g., non-nucleotide linkers, amino linkers, conjugates) and the like.
  • the 3′ terminal nucleomonomer can comprise a modified sugar moiety.
  • the 3′ terminal nucleomonomer comprises a 3′-O that can optionally be substituted by a blocking group that prevents 3′-exonuclease degradation of the oligonucleotide.
  • the 3′-hydroxyl can be esterified to a nucleotide through a 3′ ⁇ 3′ internucleotide linkage.
  • the alkyloxy radical can be methoxy, ethoxy, or isopropoxy, and preferably, ethoxy.
  • the 3′ ⁇ 3′ linked nucleotide at the 3′ terminus can be linked by a substitute linkage.
  • the 5′ most 3′ ⁇ 5′ linkage can be a modified linkage, e.g., a phosphorothioate or a P-alkyloxyphosphotriester linkage.
  • the two 5′ most 3′ ⁇ 5′ linkages are modified linkages.
  • the 5′ terminal hydroxy moiety can be esterified with a phosphorus containing moiety, e.g., phosphate, phosphorothioate, or P-ethoxyphosphate.
  • the sense strand of an oligonucleotide comprises a 5′ group that allows for RNAi activity but which renders the sense strand inactive in terms of gene targeting.
  • a 5′ modifying group is a phosphate group or a group larger than a phosphate group
  • the antisense strand of an oligonucleotide comprises a 5′ phosphate group.
  • the oligonucleotides included in the composition are high affinity oligonucleotides.
  • the term “high affinity” as used herein includes oligonucleotides that have a Tm (melting temperature) of or greater than about 60° C., greater than about 65° C., greater than about 70° C., greater than about 75° C., greater than about 80° C. or greater than about 85° C.
  • the Tm is the midpoint of the temperature range over which the oligonucleotide separates from the target nucleotide sequence. At this temperature, 50% helical (hybridized) versus coil (unhybridized) forms are present.
  • Tm is measured by using the UV spectrum to determine the formation and breakdown (melting) of hybridization. Base stacking occurs during hybridization, which leads to a reduction in UV absorption. Tm depends both on GC content of the two nucleic acid molecules and on the degree of sequence complementarity. Tm can be determined using techniques that are known in the art (see for example, Monia et al. 1993. J Biol. Chem. 268:145; Chiang et al. 1991. J Biol. Chem. 266:18162; Gagnor et al. 1987. Nucleic Acids Res. 15:10419; Monia et al. 1996. Proc. Natl. Acad. Sci. 93:15481; Publisis and Tinoco. 1989. Methods in Enzymology 180:304; Thuong et al. 1987. Proc. Natl. Acad. Sci. USA 84:5129).
  • an oligonucleotide can include an agent which increases the affinity of the oligonucleotide for its target sequence.
  • affinity enhancing agent includes agents that increase the affinity of an oligonucleotide for its target. Such agents include, e.g., intercalating agents and high affinity nucleomonomers. Intercalating agents interact strongly and nonspecifically with nucleic acids. Intercalating agents serve to stabilize RNA-DNA duplexes and thus increase the affinity of the oligonucleotides for their targets. Intercalating agents are most commonly linked to the 3′ or 5′ end of oligonucleotides.
  • intercalating agents examples include acridine, chlorambucil, benzopyridoquinoxaline, benzopyridoindole, benzophenanthridine, and phenazinium.
  • the agents may also impart other characteristics to the oligonucleotide, for example, increasing resistance to endonucleases and exonucleases.
  • a high affinity nucleomonomer is incorporated into an oligonucleotide.
  • the language “high affinity nucleomonomer” as used herein includes modified bases or base analogs that bind to a complementary base in a target nucleic acid molecule with higher affinity than an unmodified base, for example, by having more energetically favorable interactions with the complementary base, e.g., by forming more hydrogen bonds with the complementary base.
  • high affinity nucleomonomer analogs such as aminoethyoxy phenoxazine (also referred to as a G clamp), which forms four hydrogen bonds with guanine are included in the term “high affinity nucleomonomer.”
  • a high affinity nucleomonomer is illustrated below (see, e.g., Flanagan, et al., 1999. Proc. Natl. Acad. Sci. 96:3513).
  • exemplary high affinity nucleomonomers include 7-alkenyl, 7-alkynyl, 7-heteroaromatic-, or 7-alkynyl-heteroaromatic-substituted bases or the like which can be substituted for adenosine or guanosine in oligonucleotides (see, e.g., U.S. Pat. No. 5,594,121).
  • 7-substituted deazapurines have been found to impart enhanced binding properties to oligonucleotides, i.e., by allowing them to bind with higher affinity to complementary target nucleic acid molecules as compared to unmodified oligonucleotides.
  • High affinity nucleomonomers can be incorporated into the oligonucleotides of the instant invention using standard techniques.
  • an agent that increases the affinity of an oligonucleotide for its target comprises an intercalating agent.
  • an intercalating agent includes agents which can bind to a DNA double helix.
  • an intercalating agent enhances the binding of the oligonucleotide to its complementary genomic DNA target sequence.
  • the intercalating agent may also increase resistance to endonucleases and exonucleases.
  • intercalating agents are taught by Helene and Thuong (1989. Genome 31:413), and include e.g., acridine derivatives (Lacoste et al. 1997. Nucleic Acids Research. 25:1991; Kukreti et al. 1997. Nucleic Acids Research. 25:4264); quinoline derivatives (Wilson et al. 1993. Biochemistry 32:10614); benzo[f]quino[3,4-b]quioxaline derivatives (Marchand et al. 1996. Biochemistry. 35:5022; Escude et al. 1998. Proc. Natl. Acad. Sci. 95:3591).
  • Intercalating agents can be incorporated into an oligonucleotide using any convenient linkage.
  • acridine or psoralen can be linked to the oligonucleotide through any available —OH or —SH group, e.g., at the terminal 5′ position of the oligonucleotide, the 2′ positions of sugar moieties, or an OH, NH 2 , COOH, or SH incorporated into the 5-position of pyrimidines using standard methods.
  • an agent that increases the affinity of an oligonucleotide for its target when included in an RNase H activating antisense nucleotide sequence, is not positioned adjacent to an RNase activating region of the oligonucleotide, e.g., is positioned adjacent to a non-RNase activating region.
  • the agent that increases the affinity of an oligonucleotide for its target is placed at a distance as far as possible from the RNase activating domain of the chimeric antisense sequence such that the specificity of the chimeric antisense sequence is not altered when compared with the specificity of a chimeric antisense sequence which lacks the intercalating compound.
  • this can be accomplished by positioning the agent adjacent to a non-RNase activating region.
  • the specificity of the oligonucleotide can be tested by demonstrating that transcription of a non-target sequence, preferably a non-target sequence which is structurally similar to the target (e.g., has some sequence homology or identity with the target sequence but which is not identical in sequence to the target), is not inhibited to a greater degree by an oligonucleotide comprising an affinity enhancing agent than by an oligonucleotide directed against the same target that does not comprise an affinity enhancing agent.
  • the double-stranded oligonucleotides of the invention may be formed by a single, self-complementary nucleic acid strand or two separate complementary nucleic acid strands. Duplex formation can occur either inside or outside the cell containing the target gene.
  • double-stranded includes one or more nucleic acid molecules comprising a region of the molecule in which at least a portion of the nucleomonomers are complementary and hydrogen bond to form a duplex.
  • duplex includes the region of the double-stranded nucleic acid molecule(s) that is (are) hydrogen bonded to a complementary sequence.
  • the double-stranded oligonucleotides of the invention comprise a nucleotide sequence that is sense to a target gene and a complementary sequence that is antisense to the target gene.
  • the sense and antisense nucleotide sequences correspond to the target gene sequence, e.g., are identical or are sufficiently identical to effect target gene inhibition (e.g., are about at least about 98%, 96% identical, 94%, 90% identical, 85% identical, or 80% identical) to the target gene sequence.
  • the individual nucleic acid molecules can be of different lengths.
  • a double-stranded oligonucleotide of the invention is double-stranded over its entire length, i.e., with no overhanging single-stranded sequence at either end of the molecule, i.e., is blunt-ended.
  • a double-stranded oligonucleotide of the invention is not double-stranded over its entire length. For instance, when two separate nucleic acid molecules are used, one of the molecules, e.g., the first molecule comprising an antisense sequence can be longer than the second molecule hybridizing thereto (leaving a portion of the molecule single-stranded). Likewise, when a single nucleic acid molecule is used a portion of the molecule at either end can remain single-stranded.
  • a double-stranded oligonucleotide of the invention is double-stranded over at least about 70% of the length of the oligonucleotide. In another embodiment, a double-stranded oligonucleotide of the invention is double-stranded over at least about 80% of the length of the oligonucleotide. In another embodiment, a double-stranded oligonucleotide of the invention is double-stranded over at least about 90%-95% of the length of the oligonucleotide. In another embodiment, a double-stranded oligonucleotide of the invention is double-stranded over at least about 96%-98% of the length of the oligonucleotide.
  • the double-stranded duplex constructs of the invention can be further stabilized against nucleases by forming loop structures at the 5′ or 3′ end of the sense or antisense strand of the construct.
  • the construct can take the form:
  • Ns are nucleomonomers in complementary oligonucleotide strands (i.e., the top N strand is complementary to the bottom N strand) of equal length (e.g., between about 12 and about 40 nucleotides in length) and X and Y are each independently selected from a group consisting of nothing (i.e., the construct is a blunt ended construct with no loops and no overhang); from about 1 to about 20 nucleotides of 5′ overhang; from about 1 to about 20 nucleotides of 3′ overhang; a GAAA loop (tetra-loop); and a loop consisting from about 4 to about 20 nucleomonomers (where the nucleomonomers are all either Gs or A's).
  • the sequence of Ns corresponds to the target gene sequence (e.g., is homologous or identical to a nucleotide sequence that is sense or antisense to the target gene sequence), while the nucleotide sequence of the loop structure does not correspond to the target gene sequence.
  • such loops can comprise all Gs and A's and be from about 4 to about 20 nucleotides in length.
  • such a loop can be a tetra-loop having a sequence GAAA:
  • the number of Ns is about 27.
  • the oligonucleotide can be divided by having a “nick” which is two non-linked nucleomonomers at any point along the sense or antisense strand, but preferably along the sense strand.
  • the nick is at least four bases from the nearest end of the duplexed region (to provide enough thermodynamic stability).
  • a construct of the invention can take the form:
  • Ns are complementary nucleomonomers in oligonucleotide strands of equal length (e.g., between 12-40 nucleomonomers in length);
  • Zs are nucleomonomers in complementary oligonucleotide strands of between about 2 and about 8 nucleomonomers in length and which comprise a sequence which can optionally correspond to the target sequence;
  • Ms are nucleomonomers in complementary oligonucleotide strands of between about 2 and about 8 nucleomonomers in length and which can optionally correspond to the target sequence.
  • the Zs and Ms are nucleomonomers selected from the group consisting of Cs and Gs to make the end of the duplex more thermodynamically stable. Ends of duplexes can become single stranded transiently, and since duplex RNA is more stable than single-stranded RNA, the enhanced stability of the duplex on the ends will result in higher nuclease stability.
  • a preferred sequence for Z or M in the antisense strand is from 2-8 nucleomonomers in length or preferably from 3-4 nucleomonomers in length, e.g., (from 5′ to 3′) CC, GG, CG, GC, CCC, GGG, CGG, GCC, GCG, CGC, CGGG, GCCC, CCCC, GGGG, GCGC, CGCG, GGGC, CCCG, CGGG, GCCC, GGCC, or CCGG.
  • the complementary strand would have the corresponding complementary sequence.
  • a construct of the invention has the form:
  • Ns are nucleomonomers in complementary oligonucleotide strands (i.e., the top N strand is complementary to the bottom N strand) of equal length (e.g., from between about 12 to about 40 nucleomonomers in length) and X is selected from the group consisting of nothing (i.e., leaving blunt ends with no loop or overhang); 1-20 nucleotides of 5′ overhang; 1-20 nucleotides of 3′ overhang; a GAAA loop (tetra-loop); and a loop consisting of from about 4 to about 20 nucleomonomers (where the nucleomonomers are all either Gs or A's) and where Ms are nucleomonomers in complementary oligonucleotide strands of between about 2 and about 8 nucleomonomers in length (which can optionally correspond to the target sequence).
  • Ms are nucleomonomers selected from the group consisting of contain Cs and Gs.
  • a preferred sequence for M in the antisense strand is from 2-8 nucleomonomers in length or preferably from 3-4 nucleomonomers in length, e.g., (from 5′ to 3′) CC, GG, CG, GC, CCC, GGG, CGG, GCC, GCG, CGC, CGGG, GCCC, CCCC, GGGG, GCGC, CGCG, GGGC, CCCG, CGGG, GCCC, GGCC, or CCGG and the corresponding complement on the opposite strand.
  • the construct can take the form:
  • Ns are nucleomonomers in complementary oligonucleotide strands of equal length (e.g., from between about 12 to about 40 nucleomonomers in length) and Y is selected from the group consisting of nothing (i.e., leaving blunt ends with no loop or overhang; 1-20 nucleotides of 5′ overhang; 1-20 nucleotides of 3′ overhang; a GAAA loop (tetra-loop); and a loop consisting of a sequence of from about 4 to about 20 nucleomonomers (where the nucleomonomers are all either Gs or A's) and where Zs are nucleomonomers in complementary oligonucleotide strands of between about 2 and about 8 nucleomonomers in length and which comprise a sequence which can optionally correspond to the target sequence.
  • the Zs are nucleomonomers selected from the group consisting of Cs and Gs to make the end of the duplex more stable.
  • a preferred sequence for Z in the antisense strand is from 2-8 nucleomonomers in length or preferably from 3-4 nucleomonomers in length, e.g., (from 5′ to 3′) CC, GG, CG, GC, CCC, GGG, CGG, GCC, GCG, CGC, CGGG, GCCC, CCCC, GGGG, GCGC, CGCG, GGGC, CCCG, CGGG, GCCC, GGCC or CCGG (and the corresponding complement on the opposite strand).
  • GGCC on the end (and its complement) confers additional stability:
  • the invention also relates to a double-stranded oligonucleotide composition having the following structure:
  • oligoA is an oligonucleotide of a number of nucleomonomers
  • oligoB is an oligonucleotide that has the same number of nucleomonomers as oligoA and that is complementary to oligoA
  • either oligoA or oligoB corresponds to a target gene sequence.
  • X may be selected from (a) nothing; (b) an oligonucleotide of about 1 to about 20 nucleotides covalently bonded to the 5′ end of oligoA and constituting a 5′ overhang; (c) an oligonucleotide of about 1 to about 20 nucleotides covalently bonded to the 3′ end of oligoB and constituting a 3′ overhang; (d) and an oligonucleotide of about 4 to about 20 nucleomonomers covalently bonded to the 3′ end of oligoB and the 5′ end of oligoA and constituting a loop structure, where the nucleomonomers are selected from the group consisting of G and A.
  • Y may be selected from (a) nothing; (b) an oligonucleotide of about 1 to about 20 nucleotides covalently bonded to the 5′ end of oligoB and constituting a 5′ overhang; (c) an oligonucleotide of about 1 to about 20 nucleotides covalently bonded to the 3′ end of oligoA and constituting a 3′ overhang; (d) and an oligonucleotide of about 4 to about 20 nucleomonomers covalently bonded to the 3′ end of oligoA and the 5′ end of oligoB and constituting a loop structure, where the nucleomonomers are selected from the group consisting of G and A.
  • the invention includes a double-stranded oligonucleotide composition having the structure:
  • oligoA is 5′-(N) 15- 40-(M) 2-8 -3′ and oligoB is 5′-(N) 15- 40-(M) 2-8 -3′, wherein each of N and M is independently a nucleomonomer;
  • both of the sequences of Ns are complementary oligonucleotide strands of equal length having between about 15 and 40 nucleomonomers;
  • at least one of the sequences of Ns, optionally with some or all of the flanking Ms corresponds to a target gene sequence.
  • Both of the sequences of Ms are complementary oligonucleotide strands of between about 2 and about 8 nucleomonomers in length. The two M strands are optionally of the same length.
  • the group X indicated by the curved line is selected from (a) nothing; (b) an oligonucleotide of about 1 to about 20 nucleotides covalently bonded to the 5′ end of oligoA and constituting a 5′ overhang; (c) an oligonucleotide of about 1 to about 20 nucleotides covalently bonded to the 3′ end of oligoB and constituting a 3′ overhang; (d) and an oligonucleotide of about 4 to about 20 nucleomonomers covalently bonded to the 3′ end of oligoB and the 5′ end of oligoA and constituting a loop structure, where the nucleomonomers are selected from the group consisting of G and A.
  • the invention pertains to a double-stranded oligonucleotide composition having the structure:
  • oligoA is 5′-(Z) 2-8 -(N) 12-40 -3′ and oligoB is 5′-(Z) 2-8 -(N) 12-40 -3′, wherein each of N and Z is independently a nucleomonomer;
  • both of the sequences of Ns are complementary oligonucleotide strands of equal length having between about 12 and 40 nucleomonomers;
  • at least one of the sequences of Ns, optionally with some or all of the flanking Zs corresponds to a target gene sequence.
  • Both of the sequences of Zs are complementary oligonucleotide strands of between about 2 and about 8 nucleomonomers in length. The two Z strands are optionally of the same length.
  • Y is selected from (a) nothing; (b) an oligonucleotide of about 1 to about 20 nucleotides covalently bonded to the 5′ end of oligoB and constituting a 5′ overhang; (c) an oligonucleotide of about 1 to about 20 nucleotides covalently bonded to the 3′ end of oligoA and constituting a 3′ overhang; (d) and an oligonucleotide of about 4 to about 20 nucleomonomers covalently bonded to the 3′ end of oligoA and the 5′ end of oligoB and constituting a loop structure, where the nucleomonomers are selected from the group consisting of G and A.
  • the double-stranded duplex of an oligonucleotide of the invention is from between about 12 to about 50 nucleomonomers in length, i.e., the number of nucleotides of the double-stranded oligonucleotide which hybridize to the complementary sequence of the double-stranded oligonucleotide to form the double-stranded duplex structure is from about 12 to about 50 nuclemonomers in length.
  • the double-stranded duplex of an oligonucleotide of the invention is from between about 12 to about 40 nucleomonomers in length.
  • the double-stranded duplex of an oligonucleotide of the invention is at least about 25 nucleomonomers in length. In one embodiment, the double-stranded duplex is greater than about 25 nucleomonomers in length. In one embodiment, a double-stranded duplex is at least about 26, 27, 28, 29, 30, at least about 40, at least about 50, or at least about 60, at least about 70, at least about 80, or at least about 90 nucleomonomers in length. In another embodiment, the double-stranded duplex is less than about 25 nucleomonomers in length. In one embodiment, a double-stranded duplex is at least about 10, at least about 15, at least about 20, at least about 22, at least about 23 or at least about 24 nucleomonomers in length.
  • the number of Ns in each strand of the duplex is about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27. In another embodiment, the number of Ns in each strand of the duplex is about 30, 35, 40, 45, or 50. In one embodiment, the number of Ns in each strand of the duplex is about 19. In a preferred embodiment, the number of Ns in each strand of the duplex is about 27. In another embodiment, the number of Ns in each strand of the duplex is about 27 (e.g., is 26, 27, or 28). In another embodiment, the number of Ns in each strand of the duplex is 27.
  • an individual nucleic acid molecule of a double-stranded oligonucleotide of the invention is at least about 25 nucleomonomers in length.
  • the double-stranded oligonucleotide of the invention is comprised of one nucleic acid molecule, that individual molecule is at least about 25 nucleomonomers in length or when the double-stranded oligonucleotide of the invention is comprised of two separate nucleic acid molecules, the length of at least one of the individual nucleic acid molecules is at least about 25 nucleomonomers in length.
  • an individual nucleic acid molecule comprising a double-stranded oligonucleotide of the invention is greater than about 25 nucleomonomers in length. In one embodiment, an individual nucleic acid molecule comprising a double-stranded oligonucleotide of the invention is at least about 26, 27, 28, 29, 30, at least about 40, at least about 50, or at least about 60, at least about 70, at least about 80, or at least about 90 nucleomonomers in length.
  • an individual nucleic acid molecule comprising a double-stranded oligonucleotide of the invention is less than about 25 nucleomonomers in length. In one embodiment, an individual nucleic acid molecule comprising a double-stranded oligonucleotide of the invention is at least about 10, at least about 15, at least about 20, at least about 22, at least about 23 or at least about 24 nucleomonomers in length.
  • the double-stranded molecules of the invention comprise a first nucleotide sequence which is antisense to at least part of the target gene and a second nucleotide sequence which is complementary to the first nucleotide sequence; i. e., is sense to at least part of the target gene.
  • the second nucleotide sequence of the double-stranded molecule comprises a nucleotide sequence which is at least about 100% complementary to the antisense molecule.
  • the second nucleotide sequence of the double-stranded molecule comprises a nucleotide sequence which is at least about 95% complementary to the antisense molecule. In another embodiment, the second nucleotide sequence of the double-stranded molecule comprises a nucleotide sequence which is at least about 90% complementary to the antisense molecule. In another embodiment, the second nucleotide sequence of the double-stranded molecule comprises a nucleotide sequence which is at least about 80% complementary to the antisense molecule. In another embodiment, the second nucleotide sequence of the double-stranded molecule comprises a nucleotide sequence which is at least about 60% complementary to the antisense molecule. In another embodiment, the second nucleotide sequence of the double-stranded molecule comprises a nucleotide sequence which is at least about 100% complementary to the antisense molecule.
  • the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-identical sequences can be disregarded for comparison purposes).
  • gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-identical sequences can be disregarded for comparison purposes.
  • the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • the percent complementarity can be determined analogously; when a position in one sequence occupied by a nucleotide that is complementary to the nucleotide in the other sequence, then the molecules are complementary at that position.
  • the comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • the percent identity between two nucleotide sequences is determined using e.g., the GAP program in the GCG software package, using a NWSgapdna. CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between two nucleotide sequences is determined using the algorithm of E. Meyers and W. Miller ( Comput. Appl. Biosci. 4:11-17 (1988)) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
  • a first antisense sequence of the double-stranded molecule hybridizes to its complementary second sequence of the double-stranded molecule under stringent hybridization conditions.
  • hybridizes under stringent conditions is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 60% complementary to each other typically remain hybridized to each other.
  • the conditions are such that sequences at least about 70%, more preferably at least about 80%, even more preferably at least about 85% or 90% complementary to each other typically remain hybridized to each other.
  • stringent hybridization conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.
  • a preferred, non-limiting example of stringent hybridization conditions are hybridization in 6 ⁇ sodium chloride/sodium citrate (SSC) at about 45° C., followed by one or more washes in 0.2 ⁇ SSC, 0.1% SDS at 50° C., preferably at 55° C., more preferably at 60° C., and even more preferably at 65° C. Ranges intermediate to the above-recited values, e.g., at 60-65° C. or at 55-60° C. are also intended to be encompassed by the present invention.
  • formamide can be included in the hybridization solution, using methods and conditions also known in the art.
  • antisense sequence includes nucleotide sequences which bind to the “sense” strand of the nucleotide sequence of the target gene (e.g., polynucleotides such as DNA, mRNA (including pre-mRNA)) molecules.
  • the antisense sequences of the invention bind to nucleic acid molecules, they can bind to any region of a nucleic acid molecule, including e.g., introns, exons, 5′, or 3′ untranslated regions.
  • Antisense sequences that work by binding to a target and activating RNase H preferably bind within an intron, an exon, the 5′ untranslated region, or the 3′ untranslated region of a nucleic acid target molecule.
  • the oligonucleotide compositions of the invention do not activate the interferon pathway, e.g., as evidenced by the lack of induction of the double-stranded RNA, interferon-inducible protein kinase, PKR.
  • modifications are made to a double-stranded RNA molecule which would normally activate the interferon pathway such that the interferon pathway is not activated.
  • the interferon pathway is activated by double-stranded unmodified RNA.
  • the cellular recognition of double-stranded RNA is highly specific and modifying one or woth of the strands of a double-stranded duplex enable the double-stranded RNA molecule to evade the double-stranded RNA recognition machinery of the cell but would still allow for the activation of the RNAi pathway.
  • the ability of a double-stranded oligonucleotide to activate interferon could be assessed by testing for expression of the double-stranded RNA, Interferon-Inducible Protein Kinase, PKR using techniques known in the art and also testing for the ability of the double-stranded molecule to effect target gene inhibition.
  • the invention provides a method of testing for the ability of a double-stranded RNA molecule to induce interferon by testing for the ability of the oligonucleotide to activate PKR.
  • Compositions that do not activate PKR are then selected for use to inhibit gene transcription in cells, e.g., in therapeutics or functional genomics.
  • an antisense sequence used in a double-stranded oligonucleotide composition of the invention that can specifically hybridize with a nucleotide sequence within the target gene (i.e., can be complementary to a nucleotide sequence within the target gene) may achieve its affects based on, e.g.,: (1) binding to target mRNA and stericly blocking the ribosome complex from translating the mRNA; (2) binding to target mRNA and triggering mRNA cleavage by RNase H; (3) binding to double-stranded DNA in the nucleus and forming a triple helix; (4) hybridizing to open DNA loops created by RNA polymerase; (5) interfering with mRNA splicing; (6) interfering with transport of mRNA from the nucleus to the cytoplasm; or (7) interfering with translation through inhibition of the binding of initiation factors or assembly of ribosomal subunits (i.e.
  • an antisense sequence of the double-stranded oligonucleotides of the invention is complementary to a target nucleic acid sequence over at least about 80% of the length of the antisense sequence.
  • the antisense sequence of the double-stranded oligonucleotide of the invention is complementary to a target nucleic acid sequence over at least about 90-95% of the length of the antisense sequence.
  • the antisense sequence of the double-stranded oligonucleotide of the invention is complementary to a target nucleic acid sequence over the entire length of the antisense sequence.
  • an antisense sequence of the double-stranded oligonucleotide hybridizes to at least a portion of the target gene under stringent hybridization conditions.
  • antisense sequences of the invention are substantially complementary to a target nucleic acid sequence.
  • an antisense RNA molecule comprises a nucleotide sequence which is at least about 100% complementary to a portion of the target gene.
  • an antisense RNA molecule comprises a nucleotide sequence which is at least about 90% complementary to a portion of the target gene.
  • an antisense RNA molecule comprises a nucleotide sequence which is at least about 80% complementary to a portion of the target gene.
  • an antisense RNA molecule comprises a nucleotide sequence which is at least about 60% complementary to a portion of the target gene.
  • an antisense RNA molecule comprises a nucleotide sequence which is at least about 100% complementary to a portion of the target gene.
  • no loops greater than about 8 nucleotides are formed by areas of non-complementarity between the oligonucleotide and the target.
  • an antisense nucleotide sequence of the invention is complementary to a target nucleic acid sequence over at least about 80% of the length of the antisense sequence. In another embodiment, an antisense sequence of the invention is complementary to a target nucleic acid sequence over at least about 90-95% of the length of the antisense sequence. In another embodiment, an antisense sequence of the invention is complementary to a target nucleic acid sequence over the entire length of the antisense sequence.
  • the antisense sequences used in an oligonucleotide composition of the invention may be of any type, e.g., including morpholino oligonucleotides, RNase H activating oligonucleotides, or ribozymes.
  • a double-stranded oligonucleotide of the invention can comprise (i.e., be a duplex of) one nucleic acid molecule which is DNA and one nucleic acid molecule which is RNA.
  • Antisense sequences of the invention can be “chimeric oligonucleotides” which comprise an RNA-like and a DNA-like region.
  • the language “RNase H activating region” includes a region of an oligonucleotide, e.g., a chimeric oligonucleotide, that is capable of recruiting RNase H to cleave the target RNA strand to which the oligonucleotide binds.
  • the RNase activating region contains a minimal core (of at least about 3-5, typically between about 3-12, more typically, between about 5-12, and more preferably between about 5-10 contiguous nucleomonomers) of DNA or DNA-like nucleomonomers. (See, e.g., U.S. Pat. No. 5,849,902).
  • the RNase H activating region comprises about nine contiguous deoxyribose containing nucleomonomers.
  • the contiguous nucleomonomers are linked by a substitute linkage, e.g., a phosphorothioate linkage.
  • an antisense sequence of the invention is unstable, i.e., is degraded in a cell, in the absence of the second strand (or self complementary sequence) which forms a double-stranded oligonucleotide of the invention.
  • a chimeric antisense sequence comprises unmodified DNA nucleomonomers in the gap rather than phosphorothioate DNA.
  • non-activating region includes a region of an antisense sequence, e.g., a chimeric oligonucleotide, that does not recruit or activate RNase H.
  • a non-activating region does not comprise phosphorothioate DNA.
  • the oligonucleotides of the invention comprise at least one non-activating region.
  • the non-activating region can be stabilized against nucleases or can provide specificity for the target by being complementary to the target and forming hydrogen bonds with the target nucleic acid molecule, which is to be bound by the oligonucleotide.
  • Antisense sequences of the present invention may include “morpholino oligonucleotides.” Morpholino oligonucleotides are non-ionic and function by an RNase H-independent mechanism. Each of the 4 genetic bases (Adenine, Cytosine, Guanine, and Thymine/Uracil) of the morpholino oligonucleotides is linked to a 6-membered morpholine ring. Morpholino oligonucleotides are made by joining the 4 different subunit types by, e.g., non-ionic phosphorodiamidate inter-subunit linkages. An example of a 2 subunit morpholino oligonucleotide is shown below.
  • Morpholino oligonucleotides have many advantages including: complete resistance to nucleases (Antisense & Nuc. Acid Drug Dev. 1996. 6:267); predictable targeting (Biochemica Biophysica Acta. 1999. 1489:141); reliable activity in cells (Antisense & Nuc. Acid Drug Dev. 1997. 7:63); excellent sequence specificity (Antisense & Nuc. Acid Drug Dev. 1997. 7:151); minimal non-antisense activity (Biochemica Biophysica Acta. 1999. 1489:141); and simple osmotic or scrape delivery (Antisense & Nuc. Acid Drug Dev. 1997. 7:291).
  • Morpholino oligonucleotides are also preferred because of their non-toxicity at high doses. A discussion of the preparation of morpholino oligonucleotides can be found in Antisense & Nuc. Acid Drug Dev. 1997. 7:187.
  • Oligonucleotides and oligonucleotide compositions are contacted with (i.e., brought into contact with, also referred to herein as administered or delivered to) and taken up by one or more cells or a cell lysate.
  • the term “cells” includes prokaryotic and eukaryotic cells, preferably vertebrate cells, and, more preferably, mammalian cells.
  • the oligonucleotide compositions of the invention are contacted with human cells.
  • Oligonucleotide compositions of the invention can be contacted with cells in vitro, e.g., in a test tube or culture dish, (and may or may not be introduced into a subject) or in vivo, e.g., in a subject such as a malian subject. Oligonucleotides are taken up by cells at a slow rate by endocytosis, but endocytosed oligonucleotides are generally sequestered and not available, e.g., for hybridization to a target nucleic acid molecule. In one embodiment, cellular uptake can be facilitated by electroporation or calcium phosphate precipitation. However, these procedures are only useful for in vitro or ex vivo embodiments, are not convenient and, in some cases, are associated with cell toxicity.
  • delivery of oligonucleotides into cells can be enhanced by suitable art recognized methods including calcium phosphate, DMSO, glycerol or dextran, electroporation, or by transfection, e.g., using cationic, anionic, or neutral lipid compositions or liposomes using methods known in the art (see e.g., WO 90/14074; WO 91/16024; WO 91/17424; U.S. Pat. No. 4,897,355; Bergan et al. 1993. Nucleic Acids Research. 21:3567).
  • Enhanced delivery of oligonucleotides can also be mediated by the use of vectors (See e.g., Shi, Y.
  • Conjugating agents bind to the oligonucleotide in a covalent manner.
  • oligonucleotides can be derivitized or chemically modified by binding to a conjugating agent to facilitate cellular uptake.
  • covalent linkage of a cholesterol moiety to an oligonucleotide can improve cellular uptake by 5- to 10-fold which in turn improves DNA binding by about 10-fold (Boutorin et al., 1989, FEBS Letters 254:129-132).
  • Certain protein carriers can also facilitate cellular uptake of oligonucleotides, including, for example, serum albumin, nuclear proteins possessing signals for transport to the nucleus, and viral or bacterial proteins capable of cell membrane penetration. Therefore, protein carriers are useful when associated with or linked to the oligonucleotides.
  • the present invention provides for derivatization of oligonucleotides with groups capable of facilitating cellular uptake, including hydrocarbons and non-polar groups, cholesterol, long chain alcohols (i.e., hexanol), poly-L-lysine and proteins, as well as other aryl or steroid groups and polycations having analogous beneficial effects, such as phenyl or naphthyl groups, quinoline, anthracene or phenanthracene groups, fatty acids, fatty alcohols and sesquiterpenes, diterpenes, and steroids.
  • a major advantage of using conjugating agents is to increase the initial membrane interaction that leads to a greater cellular accumulation of oligonucleotides.
  • an oligonucleotide may be associated with a carrier or vehicle, e.g., liposomes or micelles, although other carriers could be used, as would be appreciated by one skilled in the art.
  • a carrier or vehicle e.g., liposomes or micelles, although other carriers could be used, as would be appreciated by one skilled in the art.
  • Liposomes are vesicles made of a lipid bilayer having a structure similar to biological membranes. Such carriers are used to facilitate the cellular uptake or targeting of the oligonucleotide, or improve the oligonucleotide's pharmacokinetic or toxicologic properties.
  • the oligonucleotides of the present invention may also be administered encapsulated in liposomes, pharmaceutical compositions wherein the active ingredient is contained either dispersed or variously present in corpuscles consisting of aqueous concentric layers adherent to lipidic layers.
  • the oligonucleotides depending upon solubility, may be present both in the aqueous layer and in the lipidic layer, or in what is generally termed a liposomic suspension.
  • the hydrophobic layer generally but not exclusively, comprises phopholipids such as lecithin and sphingomyelin, steroids such as cholesterol, more or less ionic surfactants such as diacetylphosphate, stearylamine, or phosphatidic acid, or other materials of a hydrophobic nature.
  • phopholipids such as lecithin and sphingomyelin
  • steroids such as cholesterol
  • ionic surfactants such as diacetylphosphate, stearylamine, or phosphatidic acid
  • the diameters of the liposomes generally range from about 15 nm to about 5 microns.
  • Liposomes increase intracellular stability, increase uptake efficiency and improve biological activity.
  • Liposomes are hollow spherical vesicles composed of lipids arranged in a similar fashion as those lipids which make up the cell membrane. They have an internal aqueous space for entrapping water soluble compounds and range in size from 0.05 to several microns in diameter.
  • a liposome delivery vehicle originally designed as a research tool, such as Lipofectin can deliver intact nucleic acid molecules to cells.
  • liposomes include the following: they are non-toxic and biodegradable in composition; they display long circulation half-lives; and recognition molecules can be readily attached to their surface for targeting to tissues. Finally, cost-effective manufacture of liposome-based pharmaceuticals, either in a liquid suspension or lyophilized product, has demonstrated the viability of this technology as an acceptable drug delivery system.
  • oligonucleotides of the invention can be complexed with a complexing agent to increase cellular uptake of oligonucleotides.
  • a complexing agent includes cationic lipids. Cationic lipids can be used to deliver oligonucleotides to cells.
  • cationic lipid includes lipids and synthetic lipids having both polar and non-polar domains and which are capable of being positively charged at or around physiological pH and which bind to polyanions, such as nucleic acids, and facilitate the delivery of nucleic acids into cells.
  • cationic lipids include saturated and unsaturated alkyl and alicyclic ethers and esters of amines, amides, or derivatives thereof.
  • Straight-chain and branched alkyl and alkenyl groups of cationic lipids can contain, e.g., from 1 to about 25 carbon atoms.
  • Preferred straight chain or branched alkyl or alkene groups have six or more carbon atoms.
  • Alicyclic groups include cholesterol and other steroid groups.
  • Cationic lipids can be prepared with a variety of counterions (anions) including, e.g., Cl ⁇ , Br ⁇ , I ⁇ , F ⁇ , acetate, trifluoroacetate, sulfate, nitrite, and nitrate.
  • cationic lipids examples include polyethylenimine, polyamidoamine (PAMAM) starburst dendrimers, Lipofectin (a combination of DOTMA and DOPE), Lipofectase, Lipofectamine, DOPE, Cytofectin (Gilead Sciences, Foster City, Calif.), and Eufectins (J B L, San Luis Obispo, Calif.).
  • Exemplary cationic liposomes can be made from N-[1-(2,3-dioleoloxy)-propyl]-N,N,N-trimethylammonium chloride (DOTMA), N-[1-(2,3-dioleoloxy)-propyl]-N,N,N-trimethylammonium methylsulfate (DOTAP), 3 ⁇ -[N-(N′,N′-dimethylaminoethane)carbamoyl]cholesterol (DC-Chol), 2,3,-dioleyloxy-N-[2(sperminecarboxamido)ethyl]-N,N-dimethyl-1-propanaminium trifluoroacetate (DOSPA), 1,2-dimyristyloxypropyl-3-dimethyl-hydroxyethyl ammonium bromide; and dimethyldioctadecylammonium bromide (DDAB).
  • DOTMA N-[1-(
  • DOTMA cationic lipid N-(1-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride
  • Cationic lipids have been used in the art to deliver oligonucleotides to cells (see, e.g., U.S. Pat. Nos. 5,855,910; 5,851,548; 5,830,430; 5,780,053; 5,767,099; Lewis et al. 1996. Proc. Natl. Acad. Sci. USA 93:3176; Hope et al 1998. Molecular Membrane Biology 15:1).
  • Other lipid compositions which can be used to facilitate uptake of the instant oligonucleotides can be used in connection with the claimed methods.
  • other lipid compositions are also known in the art and include, e.g, those taught in U.S. Pat. No. 4,235,871, U.S. Pat. Nos. 4,501,728; 4,837,028; 4,737,323.
  • lipid compositions can further comprise agents, e.g., viral proteins to enhance lipid-mediated transfections of oligonucleotides (Kamata, et al., 1994. Nucl. Acids. Res. 22:536).
  • agents e.g., viral proteins to enhance lipid-mediated transfections of oligonucleotides
  • oligonucleotides are contacted with cells as part of a composition comprising an oligonucleotide, a peptide, and a lipid as taught, e.g., in U.S. Pat. No. 5,736,392.
  • Improved lipids have also been described which are serum resistant (Lewis, et al., 1996. Proc. Natl. Acad. Sci. 93:3176).
  • Cationic lipids and other complexing agents act to increase the number of oligonucleotides carried into the cell through endocytosis.
  • N-substituted glycine oligonucleotides can be used to optimize uptake of oligonucleotides.
  • Peptoids have been used to create cationic lipid-like compounds for transfection (Murphy, et al., 1998. Proc. Natl. Acad. Sci. 95:1517).
  • Peptoids can be synthesized using standard methods (e.g., Zuckermann, R. N., et al. 1992. J. Am. Chem. Soc. 114:10646; Zuckermann, R. N., et al. 1992. Int. J Peptide Protein Res. 40:497).
  • Combinations of cationic lipids and peptoids, liptoids can also be used to optimize uptake of the subject oligonucleotides (Hunag, et al., 1998. Chemistry and Biology. 5:345).
  • Liptoids can be synthesized by elaborating peptoid oligonucleotides and coupling the amino terminal submonomer to a lipid via its amino group (Hunag, et al., 1998. Chemistry and Biology. 5:345).
  • a composition for delivering oligonucleotides of the invention comprises a number of arginine, lysine, histadine or ornithine residues linked to a lipophilic moiety (see e.g., U.S. Pat. No. 5,777,153).
  • composition for delivering oligonucleotides of the invention comprises a peptide having from between about one to about four basic residues. These basic residues can be located, e.g., on the amino terminal, C-terminal, or internal region of the peptide. Families of amino acid residues having similar side chains have been defined in the art.
  • amino acids with basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g., aspartic acid, glutamic acid
  • uncharged polar side chains e.g., glycine (can also be considered non-polar
  • asparagine, glutamine, serine, threonine, tyrosine, cysteine nonpolar side chains
  • nonpolar side chains e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan
  • beta-branched side chains e.g., threonine, valine, isoleucine
  • aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine
  • a majority or all of the other residues of the peptide can be selected from the non-basic amino acids, e.g., amino acids other than lysine, arginine, or histidine.
  • amino acids other than lysine, arginine, or histidine Preferably a preponderance of neutral amino acids with long neutral side chains are used.
  • a peptide such as (N-term) His-Ile-Trp-Leu-Ile-Tyr-Leu-Trp-Ile-Val-(C-term) (SEQ ID NO: ##) could be used.
  • such a composition can be mixed with the fusogenic lipid DOPE as is well known in the art.
  • the cells to be contacted with an oligonucleotide composition of the invention are contacted with a mixture comprising the oligonucleotide and a mixture comprising a lipid, e.g., one of the lipids or lipid compositions described supra for between about 12 h to about 24 h.
  • the cells to be contacted with an oligonucleotide composition are contacted with a mixture comprising the oligonucleotide and a mixture comprising a lipid, e.g., one of the lipids or lipid compositions described supra for between about 1 and about five days.
  • the cells are contacted with a mixture comprising a lipid and the oligonucleotide for between about three days to as long as about 30 days.
  • a mixture comprising a lipid is left in contact with the cells for at least about five to about 20 days.
  • a mixture comprising a lipid is left in contact with the cells for at least about seven to about 15 days.
  • an oligonucleotide composition can be contacted with cells in the presence of a lipid such as cytofectin CS or GSV(available from Glen Research; Sterling, Va.), GS3815, GS2888 for prolonged incubation periods as described herein.
  • a lipid such as cytofectin CS or GSV(available from Glen Research; Sterling, Va.), GS3815, GS2888 for prolonged incubation periods as described herein.
  • the incubation of the cells with the mixture comprising a lipid and an oligonucleotide composition does not reduce the viability of the cells.
  • the cells are substantially viable.
  • the cells are between at least about 70 and at least about 100 percent viable.
  • the cells are between at least about 80 and at least about 95% viable.
  • the cells are between at least about 85% and at least about 90% viable.
  • oligonucleotides are modified by attaching a peptide sequence that transports the oligonucleotide into a cell, referred to herein as a “transporting peptide.”
  • the composition includes an oligonucleotide which is complementary to a target nucleic acid molecule encoding the protein, and a covalently attached transporting peptide.
  • transporting peptide includes an amino acid sequence that facilitates the transport of an oligonucleotide into a cell.
  • Exemplary peptides which facilitate the transport of the moieties to which they are linked into cells are known in the art, and include, e.g., HIV TAT transcription factor, lactoferrin, Herpes VP22 protein, and fibroblast growth factor 2 (Pooga et al. 1998. Nature Biotechnology. 16:857; and Derossi et al. 1998. Trends in Cell Biology. 8:84; Elliott and O'Hare. 1997. Cell 88:223).
  • the transporting peptide comprises an amino acid sequence derived from the antennapedia protein.
  • the peptide comprises amino acids 43-58 of the antennapedia protein (Arg-Gln-Ile-Lys-Ile-Trp-Phe-Gln-Asn-Arg-Arg-Met-Lys-Trp-Lys-Lys) (SEQ ID NO: ##) or a portion or variant thereof that facilitates transport of an oligonucleotide into a cell (see, e.g., WO 91/1898; Derossi et al. 1998. Trends Cell Biol. 8:84). Exemplary variants are shown in Derossi et al., supra.
  • the transporting peptide comprises an amino acid sequence derived from the transportan, galanin (1-12)-Lys-mastoparan (1-14) amide, protein. (Pooga et al. 1998. Nature Biotechnology 16:857).
  • the peptide comprises the amino acids of the transportan protein shown in the sequence GWTLNSAGYLLGKFNLKALAALAKKIL (SEQ ID NO: ##) or a portion or variant thereof that facilitates transport of an oligonucleotide into a cell.
  • the transporting peptide comprises an amino acid sequence derived from the HIV TAT protein.
  • the peptide comprises amino acids 37-72 of the HIV TAT protein, e.g., shown in the sequence C(Acm)FITKALGISYGRKKRRQRRRPPQC (SEQ ID NO: ##) (TAT 37-60; where C(Acm) is Cys-acetamidomethyl) or a portion or variant thereof, e.g., C(Acm)GRKKRRQRRRPPQC (SEQ ID NO: ##)(TAT 48-40) or C(Acm)LGISYGRKKRRQRRPPQC (SEQ ID NO: ##) (TAT 43-60) that facilitates transport of an oligonucleotide into a cell (Vives et al. 1997. J. Biol. Chem. 272:16010).
  • the peptide (G)CFITKALGISYGRKKRRQRRRPPQGSQTH e.g., shown in the sequence
  • Portions or variants of transporting peptides can be readily tested to determine whether they are equivalent to these peptide portions by comparing their activity to the activity of the native peptide, e.g., their ability to transport fluorescently-labeled oligonucleotides to cells. Fragments or variants that retain the ability of the native transporting peptide to transport an oligonucleotide into a cell are functionally equivalent and can be substituted for the native peptides.
  • Oligonucleotides can be attached to the transporting peptide using known techniques, e.g., ( Prochiantz, A. 1996. Curr. Opin. Neurobiol. 6:629; Derossi et al. 1998. Trends Cell Biol. 8:84; Troy et al. 1996. J. Neurosci. 16:253), Vives et al. 1997. J. Biol. Chem. 272:16010).
  • oligonucleotides bearing an activated thiol group are linked via that thiol group to a cysteine present in a transport peptide (e.g., to the cysteine present in the ⁇ turn between the second and the third helix of the antennapedia homeodomain as taught, e.g., in Derossi et al. 1998. Trends Cell Biol. 8:84; Prochiantz. 1996. Current Opinion in Neurobiol. 6:629; Allinquant et al. 1995. J Cell Biol. 128:919).
  • a transport peptide e.g., to the cysteine present in the ⁇ turn between the second and the third helix of the antennapedia homeodomain as taught, e.g., in Derossi et al. 1998. Trends Cell Biol. 8:84; Prochiantz. 1996. Current Opinion in Neurobiol. 6:629; Allinquant et al. 1995. J Cell Biol. 128
  • a Boc-Cys-(Npys)OH group can be coupled to the transport peptide as the last (N-terminal) amino acid and an oligonucleotide bearing an SH group can be coupled to the peptide (Troy et al. 1996. J. Neurosci. 16:253).
  • a linking group can be attached to a nucleomonomer and the transporting peptide can be covalently attached to the linker.
  • a linker can function as both an attachment site for a transporting peptide and can provide stability against nucleases. Examples of suitable linkers include substituted or unsubstituted C 1 -C 20 alkyl chains, C 2 -C 20 alkenyl chains, C 2 -C 20 alkynyl chains, peptides, and heteroatoms (e.g., S, O, NH, etc.).
  • linkers include bifunctional crosslinking agents such as sulfosuccinimidyl-4-(maleimidophenyl)-butyrate (SMPB) (see, e.g., Smith et al. Biochem J 1991. 276: 417-2).
  • SMPB sulfosuccinimidyl-4-(maleimidophenyl)-butyrate
  • oligonucleotides of the invention are synthesized as molecular conjugates which utilize receptor-mediated endocytotic mechanisms for delivering genes into cells (see, e.g., Bunnell et al. 1992. Somatic Cell and Molecular Genetics. 18:559 and the references cited therein).
  • the delivery of oligonucleotides can also be improved by targeting the oligonucleotides to a cellular receptor.
  • the targeting moieties can be conjugated to the oligonucleotides or attached to a carrier group (i.e., poly(L-lysine) or liposomes) linked to the oligonucleotides. This method is well suited to cells that display specific receptor-mediated endocytosis.
  • oligonucleotide conjugates to 6-phosphomannosylated proteins are internalized 20-fold more efficiently by cells expressing mannose 6-phosphate specific receptors than free oligonucleotides.
  • the oligonucleotides may also be coupled to a ligand for a cellular receptor using a biodegradable linker.
  • the delivery construct is mannosylated streptavidin which forms a tight complex with biotinylated oligonucleotides.
  • Mannosylated streptavidin was found to increase 20-fold the internalization of biotinylated oligonucleotides. (Vlassov et al. 1994. Biochimica et Biophysica Acta 1197:95-108).
  • polylysine component can be conjugated to the polylysine component of polylysine-based delivery systems.
  • transferrin-polylysine, adenovirus-polylysine, and influenza virus hemagglutinin HA-2 N-terminal fusogenic peptides-polylysine conjugates greatly enhance receptor-mediated DNA delivery in eucaryotic cells.
  • Mannosylated glycoprotein conjugated to poly(L-lysine) in aveolar macrophages has been employed to enhance the cellular uptake of oligonucleotides. Liang et al. 1999. Pharmazie 54:559-566.
  • oligonucleotide uptake is seen in promyelocytic leukaemia (HL-60) cells and human melanoma (M-14) cells. Ginobbi et al. 1997. Anticancer Res. 17:29.
  • liposomes coated with maleylated bovine serum albumin, folic acid, or ferric protoporphyrin IX show enhanced cellular uptake of oligonucleotides in murine macrophages, KB cells, and 2.2.15 human hepatoma cells. Liang et al. 1999. Pharmazie 54:559-566.
  • Liposomes naturally accumulate in the liver, spleen, and reticuloendothelial system (so-called, passive targeting). By coupling liposomes to various ligands such as antibodies are protein A, they can be actively targeted to specific cell populations. For example, protein A-bearing liposomes may be pretreated with H-2K specific antibodies which are targeted to the mouse major histocompatibility complex-encoded H-2K protein expressed on L cells. (Vlassov et al. 1994. Biochimica et Biophysica Acta 1197:95-108).
  • the double-stranded oligonucleotides of the invention are stabilized, i.e., substantially resistant to endonuclease and exonuclease degradation.
  • An oligonucleotide is defined as being substantially resistant to nucleases when it is at least about 3-fold more resistant to attack by an endogenous cellular nuclease, and is highly nuclease resistant when it is at least about 6-fold more resistant than a corresponding, single-stranded oligonucleotide. This can be demonstrated by showing that the oligonucleotides of the invention are substantially resist nucleases using techniques which are known in the art.
  • oligonucleotides of the invention function when delivered to a cell, e.g., that they reduce transcription or translation of target nucleic acid molecules, e.g., by measuring protein levels or by measuring cleavage of mRNA.
  • Assays which measure the stability of target RNA can be performed at about 24 hours post-transfection (e.g., using Northern blot techniques, RNase Protection Assays, or QC-PCR assays as known in the art). Alternatively, levels of the target protein can be measured.
  • RNA or protein levels of a control, non-targeted gene will be measured (e.g., actin, or preferably a control with sequence similarity to the target) as a specificity control.
  • RNA or protein measurements can be made using any art-recognized technique. Preferably, measurements will be made beginning at about 16-24 hours post transfection. (M. Y. Chiang, et al. 1991. J. Biol Chem. 266:18162-71; T. Fisher, et al. 1993. Nucleic Acids Research. 21 3857).
  • RNA encoding a particular protein can be measured using techniques which are known in the art, for example, by detecting an inhibition in gene transcription or protein synthesis. For example, Nuclease S1 mapping can be performed.
  • Northern blot analysis can be used to measure the presence of RNA encoding a particular protein. For example, total RNA can be prepared over a cesium chloride cushion (see, e.g., Ausebel et al., 1987. Current Protocols in Molecular Biology (Greene & Wiley, New York)). Northern blots can then be made using the RNA and probed (see, e.g., Id.).
  • the level of the specific mRNA produced by the target protein can be measured, e.g., using PCR.
  • Western blots can be used to measure the amount of target protein present.
  • a phenotype influenced by the amount of the protein can be detected. Techniques for performing Western blots are well known in the art, see, e.g., Chen et al. J. Biol. Chem. 271:28259.
  • the promoter sequence of a target gene can be linked to a reporter gene and reporter gene transcription (e.g., as described in more detail below) can be monitored.
  • reporter gene transcription e.g., as described in more detail below
  • oligonucleotide compositions that do not target a promoter can be identified by fusing a portion of the target nucleic acid molecule with a reporter gene so that the reporter gene is transcribed.
  • By monitoring a change in the expression of the reporter gene in the presence of the oligonucleotide composition it is possible to determine the effectiveness of the oligonucleotide composition in inhibiting the expression of the reporter gene. For example, in one embodiment, an effective oligonucleotide composition will reduce the expression of the reporter gene.
  • a “reporter gene” is a nucleic acid that expresses a detectable gene product, which may be RNA or protein. Detection of mRNA expression may be accomplished by Northern blotting and detection of protein may be accomplished by staining with antibodies specific to the protein. Preferred reporter genes produce a readily detectable product.
  • a reporter gene may be operably linked with a regulatory DNA sequence such that detection of the reporter gene product provides a measure of the transcriptional activity of the regulatory sequence.
  • the gene product of the reporter gene is detected by an intrinsic activity associated with that product.
  • the reporter gene may encode a gene product that, by enzymatic activity, gives rise to a detectable signal based on color, fluorescence, or luminescence. Examples of reporter genes include, but are not limited to, those coding for chloramphenicol acetyl transferase (CAT), luciferase, ⁇ -galactosidase, and alkaline phosphatase.
  • CAT chloramphenicol acety
  • reporter genes suitable for use in the present invention. These include, but are not limited to, chloramphenicol acetyltransferase (CAT), luciferase, human growth hormone (hGH), and beta-galactosidase. Examples of such reporter genes can be found in F. A. Ausubel et al., Eds., Current Protocols in Molecular Biology, John Wiley & Sons, New York, (1989). Any gene that encodes a detectable product, e.g., any product having detectable enzymatic activity or against which a specific antibody can be raised, can be used as a reporter gene in the present methods.
  • CAT chloramphenicol acetyltransferase
  • hGH human growth hormone
  • beta-galactosidase beta-galactosidase
  • One reporter gene system is the firefly luciferase reporter system.
  • the luciferase assay is fast and sensitive. In this assay, a lysate of the test cell is prepared and combined with ATP and the substrate luciferin. The encoded enzyme luciferase catalyzes a rapid, ATP dependent oxidation of the substrate to generate a light-emitting product. The total light output is measured and is proportional to the amount of luciferase present over a wide range of enzyme concentrations.
  • CAT is another frequently used reporter gene system; a major advantage of this system is that it has been an extensively validated and is widely accepted as a measure of promoter activity. (Gorman C. M., Moffat, L. F., and Howard, B. H. 1982. Mol. Cell. Biol., 2:1044-1051).
  • test cells are transfected with CAT expression vectors and incubated with the candidate substance within 2-3 days of the initial transfection. Thereafter, cell extracts are prepared. The extracts are incubated with acetyl CoA and radioactive chloramphenicol. Following the incubation, acetylated chloramphenicol is separated from nonacetylated form by thin layer chromatography. In this assay, the degree of acetylation reflects the CAT gene activity with the particular promoter.
  • Another suitable reporter gene system is based on immunologic detection of hGH. This system is also quick and easy to use. (Selden, R., Burke-Howie, K. Rowe, M. E., Goodman, H. M., and Moore, D. D. (1986), Mol. Cell, Biol., 6:3173-3179 incorporated herein by reference).
  • the hGH system is advantageous in that the expressed hGH polypeptide is assayed in the media, rather than in a cell extract. Thus, this system does not require the destruction of the test cells. It will be appreciated that the principle of this reporter gene system is not limited to hGH but rather adapted for use with any polypeptide for which an antibody of acceptable specificity is available or can be prepared.
  • nuclease stability of a double-stranded oligonucleotide of the invention is measured and compared to a control, e.g., an RNAi molecule typically used in the art (e.g., a duplex oligonucleotide of less than 25 nucleotides in length and comprising 2 nucleotide base overhangs) or an unmodified RNA duplex with blunt ends.
  • a control e.g., an RNAi molecule typically used in the art (e.g., a duplex oligonucleotide of less than 25 nucleotides in length and comprising 2 nucleotide base overhangs) or an unmodified RNA duplex with blunt ends.
  • Oligonucleotides of the invention can be synthesized by any method known in the art, e.g., using enzymatic synthesis and chemical synthesis.
  • the oligonucleotides can be synthesized in vitro (e.g., using enzymatic synthesis and chemical synthesis) or in vivo (using recombinant DNA technology well known in the art).
  • chemical synthesis is used.
  • Chemical synthesis of linear oligonucleotides is well known in the art and can be achieved by solution or solid phase techniques. Preferably, synthesis is by solid phase methods. Oligonucleotides can be made by any of several different synthetic procedures including the phosphoramidite, phosphite triester, H-phosphonate, and phosphotriester methods, typically by automated synthesis methods.
  • Oligonucleotide synthesis protocols are well known in the art and can be found, e.g., in U.S. Pat. No. 5,830,653; WO 98/13526; Stec et al. 1984. J. Am. Chem. Soc. 106:6077; Stec et al. 1985. J. Org. Chem. 50:3908; Stec et al. J. Chromatog. 1985. 326:263; LaPlanche et al. 1986. Nuc. Acid. Res. 1986. 14:9081; Fasman G. D., 1989. Practical Handbook of Biochemistry and Molecular Biology. 1989. CRC Press, Boca Raton, Fla.; Lamone. 1993. Biochem. Soc.
  • the synthesis method selected can depend on the length of the desired oligonucleotide and such choice is within the skill of the ordinary artisan.
  • the phosphoramidite and phosphite triester method can produce oligonucleotides having 175 or more nucleotides while the H-phosphonate method works well for oligonucleotides of less than 100 nucleotides. If modified bases are incorporated into the oligonucleotide, and particularly if modified phosphodiester linkages are used, then the synthetic procedures are altered as needed according to known procedures. In this regard, Uhlmann et al.
  • the oligonucleotides may be purified by polyacrylamide gel electrophoresis, or by any of a number of chromatographic methods, including gel chromatography and high pressure liquid chromatography.
  • oligonucleotides may be subjected to DNA sequencing by any of the known procedures, including Maxam and Gilbert sequencing, Sanger sequencing, capillary electrophoresis sequencing the wandering spot sequencing procedure or by using selective chemical degradation of oligonucleotides bound to Hybond paper. Sequences of short oligonucleotides can also be analyzed by laser desorption mass spectroscopy or by fast atom bombardment (McNeal, et al., 1982, J. Am. Chem.
  • oligonucleotides synthesized can be verified by testing the oligonucleotide by capillary electrophoresis and denaturing strong anion HPLC (SAX-HPLC) using, e.g., the method of Bergot and Egan. 1992. J. Chrom. 599:35.
  • SAX-HPLC denaturing strong anion HPLC
  • This invention also features methods of inhibiting expression of a protein in a cell including contacting the cell with one of the above-described oligonucleotide compositions.
  • oligonucleotides of the invention can be used in a variety of in vitro and in vivo situations to specifically inhibit protein expression.
  • the instant methods and compositions are suitable for both in vitro and in vivo use.
  • the methods of the invention may be used for determining the function of a gene in a cell or an organism or for modulating the function of a gene in a cell or an organism, being capable of responding to or mediating RNA interference.
  • the cell is preferably a eukaryotic cell or a cell line, e.g., an animal cell such as a mammalian cell, e.g., an embryonic cell, a pluripotent stem cell, a tumor cell, e.g., a teratocarcinoma cell, or a virus-infected cell.
  • the organism is preferably a eukaryotic organism, e.g., an animal such as a mammal, particularly a human.
  • the invention includes methods to inhibit expression of a target gene in a cell in vitro.
  • methods to inhibit expression of a target gene in a cell in vitro may include introduction of RNA into a cell in an amount sufficient to inhibit expression of the target gene, where the RNA is a double-stranded molecule of the invention.
  • such an RNA molecule may have a first strand consisting essentially of a ribonucleotide sequence that corresponds to a nucleotide sequence of the target gene, and a second strand consisting essentially of a ribonucleotide sequence that is complementary to the nucleotide sequence of the target gene, in which the first and the second strands are separate complementary strands or are joined by a loop, and they hybridize to each other to form said double-stranded molecule, such that the duplex composition inhibits expression of the target gene.
  • the duplex composition may include modified nucleomonomers as discussed above.
  • the invention also relates to a method to inhibit expression of a target gene in an invertebrate organism.
  • Such methods include providing an invertebrate organism containing a target cell that contains the target gene, in which the target cell is susceptible to RNA interference and the target gene is expressed in the target cell.
  • Such methods further include contacting the invertebrate organism with an RNA composition of the invention.
  • the RNA may be a double-stranded molecule with a first strand consisting essentially of a ribonucleotide sequence that corresponds to a nucleotide sequence of the target gene and a second strand consisting essentially of a ribonucleotide sequence that is complementary to the nucleotide sequence of the target gene.
  • the first and the second ribonucleotide sequences may be separate complementary strands or joined by a loop, and they hybridize to each other to form the double-stranded molecule.
  • such methods include a step of introducing the duplex RNA composition into the target cell to thereby inhibiting expression of the target gene.
  • the oligonucleotides of the invention can be used to inhibit gene function in vitro in a method for identifying the functions of genes. In this manner, the transcription of genes that are identified, but for which no function has yet been shown, can be inhibited to thereby determine how the phenotype of a cell is changed when the gene is not transcribed. Such methods are useful for the validation of genes as targets for clinical treatment, e.g., with oligonucleotides or with other therapies.
  • nucleic acid probes e.g., in the form of arrays
  • Probes can also be used detect peptides, proteins, or protein domains, e.g., antibodies can be used to detect the expression of a particular protein.
  • the function of a protein e.g., enzymatic activity
  • the phenotype of a cell can be evaluated to determine whether or not a target protein is expressed. For example, the ability of a composition to affect a phenotype of a cell that is associated with cancer can be tested.
  • one or more additional agents e.g., activating agents, inducing agents, proliferation enhancing agents, tumor promoters
  • activating agents e.g., activating agents, inducing agents, proliferation enhancing agents, tumor promoters
  • additional agents e.g., activating agents, inducing agents, proliferation enhancing agents, tumor promoters
  • compositions of the invention can be used to monitor biochemical reactions such as, e.g., interactions of proteins, nucleic acids, small molecules, or the like, for example the efficiency or specificity of interactions between antigens and antibodies; or of receptors (such as purified receptors or receptors bound to cell membranes) and their ligands, agonists or antagonists; or of enzymes (such as proteases or kinases) and their substrates, or increases or decreases in the amount of substrate converted to a product; as well as many others.
  • biochemical assays can be used to characterize properties of the probe or target, or as the basis of a screening assay.
  • the samples can be assayed, for example using probes which are fluorogenic substrates specific for each protease of interest. If a target protease binds to and cleaves a substrate, the substrate will fluoresce, usually as a result, e.g., of cleavage and separation between two energy transfer pairs, and the signal can be detected.
  • proteases e.g., proteases involved in blood clotting such as proteases Xa and VIIa
  • probes which are fluorogenic substrates specific for each protease of interest. If a target protease binds to and cleaves a substrate, the substrate will fluoresce, usually as a result, e.g., of cleavage and separation between two energy transfer pairs, and the signal can be detected.
  • samples containing one or more kinases of interest can be assayed, e.g., using probes are peptides which can be selectively phosphorylated by one of the kinases of interest.
  • probes are peptides which can be selectively phosphorylated by one of the kinases of interest.
  • reactions can be stopped, e.g., by washing and the phosphorylated substrates can be detected by, for example, incubating them with detectable reagents such as, e.g., fluorescein-labeled anti-phosphotyrosine or anti-phosphoserine antibodies and the signal can be detected.
  • detectable reagents such as, e.g., fluorescein-labeled anti-phosphotyrosine or anti-phosphoserine antibodies and the signal can be detected.
  • compositions of the invention can be used to screen for agents which modulate a pattern of gene expression.
  • Arrays of oligonucleotides can be used, for example, to identify mRNA species whose pattern of expression from a set of genes is correlated with a particular physiological state or developmental stage, or with a disease condition (“correlative” genes, RNAs, or expression patterns).
  • correlate or “correlative,” it is meant that the synthesis pattern of RNA is associated with the physiological condition of a cell, but not necessarily that the expression of a given RNA is responsible for or is causative of a particular physiological state.
  • mRNAs can be identified which are modulated (e.g., upregulated or downregulated) in cells which serve as a model for a particular disease state.
  • This altered pattern of expression as compared to that in a normal cell, which does not exhibit a pathological phenotype, can serve as a indicator of the disease state (“indicator” or “correlatvie” genes, RNAs, or expression patterns).
  • compositions which modulate the chosen indicator expression pattern can indicate that a particular target gene is a potential target for therapeutic intervention.
  • compositions may be useful as therapeutic agents to modulate expression patters of cells in an in vitro expression system or in in vivo therapy.
  • modulate means to cause to increase or decrease the amount or activity of a molecule or the like which is involved in a measurable reaction.
  • a series of cells e.g., from a disease model
  • a series of agents e.g., for a period of time ranging from about 10 minutes to about 48 hours or more
  • routine, art-recognized methods e.g., commercially available kits
  • total RNA or mRNA extracts can be made.
  • standard procedures such as RT-PCR amplification can be used (see, e.g., Innis et al eds., (1996) PCR Protocols: A Guide to Methods in Amplification, Academic Press, New York).
  • the extracts (or amplified products from them) can be allowed to contact (e.g., incubate with) probes for appropriate indicator RNAs, and those agents which are associated with a change in the indicator expression pattern can be identified.
  • agents can be identified which modulate expression patterns associated with particular physiological states or developmental stages.
  • agents can be man-made or naturally-occurring substances, including environmental factors such as substances involved in embryonic development or in regulating physiological reactions.
  • the methods described herein can be performed in a “high throughput” manner, in which a large number of target genes (e.g., as many as about 1000 or more, depending on the particular format used) are assayed rapidly and concurrently. Further, many assay formats (e.g., plates or surfaces) can be processed at one time. For example, because the oligonucleotides of the invention do not need to be tested individually before incorporating them into a composition, they can be readily synthesized and large numbers of target genes can be tested at one time.
  • a large number of samples each comprising a biological sample containing a target nucleic acid molecule (e.g., a cell) and a composition of the invention can be added to separate regions of an assay format and assays can be performed on each of the samples.
  • a target nucleic acid molecule e.g., a cell
  • the optimal course of administration or delivery of the oligonucleotides may vary depending upon the desired result and/or on the subject to be treated.
  • administration refers to contacting cells with oligonucleotides and can be performed in vitro or in vivo.
  • the dosage of oligonucleotides may be adjusted to optimally reduce expression of a protein translated from a target nucleic acid molecule, e.g., as measured by a readout of RNA stability or by a therapeutic response, without undue experimentation.
  • expression of the protein encoded by the nucleic acid target can be measured to determine whether or not the dosage regimen needs to be adjusted accordingly.
  • an increase or decrease in RNA or protein levels in a cell or produced by a cell can be measured using any art recognized technique. By determining whether transcription has been decreased, the effectiveness of the oligonucleotide in inducing the cleavage of a target RNA can be determined.
  • any of the above-described oligonucleotide compositions can be used alone or in conjunction with a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier includes appropriate solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, it can be used in the therapeutic compositions. Supplementary active ingredients can also be incorporated into the compositions.
  • Oligonucleotides may be incorporated into liposomes or liposomes modified with polyethylene glycol or admixed with cationic lipids for parenteral administration. Incorporation of additional substances into the liposome, for example, antibodies reactive against membrane proteins found on specific target cells, can help target the oligonucleotides to specific cell types.
  • the present invention provides for administering the subject oligonucleotides with an osmotic pump providing continuous infusion of such oligonucleotides, for example, as described in Rataiczak et al. (1992 Proc. Natl. Acad. Sci. USA 89:11823-11827).
  • an osmotic pump providing continuous infusion of such oligonucleotides, for example, as described in Rataiczak et al. (1992 Proc. Natl. Acad. Sci. USA 89:11823-11827).
  • Such osmotic pumps are commercially available, e.g., from Alzet Inc. (Palo Alto, Calif.). Topical administration and parenteral administration in a cationic lipid carrier are preferred.
  • the formulations of the present invention can be administered to a patient in a variety of forms adapted to the chosen route of administration, e.g., parenterally, orally, or intraperitoneally.
  • Parenteral administration which is preferred, includes administration by the following routes: intravenous; intramuscular; interstitially; intraarterially; subcutaneous; intra ocular; intrasynovial; trans epithelial, including transdermal; pulmonary via inhalation; ophthalmic; sublingual and buccal; topically, including ophthalmic; dermal; ocular; rectal; and nasal inhalation via insufflation.
  • compositions for parenteral administration include aqueous solutions of the active compounds in water-soluble or water-dispersible form.
  • suspensions of the active compounds as appropriate oily injection suspensions may be administered.
  • Suitable lipophilic solvents or vehicles include fatty oils, for example, sesame oil, or synthetic fatty acid esters, for example, ethyl oleate or triglycerides.
  • Aqueous injection suspensions may contain substances which increase the viscosity of the suspension include, for example, sodium carboxymethyl cellulose, sorbitol, or dextran, optionally, the suspension may also contain stabilizers.
  • the oligonucleotides of the invention can be formulated in liquid solutions, preferably in physiologically compatible buffers such as Hank's solution or Ringer's solution.
  • the oligonucleotides may be formulated in solid form and redissolved or suspended immediately prior to use. Lyophilized forms are also included in the invention.
  • compositions for topical administration include transdermal patches, ointments, lotions, creams, gels, drops, sprays, suppositories, liquids and powders.
  • conventional pharmaceutical carriers, aqueous, powder or oily bases, or thickeners may be used in pharmaceutical preparations for topical administration.
  • compositions for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets or tablets.
  • thickeners, flavoring agents, diluents, emulsifiers, dispersing aids, or binders may be used in pharmaceutical preparations for oral administration.
  • penetrants appropriate to the barrier to be permeated are used in the formulation.
  • penetrants are known in the art, and include, for example, for transmucosal administration bile salts and fusidic acid derivatives, and detergents.
  • Transmucosal administration may be through nasal sprays or using suppositories.
  • the oligonucleotides are formulated into conventional oral administration forms such as capsules, tablets, and tonics.
  • topical administration the oligonucleotides of the invention are formulated into ointments, salves, gels, or creams as known in the art.
  • Drug delivery vehicles can be chosen e.g., for in vitro, for systemic, or for topical administration. These vehicles can be designed to serve as a slow release reservoir or to deliver their contents directly to the target cell.
  • An advantage of using some direct delivery drug vehicles is that multiple molecules are delivered per uptake. Such vehicles have been shown to increase the circulation half-life of drugs that would otherwise be rapidly cleared from the blood stream.
  • Some examples of such specialized drug delivery vehicles which fall into this category are liposomes, hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres.
  • the described oligonucleotides may be administered systemically to a subject.
  • Systemic absorption refers to the entry of drugs into the blood stream followed by distribution throughout the entire body.
  • Administration routes which lead to systemic absorption include: intravenous, subcutaneous, intraperitoneal, and intranasal. Each of these administration routes delivers the oligonucleotide to accessible diseased cells.
  • the therapeutic agent drains into local lymph nodes and proceeds through the lymphatic network into the circulation.
  • the rate of entry into the circulation has been shown to be a function of molecular weight or size.
  • the use of a liposome or other drug carrier localizes the oligonucleotide at the lymph node.
  • the oligonucleotide can be modified to diffuse into the cell, or the liposome can directly participate in the delivery of either the unmodified or modified oligonucleotide into the cell.
  • Preferred delivery methods include liposomes (10-400 nm), hydrogels, controlled-release polymers, and other pharmaceutically applicable vehicles, and microinjection or electroporation (for ex vivo treatments).
  • the pharmaceutical preparations of the present invention may be prepared and formulated as emulsions.
  • Emulsions are usually heterogenous systems of one liquid dispersed in another in the form of droplets usually exceeding 0.1 ⁇ m in diameter.
  • the emulsions of the present invention may contain excipients such as emulsifiers, stabilizers, dyes, fats, oils, waxes, fatty acids, fatty alcohols, fatty esters, humectants, hydrophilic colloids, preservatives, and anti-oxidants may also be present in emulsions as needed. These excipients may be present as a solution in either the aqueous phase, oily phase or itself as a separate phase.
  • excipients such as emulsifiers, stabilizers, dyes, fats, oils, waxes, fatty acids, fatty alcohols, fatty esters, humectants, hydrophilic colloids, preservatives, and anti-oxidants may also be present in emulsions as needed.
  • excipients may be present as a solution in either the aqueous phase, oily phase or itself as a separate phase.
  • Examples of naturally occurring emulsifiers that may be used in emulsion formulations of the present invention include lanolin, beeswax, phosphatides, lecithin and acacia. Finely divided solids have also been used as good emulsifiers especially in combination with surfactants and in viscous preparations. Examples of finely divided solids that may be used as emulsifiers include polar inorganic solids, such as heavy metal hydroxides, nonswelling clays such as bentonite, attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum silicate and colloidal magnesium aluminum silicate, pigments and nonpolar solids such as carbon or glyceryl tristearate.
  • polar inorganic solids such as heavy metal hydroxides, nonswelling clays such as bentonite, attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum silicate and colloidal magnesium aluminum silicate, pigments and
  • Examples of preservatives that may be included in the emulsion formulations include methyl paraben, propyl paraben, quaternary ammonium salts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boric acid.
  • Examples of antioxidants that may be included in the emulsion formulations include free radical scavengers such as tocopherols, alkyl gallates, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium metabisulfite, and antioxidant synergists such as citric acid, tartaric acid, and lecithin.
  • compositions of oligonucleotides are formulated as microemulsions.
  • a microemulsion is a system of water, oil and amphiphile which is a single optically isotropic and thermodynamically stable liquid solution.
  • microemulsions are prepared by first dispersing an oil in an aqueous surfactant solution and then adding a sufficient amount of a 4th component, generally an intermediate chain-length alcohol to form a transparent system.
  • Surfactants that may be used in the preparation of microemulsions include, but are not limited to, ionic surfactants, non-ionic surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol fatty acid esters, tetraglycerol monolaurate (ML310), tetraglycerol monooleate (MO310), hexaglycerol monooleate (PO310), hexaglycerol pentaoleate (PO500), decaglycerol monocaprate (MCA750), decaglycerol monooleate (MO750), decaglycerol sequioleate (SO750), decaglycerol decaoleate (DA0750), alone or in combination with cosurfactants.
  • ionic surfactants etraglycerol monolaurate
  • MO310 tetraglycerol monooleate
  • PO310 hexaglycerol monooleate
  • PO500 he
  • the cosurfactant usually a short-chain alcohol such as ethanol, 1-propanol, and 1-butanol, serves to increase the interfacial fluidity by penetrating into the surfactant film and consequently creating a disordered film because of the void space generated among surfactant molecules.
  • a short-chain alcohol such as ethanol, 1-propanol, and 1-butanol
  • Microemulsions may, however, be prepared without the use of cosurfactants and alcohol-free self-emulsifying microemulsion systems are known in the art.
  • the aqueous phase may typically be, but is not limited to, water, an aqueous solution of the drug, glycerol, PEG300, PEG400, polyglycerols, propylene glycols, and derivatives of ethylene glycol.
  • the oil phase may include, but is not limited to, materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C 8 -C 12 ) mono, di, and tri-glycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C 8 -C 10 glycerides, vegetable oils and silicone oil.
  • materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C 8 -C 12 ) mono, di, and tri-glycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C 8 -C 10 glycerides, vegetable oils and silicone oil.
  • Microemulsions are particularly of interest from the standpoint of drug solubilization and the enhanced absorption of drugs.
  • Lipid based microemulsions both oil/water and water/oil have been proposed to enhance the oral bioavailability of drugs.
  • Microemulsions offer improved drug solubilization, protection of drug from enzymatic hydrolysis, possible enhancement of drug absorption due to surfactant-induced alterations in membrane fluidity and permeability, ease of preparation, ease of oral administration over solid dosage forms, improved clinical potency, and decreased toxicity (Constantinides et al., Pharmaceutical Research, 1994, 11:1385; Ho et al., J. Pharm. Sci., 1996, 85:138-143). Microemulsions have also been effective in the transdermal delivery of active components in both cosmetic and pharmaceutical applications.
  • microemulsion compositions and formulations of the present invention will facilitate the increased systemic absorption of oligonucleotides from the gastrointestinal tract, as well as improve the local cellular uptake of oligonucleotides within the gastrointestinal tract, vagina, buccal cavity and other areas of administration.
  • the present invention employs various penetration enhancers to effect the efficient delivery of nucleic acids, particularly oligonucleotides, to the skin of animals.
  • nucleic acids particularly oligonucleotides
  • the present invention employs various penetration enhancers to effect the efficient delivery of nucleic acids, particularly oligonucleotides, to the skin of animals.
  • non-lipophilic drugs may cross cell membranes if the membrane to be crossed is treated with a penetration enhancer.
  • penetration enhancers also act to enhance the permeability of lipophilic drugs.
  • Five categories of penetration enhancers that may be used in the present invention include: surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants.
  • Other agents may be utilized to enhance the penetration of the administered oligonucleotides include: glycols such as ethylene glycol and propylene glycol, pyrrols such as 2-15 pyrrol, azones, and terpenes such as limonene, and menthone.
  • the oligonucleotides, especially in lipid formulations, can also be administered by coating a medical device, for example, a catheter, such as an angioplasty balloon catheter, with a cationic lipid formulation. Coating may be achieved, for example, by dipping the medical device into a lipid formulation or a mixture of a lipid formulation and a suitable solvent, for example, an aqueous-based buffer, an aqueous solvent, ethanol, methylene chloride, chloroform and the like. An amount of the formulation will naturally adhere to the surface of the device which is subsequently administered to a patient, as appropriate. Alternatively, a lyophilized mixture of a lipid formulation may be specifically bound to the surface of the device. Such binding techniques are described, for example, in K. Ishihara et al., Journal of Biomedical Materials Research, Vol. 27, pp. 1309-1314 (1993), the disclosures of which are incorporated herein by reference in their entirety.
  • the useful dosage to be administered and the particular mode of administration will vary depending upon such factors as the cell type, or for in vivo use, the age, weight and the particular animal and region thereof to be treated, the particular oligonucleotide and delivery method used, the therapeutic or diagnostic use contemplated, and the form of the formulation, for example, suspension, emulsion, micelle or liposome, as will be readily apparent to those skilled in the art.
  • dosage is administered at lower levels and increased until the desired effect is achieved.
  • the amount of lipid compound that is administered can vary and generally depends upon the amount of oligonucleotide agent being administered.
  • the weight ratio of lipid compound to oligonucleotide agent is preferably from about 1:1 to about 15:1, with a weight ratio of about 5:1 to about 10:1 being more preferred.
  • the amount of cationic lipid compound which is administered will vary from between about 0.1 milligram (mg) to about 1 gram (g).
  • mg milligram
  • g 1 gram
  • the agents of the invention are administered to subjects or contacted with cells in a biologically compatible form suitable for pharmaceutical administration.
  • biologically compatible form suitable for administration is meant that the oligonucleotide is administered in a form in which any toxic effects are outweighed by the therapeutic effects of the oligonucleotide.
  • oligonucleotides can be administered to subjects. Examples of subjects include mammals, e.g., humans and other primates; cows, pigs, horses, and farming (agricultural) animals; dogs, cats, and other domesticated pets; mice, rats, and transgenic non-human animals.
  • an active amount of an oligonucleotide of the present invention is defined as an amount effective, at dosages and for periods of time necessary to achieve the desired result.
  • an active amount of an oligonucleotide may vary according to factors such as the type of cell, the oligonucleotide used, and for in vivo uses the disease state, age, sex, and weight of the individual, and the ability of the oligonucleotide to elicit a desired response in the individual.
  • Establishment of therapeutic levels of oligonucleotides within the cell is dependent upon the rates of uptake and efflux or degradation. Decreasing the degree of degradation prolongs the intracellular half-life of the oligonucleotide.
  • chemically-modified oligonucleotides e.g., with modification of the phosphate backbone, may require different dosing.
  • oligonucleotide The exact dosage of an oligonucleotide and number of doses administered will depend upon the data generated experimentally and in clinical trials. Several factors such as the desired effect, the delivery vehicle, disease indication, and the route of administration, will affect the dosage. Dosages can be readily determined by one of ordinary skill in the art and formulated into the subject pharmaceutical compositions. Preferably, the duration of treatment will extend at least through the course of the disease symptoms.
  • Dosage periods may be adjusted to provide the optimum therapeutic response.
  • the oligonucleotide may be repeatedly administered, e.g., several doses may be administered daily or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation.
  • One of ordinary skill in the art will readily be able to determine appropriate doses and schedules of administration of the subject oligonucleotides, whether the oligonucleotides are to be administered to cells or to subjects.
  • the oligonucleotide compositions of the present invention can be used to treat any disease involving the expression of a protein.
  • diseases that can be treated by oligonucleotide compositions include: cancer, retinopathies, autoimmune diseases, inflammatory diseases (i.e., ICAM-1 related disorders, Psoriasis, Ulcerative Colitus, Crohn's disease), viral diseases (i.e., HIV, Hepatitis C), and cardiovascular diseases.
  • in vitro treatment of cells with oligonucleotides can be used for ex vivo therapy of cells removed from a subject (e.g., for treatment of leukemia or viral infection) or for treatment of cells which did not originate in the subject, but are to be administered to the subject (e.g., to eliminate transplantation antigen expression on cells to be transplanted into a subject).
  • in vitro treatment of cells can be used in non-therapeutic settings, e.g., to evaluate gene function, to study gene regulation and protein synthesis or to evaluate improvements made to oligonucleotides designed to modulate gene expression or protein synthesis.
  • In vivo treatment of cells can be useful in certain clinical settings where it is desirable to inhibit the expression of a protein.
  • antisense therapy is reported to be suitable (see, e.g., U.S. Pat. No. 5,830,653) as well as respiratory syncytial virus infection (WO 95/22,553) influenza virus (WO 94/23,028), and malignancies (WO 94/08,003).
  • respiratory syncytial virus infection WO 95/22,553 influenza virus
  • malignancies WO 94/08,003
  • Other examples of clinical uses of antisense sequences are reviewed, e.g., in Glaser. 1996. Genetic Engineering News 16:1.
  • Exemplary targets for cleavage by oligonucleotides include, e.g., protein kinase Ca, ICAM-1, c-raf kinase, p53, c-myb, and the bcr/abl fusion gene found in chronic myelogenous leukemia.
  • a gapped antisense oligonucleotide comprising 2′-O-methyl RNA arms and an unmodified DNA gap was synthesized.
  • a complementary oligonucleotide was also synthesized using unmodified RNA.
  • a double-stranded duplex was formed and the composition was found to inhibit expression of the target gene.
  • Twenty one and 27-mers were designed to target each of two sites on the p53 molecule (89-90 site, and 93-94 site).
  • the double-stranded molecules were designed with or without 3′-deoxy TT overhangs.
  • the test oligonucleotides were 21-mers with 2 nucleotide 3′ deoxy TT overhangs and without overhangs (blunt ends); and 27-mers with 2 nucleotide 3′ deoxy TT overhangs and without overhangs (blunt ends).
  • Two positive controls were included in the experiment (p53) and two negative controls were also included (FITC)
  • FIG. 1 shows the result of an experiment comparing the ability of different oligonucleotide constructs to inhibit p53 and shows that length or the presence or absence of a 3′ deoxy TT overhang did not affect the activity of the oligonucleotide. The results in FIG.
  • HMVEC cells were transfected using 100 nM oligomer complexed with 2ug/mL of Lipofecatmine 2000 in media containing serum for 24 hours. Twenty-four hours after transfection, the cells were lysed and the RNA was isolated for analysis by RT-PCR. No significant toxicity was observed.
  • the results in FIG. 1B show the amount of ⁇ -3-integrin mRNA normalized to the amount of GAPDH, as determined by RT-PCR analysis.
  • Double-Stranded RNA, Interferon-Inducible Protein Kinase, PKR Activation of the Double-Stranded RNA, Interferon-Inducible Protein Kinase, PKR
  • PKR is activated by double-stranded RNA molecules. Active PKR leads to the inhibition of protein synthesis, activation of transcription, and a variety of other cellular effects, including signal transduction, cell differentiation, cell growth inhibition, apoptosis, and antiviral effects.
  • the effect of p53-targetd double-stranded RNA molecules on PKR expression was tested. The level of mRNA was determined using RT-PCR analysis. As shown in FIG. 2, no correlation was observed between the length of the double-stranded oligonucleotide and the level of PKR induction. Accordingly, long oligonucleotides can be used without activating PKR, a marker for interferon induction.
  • Oligonucleotide duplexes were modified at either the 3′ or 5′ end with FITC groups. The modifications were made on either the antisense strand or the sense strand. 5′ or 3′ modification of the sense strand had no effect on the percent inhibition of p53 mRNA. 3′ modification of the antisense strand had little affect on activity, while 5′ modification of the antisense strand reduced activity significantly. 3′ modification of both strands also had little affect on activity, while 3′ and 5′ modification of both strands reduced activity. See FIG. 3.
  • A549 cells were transfected with modified or unmodified RNA duplexes complexed at 100 nM with 2 ug/mL Lipofectamine 2000 (Invitrogen) and were transfected for 24 hours.
  • the A549 cells were plated at 20,000/well in 48 well plates. After 24 hours, FITC-labeled double-stranded oligonucleotides were visible in A549 cells; the inclusion of a 2′-O-Me group did not affect uptake.
  • the Table below shows the results of this experiment.
  • 2′-O-Me Oligonucleotide Duplexes Anti- sense/Sense Anti- Anti- Anti-sense/ 2′-O-Me/2′-O- sense/Sense sense/Sense Sense Me 2′-O-Me/RNA RNA/2′-O-Me RNA/RNA targeted 18639/18640 18639/16194 16193/18640 18876 non- 19039/19040 19039/19044 19043/19040 18850 & targeted 16197/16198 FITC-2′-O-Me/ FITC-2′-O-Me/ FITC-2′-O-Me/ 2′-O-Me/ FITC 2′-O-Me FITC 2′-O-Me FITC 2′-O-Me FITC 2′-O-Me FITC 2′-O-Me FITC-RNA FITC-RNA non- 19209 19037/19042 19037/19044 19039/19042 targeted
  • siRNAs targeting p53 were not toxic to cells when compared to standard 21-mer siRNAs having 3′ deoxy TT overhangs. In this experiment, both siRNA constructs inhibited p53 to a similar extent (83% inhibition for 27-mer vs. 90% inhibition for 21-mer). siRNAs were designed to target p53 and were constructed as blunt-end 27-mers or as 21-mers with 3′ deoxy TT overhangs. A549 cells were plated at 20,000 cells per well in 48-well plates on the day prior to transfection. On the day of transfection, cells were approximately 60-70% confluent. Cells were transfected with 100 nM siRNAs complexed with 2 ug/mL Lipofectamine 2000 for 24 hours.
  • siRNA sequences used were as follows: 21-mer with overhangs targeted (5′-3′): ACCUCAAAGCUGUUCCGUCTT (SEQ ID NO: ##) GACGGAACAGCUUUGAGGUTT (SEQ ID NO: ##) Blunt-end 27-mer targeted (5′-3′): ACGCACACCUCAAAGCUGUUCCGUCCC (SEQ ID NO: ##) GGGACGGAACAGCTTTGAGGTGTGCGT (SEQ ID NO: ##)
  • siRNAs targeting p53 were designed to target p53 and were constructed as blunt-end 27-mers.
  • the corresponding control consisted of chemistry-matched, scrambled sequences with a similar base-pair composition.
  • A549 cells were plated at 20,000 cells per well in 48-well plates on the day prior to transfection. On the day of transfection, cells were approximately 60-70% confluent. Cells were transfected with 100 nM siRNAs complexed with 2 ug/mL Lipofectamine 2000 for 24 hours. Following transfection, the cells were stained with Dead Red stain to visualize the extent of cell death.
  • siRNA sequences used were as follows: Blunt-end 27-mer targeted (5′-3′ on top): ACGCACACCUCAAAGCUGUUCCGUCCC (SEQ ID NO: ##) GGGACGGAACAGCTTTGAGGTGTGCGT (SEQ ID NO: ##) Corresponding control (5′-3′ on top): CCCTGCCTTGTCGAAACTCCACACGCA (SEQ ID NO: ##) TGCGTGTGGAGTTTCGACAAGGCAGGG (SEQ ID NO: ##)
  • siRNAs targeting p53 were not observed to be toxic to cells in comparison with a control nucleic acid and no treatment, as determined by Dead Red staining.
  • siRNAs were designed to target p53 and were constructed as blunt-end 32-mers.
  • the corresponding control consisted of chemistry-matched, scrambled sequences with a similar base-pair composition.
  • A549 cells were plated at 20,000 cells per well in 48-well plates on the day prior to transfection. On the day of transfection, cells were approximately 60-70% confluent. Cells were transfected with 100 nM siRNAs complexed with 2 ug/mL Lipofectamine 2000 for 24 hours.
  • siRNA sequences used were as follows: Targeted blunt-end 32-mer (5′-3′ on top:) CCCTCACGCACACCUCAAAGCUGUUCCGUCCC (SEQ ID NO: ##) GGGACGGAACAGCTTTGAGGTGTGCGTGAGGG (SEQ ID NO: ##) Corresponding control (5′-3′ on top): CCCTGCCTTGTCGAAACTCCACACGCACTCCC (SEQ ID NO: ##) GGGAGTGCGTGTGGAGTTTCGACAAGGCAGGG (SEQ ID NO: ##)
  • FIG. 6 depicts the results of inhibition of p53 by 32- and 37-mer blunt-end siRNAs in comparison with various control experiments.
  • siRNAs were designed to target each of two sites (93-93 site) and (89-90 site) along the coding region of p53.
  • siRNAs were constructed as blunt-end 32-mers or blunt-end 37-mers.
  • Positive control siRNAs were 21-mers with 3′ deoxy TT overhangs.
  • Corresponding controls consisted of chemistry-matched, scrambled sequences with a similar base-pair composition.
  • A549 cells were plated at 20,000 cells per well in 48-well plates on the day prior to transfection. On the day of transfection, cells were approximately 60-70% confluent.
  • siRNA sequences used were as follows (depicted with the 5′-3′ strand on top): Targeted 32-mer (89-90 site): CCCTCACGCACACCUCAAAGCUGUUCCGUCCC (SEQ ID NO: ##) GGGACGGAACAGCTTTGAGGTGTGCGTGAGGG (SEQ ID NO: ##) 32-mer control (89-90 site): CCCTGCCTTGTCGAAACTCCACACGCACTCCC (SEQ ID NO: ##) GGGAGTGCGTGTGGAGTTTCGACAAGGCAGGG (SEQ ID NO: ##) 32-mer targeted (93-94 site): CCCUUCUGUCUUGAACAUGAGTTTTTTATGGC (SEQ ID NO: ##) GCCATAAAAAACTCATGTTCAAGACAGAAGGG (SEQ ID NO: ##) 32-mer control (93-94 site): CGGTATTTTTTGAGTACAAGTTCTGTCTTCCC (SEQ ID NO: ##) GGGAAGACAGAACT
  • the single-stranded control oligomer was transfected at 800 nM. Accumulation was observed in the nucleus at 6 hours post transfection, however by 25 hours the fluorescence of the single-stranded oligomer had largely dissipated, indicating the oligomer was no longer intact (Fisher, T., T. Terhorst, et al. (1993). “Intracellular disposition and metabolism of fluorescently-labeled unmodifieed and modified oligonucleotides microinjected into mammalian cells.” NAR 21: 3857-3865).
  • the oligomers were all 2′-O-CH 3 with a phosphodiester backbone containing 6-carboxyfluorescein (6-FAM) tethered to the 5′ hydroxyl.
  • 6-FAM 6-carboxyfluorescein
  • the single-stranded control oligomer was transfected at 800 nM complexed with 4 ug/mL of Lipofectamine 2000, and the double-stranded complex was transfected at 100 nM complexed with 1 ug/mL of Lipofectamine 2000.
  • RNA complexes were transfected in A549 cells with 100 nM oligomer complexed with 2 ug/mL Lipofecatmine 2000 as described below. Cells were continuously transfected for 24 hours and fluorescent uptake was assessed at 6 and 24 hours.
  • Oligomers were 2′-O-methyl modified RNA with 5′ 6-FAM (FITC-2′-OMe), 19-mer RNA with two deoxynucleotides on the 3′ end with 5′ 6-FAM (FITC-RNA) or 19-mer RNA with two deoxynucleotides on the 3′ end (RNA) complexed.
  • the FITC-2′-O-methyl duplexes show localization in the nucleus and the FITC-2′-O-methyl/RNA and 2′-O-methyl/FITC-RNA complexes show a more diffuse pattern of uptake (these RNA/2′-O-methyl complexes are a substrate for the RISC complex and are therefore retained in the cytoplasm where the RISC complex has been reported to be active).
  • the FITC-2′-O-methyl/RNA and 2′-O-methyl/FITC-RNA complexes were still visible in the cell, whereas typically not even the single-stranded FITC-2′-O- was visible, even when transfected at significantly higher concentrations, demonstrating that the 2′-O-methyl RNA protects the RNA strand from degradation in the cell.
  • RNA oligomers having a phosphodiester backbone with 2′-O-methyl nucleotides were synthesized using standard phosphoramidite chemistry. Oligomers were purified by denaturing polyacrylamide gel electrophoresis (PAGE). Purity of oligomers was confirmed by (PAGE) and mass spectrometry. All oligomers were greater than 90% full length, and mass data obtained was consistent with expected values.
  • Target-specific siRNA duplexes consisted of 21-nt sense and 21-nt antisense strands with symmetric 2-nt 3′ deoxy TT overhangs. 21-nt RNAs were chemically synthesized using phosphoramidite chemistry.
  • sense- and antisense oligomers were combined in equal volumes in annealing buffer (30 mM HEPES pH 7.0, 100 mM potassium acetate, and 2 mM magnesium acetate), heat-denatured at 90° C. for 1 min and annealed at 37° C. for one hour. Duplexes were stored at 80° C. until used.
  • A549 cells were cultured at 37° C. in Dulbecco's Modified Eagle Medium (DMEM, Life Technologies #11960-044) supplemented with 2 mM L-glutamine, 100 units/mL penicillin, 100 ⁇ g/mL streptomycin, and 10% fetal bovine serum (FBS).
  • HeLa cells were cultured at 37° C. in Minimal Essential Medium (MEM, Life Technologies #10370-021) supplemented with 2 mM L-glutamine, 1.5 g/L sodium bicarbonate, 1.0 mM sodium pyruvate, 100 units/mL penicillin, 100 ⁇ g/mL streptomycin, and 10% FBS.

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