WO1997006662A2 - Inverted chimeric and hybrid oligonucleotides - Google Patents

Inverted chimeric and hybrid oligonucleotides Download PDF

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Publication number
WO1997006662A2
WO1997006662A2 PCT/US1996/013371 US9613371W WO9706662A2 WO 1997006662 A2 WO1997006662 A2 WO 1997006662A2 US 9613371 W US9613371 W US 9613371W WO 9706662 A2 WO9706662 A2 WO 9706662A2
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Prior art keywords
oligonucleotide
composition
oligonucleotides
gene expression
side effects
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WO1997006662A3 (en
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Sudhir Agrawal
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Aceragen Inc
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Hybridon Inc
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Priority to DE69628864T priority Critical patent/DE69628864T2/de
Priority to JP50953597A priority patent/JP4177455B2/ja
Priority to AU69538/96A priority patent/AU6953896A/en
Priority to DK96930536T priority patent/DK1019428T3/da
Priority to AT96930536T priority patent/ATE243706T1/de
Priority to CA2229811A priority patent/CA2229811C/en
Priority to EP96930536A priority patent/EP1019428B1/en
Publication of WO1997006662A2 publication Critical patent/WO1997006662A2/en
Publication of WO1997006662A3 publication Critical patent/WO1997006662A3/en
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1137—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against enzymes
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/31—Chemical structure of the backbone
    • C12N2310/315—Phosphorothioates
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/321—2'-O-R Modification
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/322—2'-R Modification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/34—Spatial arrangement of the modifications
    • C12N2310/341—Gapmers, i.e. of the type ===---===
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/34—Spatial arrangement of the modifications
    • C12N2310/345—Spatial arrangement of the modifications having at least two different backbone modifications
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/34—Spatial arrangement of the modifications
    • C12N2310/346—Spatial arrangement of the modifications having a combination of backbone and sugar modifications

Definitions

  • the invention relates to modified oligonucleotides that are useful for studies of gene: expression and for the antisense therapeutic approach.
  • USA 7j5: 280-284 and 285-288 (1978) disclose that a 13-mer synthetic oligonucleotide that is complementary to a part of the Rous sarcoma virus (RSV) genome can inhibit RSV replication in infected cell cultures and can inhibit RSV-mediated transformation of primary chick fibroblasts into malignant sarcoma cells. Since these early studies, the ability of antisense oligonucleotides to inhibit virus propagation has become firmly established.
  • US Patent No. 4,806,463 teaches that human immunodeficiency virus propagation can be inhibited by oligonucleotides that are complementary to any of various regions of the HIV genome. US Patent No.
  • 5,194,428 discloses inhibition of influenza virus replication by phosphorothioate oligonucleotides complementary to the influenza virus polymerase 1 gene. Agrawal, Trends in Biotechnology 10 . : 152-158 (1992) reviews the use of antisense oligonucleotides as antiviral agents. Antisense oligonucleotides have also been developed as anti-parasitic agents. PCT publication no. WO93/13740 discloses the use of antisense oligonucleotides to inhibit propagation of drug-resistant malarial parasites. Tao et al . , Antisense Research and Development 5_: 123-129 (1995) teaches inhibition of propagation of a schistosome parasite by antisense oligonucleotides.
  • oligonucleotides containing the CG dinucleotide flanked by certain other sequences have a mitogenic effect in vivo .
  • Galbraith et al. Antisense Research and Development 4.: 201- 206 (1994) disclose complement activation by oligonucleotides.
  • oligonucleotides may potentially interfere with blood clotting. There is, therefor, a need for modified oligonucleotides that retain gene expression inhibition properties while producing fewer side effects than conventional oligonucleotides.
  • the invention relates to modified oligonucleotides that are useful for studies of gene expression and for the antisense therapeutic approach.
  • the invention provides modified oligonucleotides that inhibit gene expression and that produce fewer side effects than conventional oligonucleotides.
  • the invention provides modified oligonucleotides that demonstrate reduced mitogenicity, reduced activation of complement and reduced antithrombotic properties, relative to conventional oligonucleotides.
  • the invention provides inverted hybrid and inverted chimeric oligonucleotides and compositions of matter for inhibiting specific gene expression with reduced side effects.
  • Such inhibition of gene expression can be used as an alternative to mutant analysis for determining the biological function of specific genes.
  • Such inhibition of gene expression can also be used to therapeutically treat diseases that are caused by expression of the genes of a virus or a pathogen, or by the inappropriate expression of cellular genes.
  • the composition of matter comprises modified oligonucleotides having one or more 2'-0-substituted RNA region flanked by one or more oligodeoxyribonucleotide phosphorothioate region.
  • the 2'-O-substituted RNA region is in between two oligodeoxyribonucleotide regions, a structure that is "inverted" relative to traditional hybrid oligonucleotides.
  • the composition of matter comprises modified oligonucleotides having one or more nonionic oligonucleotide region flanked by one or more region of oligonucleotide phosphorothioate.
  • the nonionic region contains alkylphosphonate and/or phosphoramidate and/ or phosphotriester internucleoside linkages.
  • the nonionic oligonucleotide region is in between two oligonucleotide phosphorothioate regions, a structure that is "inverted" relative to traditional chimeric oligonucleotides.
  • the invention provides a method for modulating gene expression in a mammal with reduced side effects.
  • a composition of matter according to the first aspect of the invention is administered to the mammal, wherein the oligonucleotide is complementary to a gene that is being expressed in the mammal.
  • one or more measurement is taken of biological effects selected from the group consisting of complement activation, mitogenesis and inhibition of thrombin clot formation.
  • the invention provides a method for therapeutically treating, with reduced side effects, a disease caused by aberrant gene expression, the method comprising administering to an individual having the disease a composition of matter according to the first aspect of the invention, wherein the oligonucleotide is complementary to a gene that is aberrantly expressed, wherein such aberrant expression causes the disease.
  • aberrant gene expression means expression in a host organism of a gene required for the propagation of a virus or a prokaryotic or eukaryotic pathogen, or inappropriate expression of a host cellular gene.
  • Inappropriate host cellular gene expression includes expression of a mutant allele of a cellular gene, or underexpression or overexpression of a normal allele of a cellular gene, such that disease results from such inappropriate host cellular gene expression.
  • one or more measurement is taken of biological effects selected from the group consisting of complement activation, mitogenesis and inhibition of thrombin clot formation.
  • Figure 1 shows inverted hybrid oligonucleotides, hybrid oligonucleotides and oligonucleotide phosphodiesters and phosphorothioates used in the current studies.
  • 2'-0- methylribo-nucleotides are outlined and phosphodiester- linked nucleotides are underlined; all others are phosphorothioate-linked nucleotides.
  • Figure 2 shows mixed backbone, chimeric and inverted chimeric oligonucleotides used in the current studies. Methylphosphonate-linked nucleotides are underlined; all others are phosphorothioate linked nucleotides.
  • Figure 3 shows thymidine uptake by mouse spleenocytes as a function of concentration of phosphorothioate oligonucleotide or any of various inverted hybrid oligonucleotides.
  • Figure 4 shows extent of inhibition of complement- mediated hemolysis observed when serum is treated with phosphorothioate oligonucleotide or any of various inverted hybrid oligonucleotides.
  • Figure 5 shows prolongation of aPTT obtained when normal human serum is treated with phosphorothioate oligonucleotides or with any of various inverted hybrid oligonucleotides.
  • Figure 6 shows thymidine uptake by mouse spleenocytes as a function of concentration of phosphorothioate oligonucleotide or any of various inverted chimeric oligonucleotides.
  • Figure 7 shows extent of inhibition of complement- mediated hemolysis observed when serum is treated with phosphorothioate oligonucleotide or any of various inverted chimeric oligonucleotides.
  • Figure 8 shows prolongation of aPTT obtained when normal human serum is treated with phosphorothioate oligonucleotides or with any of various inverted chimeric oligonucleotides .
  • the invention relates to modified oligonucleotides that are useful for studies of gene expression and for the antisense therapeutic approach.
  • the invention provides modified oligonucleotides that inhibit gene expression and that produce fewer side effects than conventional oligonucleotides.
  • the invention provides modified oligonucleotides that demonstrate reduced itogenicity, reduced activation of complement and reduced antithrombotic properties, relative to conventional oligonucleotides.
  • the invention provides inverted hybrid and inverted chimeric oligonucleotides and compositions of matter for inhibiting specific gene expression with reduced side effects.
  • Such inhibition of gene expression can be used as an alternative to mutant analysis or gene "knockout" experiments for determining the biological function of specific genes.
  • Such inhibition of gene expression can also be used to therapeutically treat diseases that are caused by expression of the genes of a virus or a pathogen, or by the inappropriate expression of cellular genes.
  • a composition of matter for inhibiting specific gene expression with reduced side effects comprises a modified oligonucleotide that is complementary to a portion of a genomic region or gene for which inhibition of expression is desired, or to RNA transcribed from such a gene.
  • oligonucleotide includes polymers of two or more deoxyribonucleotide, ribonucleotide, or 2'-O-substituted ribonucleotide monomers, or any combination thereof.
  • oligonucleotide also encompasses such polymers having chemically modified bases or sugars and/ or having additional substituents, including without limitation lipophilic groups, intercalating agents, diamines and adama ⁇ tane.
  • oligonucleotides will have from about 12 to about 50 nucleotides, most preferably from about 17 to about 35 nucleotides.
  • complementary means having the ability to hybridize to a genomic region, a gene, or an RNA transcript thereof under physiological conditions. Such hybridization is ordinarily the result of base-specific hydrogen bonding between complementary strands, preferably to form Watson-Crick or Hoogsteen base pairs, although other modes of hydrogen bonding, as well as base stacking can also lead to hybridization.
  • RNA transcript sequence to which the modified oligonucleotide sequence is complementary will depend upon the biological effect that is sought to be modified.
  • the genomic region, gene, or RNA transcript thereof may be from a virus.
  • viruses include, without limitation, human immunodeficiency virus (type 1 or 2), influenza virus, herpes simplex virus (type 1 or 2), Epstein-Barr virus, cytomegalovirus, respiratory syncytial virus, influenza virus, hepatitis B virus, hepatitis C virus and papilloma virus.
  • the genomic region, gene, or RNA transcript thereof may be from endogenous mammalian (including human) chromosomal DNA.
  • Preferred examples of such genomic regions, genes or RNA transcripts thereof include, without limitation, sequences encoding vascular endothelial growth factor (VEGF) , beta amyloid, DNA methyltransferase,- protein kinase A, ApoE4 protein, p- glycoprotein, c-MYC protein, BCL-2 protein and CAP .
  • VEGF vascular endothelial growth factor
  • beta amyloid DNA methyltransferase
  • beta protein kinase A kinase A
  • ApoE4 protein p- glycoprotein
  • c-MYC protein c-MYC protein
  • BCL-2 protein and CAP vascular endothelial growth factor
  • the genomic region, gene, or RNA transcript thereof may be from a eukaryotic or prokaryotic pathogen including, without limitation, Plasmod
  • Plasmodium malar ie Plasmodium ovale, Schistosoma spp . , and Mycobacterium tuberculosis .
  • composition of matter for inhibiting gene expression with reduced side effects may optionally contain any of the well known pharmaceutically acceptable carriers or diluents.
  • This composition of matter may further contain one or more additional oligonucleotides according to the invention, which additional oligonucleotide may be either an inverted hybrid oligonucleotide or an inverted chimeric oligonucleotide.
  • this composition may contain one or more traditional antisense oligonucleotide, such as an oligonucleotide phosphorthioate, a hybrid oligonucleotide, or a chimeric oligonucleotide, or it may contain any other pharmacologically active agent.
  • the composition of matter comprises modified oligonucleotides having one or more 2'-O-substituted RNA region flanked by one or more oligodeoxyribonucleotide phosphorothioate region.
  • the 2'-O-substituted RNA region is in between two oligodeoxyribonucleotide phosphorothioate regions, a structure that is "inverted" relative to traditional hybrid oligonucleotides. Accordingly, oligonucleotides according to this embodiment are designated inverted hybrid oligonucleotides.
  • the 2'-O-substituted RNA region preferably has from about four to about 10 or 13 2'-O- substituted nucleosides joined to each other by 5' to 3' internucleoside linkages, and most preferably from about four to about eight such 2'-O-substituted nucleosides.
  • the overall size of the inverted hybrid oligonucleotide will be from about 15 to about 35 or 50 nucleotides.
  • the 2 '-O-substituted ribonucleosides will be linked to each other through a 5' to 3' phosphorothioate, phosphotriester, or phosphodiester linkage.
  • the term "2'-0- substituted" means substitution of the 2' position of the pentose moiety with an -O-lower alkyl group containing 1-6 saturated or unsaturated carbon atoms, or with an -O-aryl or allyl group having 2-6 carbon atoms, wherein such alkyl, aryl or allyl group may be unsubstituted or may be substituted, e.g., with halo, hydroxy, trifluoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxyl, carbalkoxyl, or amino groups; or with a hydroxy, an amino or a halo group, but not with a 2 '-H group.
  • the phosphorothioate flanking region or regions has from about four to about 46 nucleosides joined to each other by 5' to 3 ' phosphorothioate linkages, and preferably from about 5 to about 26 such phosphorothioate-linked nucleosides. Most preferably, the phosphorothioate regions will have from about 5 to about 15 phosphorothioate-linked nucleosides.
  • the phosphorothioate linkages may be mixed R and S
  • P P enantiomers or they may be stereoregular or substantially stereoregular in either R or S form (see Iyer efc al . ,
  • the composition of matter comprises modified oligonucleotides having one or more nonionic oligonucleotide region flanked by one or more region of oligonucleotide phosphorothioate.
  • the nonionic region contains alkylphosphonate and/or phosphoramidate and/or phosphotriester internucleoside linkages.
  • the nonionic oligonucleotide region is in between two oligonucleotide phosphorothioate regions, a structure that is "inverted" relative to traditional chimeric oligonucleotides.
  • oligonucleotides according to this embodiment are designated inverted chimeric oligonucleotides.
  • the nonionic region has from about four to about 10 or 12 nucleosides joined to each other by 5' to 3' nonionic linkages, preferably alkylphosphonate, phosphoramidate or phosphotriester linkages, and preferably from about four to about eight such nonionic-linked nucleosides.
  • the phosphorothioate flanking region or regions has from about four to about 46 nucleosides joined to each other by 5' to 3 ' phosphorothioate linkages, and preferably from about eight to about 26 such phosphorothioate-linked nucleosides. Most preferably, the phosphorothioate regions will have from about 5 to about 15 phosphorothioate-linked nucleosides .
  • the phosphorothioate linkages may be mixed R and S enantiomers, or they may be
  • the oligonucleotide has a nonionic region having from about 6 to about 8 methylphosphonate-linked nucleosides, flanked on either side by phosphorothioate regions, each having from about 6 to about 10 phosphorothioate-linked nucleosides.
  • 2 '-O-substituted ribonucleotide regions may well include from one to all nonionic internucleoside linkages .
  • nonionic regions may have from one to all 2'-
  • oligonucleotides according to the invention may contain combinations of one or more 2 '-O-substituted ribonucleotide region and one or more nonionic region, either or both being flanked by phosphorothioate regions.
  • the invention provides a method for modulating gene expression in a mammal with reduced side effects .
  • a composition of matter according to the first aspect of the invention is administered to the mammal, wherein the oligonucleotide is complementary to a gene that is being expressed in the mammal.
  • such adminisration may be parenteral, oral, intranasal or intrarectal.
  • one or more measurement is taken of biological side effects selected from the group consisting of complement activation, mitogenesis and inhibition of thrombin clot formation.
  • the invention provides a method for therapeutically treating, with reduced side effects, a disease caused by aberrant gene expression, the method comprising administering to an individual having the disease a composition of matter according to the first aspect of the invention, wherein the oligonucleotide is complementary to a gene that is aberrantly expressed, wherein such aberrant expression causes the disease.
  • aberrant gene expression means expression in a host organism of a gene required for the propagation of a virus or a prokaryotic or eukaryotic pathogen, or inappropriate expression of a host cellular gene.
  • Inappropriate host cellular gene expression includes expression of a mutant allele of a cellular gene, or underexpression or overexpression of a normal allele of a cellular gene, such that disease results from such inappropriate host cellular gene expression.
  • such administation should be parenteral, oral, sublingual, transdermal, topical, intranasal or intrarectal.
  • Administration of the therapeutic compositions can be carried out using known procedures at dosages and for periods of time effective to reduce symptoms or surrogate markers of the disease.
  • the therapeutic composition is preferably administered at a sufficient dosage to attain a blood level of oligonucleotide from about 0.01 micromolar to about 10 micromolar.
  • a total dosage of oligonucleotide will range from about 0.1 mg oligonucleotide per patient per day to about 200 mg oligonucleotide per kg body weight per day. It may desirable to administer simultaneously, or sequentially a therapeutically effective amount of one or more of the therapeutic compositions of the invention to an individual as a single treatment episode. In a preferred embodiment, after the composition of matter is administered, one or more measurement is taken of biological effects selected from the group consisting of complement activation, mitogenesis and inhibition of thrombin clot formation.
  • Oligonucleotide phosphorothioates were synthesized using an automated DNA synthesizer (Model 8700, Biosearch, Bedford,MA) using a beta-cyanoethyl phosphoramidite approach on a 10 micromole scale. To generate the phosphorothioate linkages, the intermediate phosphite linkage obtained after each coupling was oxidized using 3H, 1,2-benzodithiole-3H- one-1, 1-dioxide (See Beaucage, In Protocols for
  • Oligonucleotides and Analogs Synthesis and Properties, Agrawal (editor), Humana Press, Totowa, NJ, pp. 33-62 (1993) .) Similar synthesis was carried out to generate phosphodiester linkages, except that a standard oxidation was carried out using standard iodine reagent.
  • Inverted hybrid oligonucleotides were synthesized similarly, except that the segment containing 2'-O- methylribonucleotides was assembled using 2'-0- methylribonucleoside phosphoramidite, followed by oxidation to a phosphorothioate or phosphodiester linkage as described above. Deprotection and purification of oligonucleotides was carried out according to standard procedures, (See Padmapriya et al . , Antisense Res. & Dev. 4: 185-199 (1994)), except for oligonucleotides containing methylphosphonate- containing regions.
  • the CPG- bound oligonucleotide was treated with concentrated ammonium hydroxide for 1 hour at room temperature, and the supernatant was removed and evaporated to obtain a pale yellow residue, which was then treated with a mixture of ethylenediamine/ethanol (1:1 v/v) for 6 hours at room temperature and dried again under reduced pressure.
  • Venous blood was collected from healthy adult human volunteers. Serum was prepared for hemolytic complement assay by collecting blood into vacutainers (Becton Dickinson #6430 Franklin Lakes, NJ) without commercial additives. Blood was allowed to clot at room temperature for 30 minutes, chilled on ice for 15 minutes, then centrifuged at 4 * C to separate serum. Harvested serum was kept on ice for same day assay or, alternatively, stored at -70'C.
  • FBS was first heated for 30 minutes at 65"C (phosphodiester-containing oligonucleotides) or 56"C (all other oligonucleotides) .
  • Cells were plated in 96 well dishes at 100,000 cells per well (volume of 100 microliters/ well) . Oligonucleotides in
  • 35 methyl region appeared to be slightly less immunogenic than those containing phosphorothioate linkages in that region. No significant difference in mitogenicity was observed when the 2'-O-methylribonucleotide region was pared down from 13 to 11 or to 9 nucleotides. Inverted chimeric oligonucleotides were also generally less mitogenic than phosphorothioate oligonucleotides. In addition, these oligonucleotides appeared to be less mitogenic than traditional chimeric oligonucleotides, at least in cases in which the traditional chimeric oligonucleotides had significant numbers of methylphosphonate linkages near the 3' end.
  • Venous blood was collected from healthy adult human volunteers.
  • Plasma for clotting time assay was prepared by collecting blood into siliconized vacutainers with sodium citrate (Becton Dickinson #367705), followed by two centifugations at 4'C to prepare platelet-poor plasma. Plasma aliquots were kept on ice, spiked with various test compounds, and either tested immediately or quickly frozen on dry ice for subsequent storage at -20'C prior to coagulation assay.
  • Activated partial thromboplastin time was performed in duplicate on an Electra 1000C (Medical Laboratory Automation, Mount Vernon, NY) according to the manufacturer's recommended procedures, using Actin FSL (Baxter Dade, Miami, FL) and calcium to initiate clot formation, which was measured photometrically. Prolongation of aPTT was taken as an indication of clotting inhibition side effect produced by the oligonucleotide. The results are shown in Figure 5 for inverted hybrid oligonucleotides and in Figure 8 for inverted chimeric oligonucleotides. Traditional phosphorothioate oligonucleotides produce the greatest prolongation of aPTT, of all of the oligonucleotides tested.
  • Rhesus monkeys (4-9 kg body weight) are acclimatized to laboratory conditions for at least 7 days prior to the study. On the day of the study, each animal is lightly sedated with ketamine-HCl (10 mg/kg) and diazepam (0.5 mg/ kg) . Surgical level anasthesia is induced and maintained by continuous ketamine intravenous drip throughout the procedure. Phosphorothioate oligonucleotide or inverted hybrid or inverted chimeric oligonucleotide is dissolved in normal saline and infused intravenously via a cephalic vein catheter, using a programmable infusion pump at a delivery rate of 0.42 ml/ minute.
  • oligonucleotide doses of 0, 0.5, 1, 2, 5 and 10 mg/ kg are administered to two animals each over a 10 minute infusion period.
  • Arterial blood samples are collected 10 minutes prior to oligonucleotide administration and 2, 5, 10, 20, 40 and 60 minutes after the start of the infusion, as well as 24 hours later.
  • Serum is used for determining complement CH50, using the conventional complement-dependent lysis of sheep ertyhrocyte procedure (see Kabat and Mayer, 1961, supra) .
  • phosphorothioate oligonucleotide causes a decrease in serum complement CH50 beginning within 5 minutes of the start of infusion.
  • CDI mice are injected intraperitoneally with a dose of 50 mg/kg body weight of phosphorothioate oligonucleotide, inverted hybrid oligonucleotide or inverted chimeric oligonucleotide. Forty-eight hours later, the animals are euthanized and the spleens are removed and weighed. Animals treated with inverted hybrid or inverted hybrid oligonucleotides are expected to show no significant increase in spleen weight, while those treated with oligonucleotide phosphorothioates are expected to show modest increases in spleen weight.
  • Rhesus monkeys are treated as in example 5. From the whole blood samples taken, plasma for clotting assay is prepared, and the assay performed, as described in example 4. It is expected that prolongation of aPTT will be substantially reduced for both inverted hybrid oligonucleotides and for inverted chimeric oligonucleotides, relative to traditional oligonucleotide phosphorothioates.
  • the samples were heated to 95'C, then cooled gradually to room temperature to allow annealing to form duplexes .
  • Annealed duplexes were incubated for 10 minutes at 37"C, then 5 units RNase H was added and data collection commenced over a three hour period. Data was collected using a GBC 920 (GBC Scientific Equipment, Victoria, Australia) spectrophotometer at 259 nm. RNase H degradation was determined by hyperchromic shift.
  • HyblO ⁇ (inv. hyb.) 15.4 sec.
  • Hybll ⁇ (inv. chim.) 11.5 sec.
  • Hybl09 (inv. hyb.) 7.9 sec.
  • Hybll9 (inv. chim.) 14.4 sec.
  • HybllO (inv. hyb.) 10.4 sec.
  • Hybl20 (inv. chim.) 9.3 sec.
  • Hyblll (inv. hyb.) 12.9 sec.
  • Hybl21 (3' MP) 21.2 sec.
  • Hybll2 (inv. hyb.) 12.5 sec.
  • Hybl22 (chimeric) 23.0 sec.
  • Hybll3 (inv. hyb.) 10.9 sec.
  • Hybl23 (chimeric) 41.8 sec.
  • Hybll4 inv. hyb. 20.3 sec.
  • Hybl24 chimeric not detect.
  • phosphodiester oligonucleotides behaved as very good co-substrates for RNase H-mediated degradation of
  • RNA with a degradative half-life of 8.8 seconds.
  • Phosphorothioate oligonucleotides produced an increased half-life of 22.4 seconds.
  • introducing a 2 '-O-methyl segment into the middle of the oligonucleotide always resulted in improved RNase H- mediated degradation.
  • the best RNase H activity was observed, with a half-life of 7.9 seconds.
  • Tm Thermal melting
  • Tm experiments were performed in a buffer containing 10 mM PIPES, pH 7.0, 1 mM EDTA, 1 M NaCI.
  • a VWR 1166 (VWR, Boston, MA) refrigerated bath was connected to the peltier-effeet temperature controller to absorb the heat.
  • Oligonucleotide strand concentration was determined using absorbance values at 260 nm, taking into account extinction coefficients.
  • HyblO ⁇ (inv. hyb.) ' 76.4 Hybll8 (inv. chim.) 57.9
  • Hybl09 (inv. hyb.) 80.0 Hybll9 (inv. chim.) 57.7 HybllO (inv. hyb.) 74.2 Hybl20 (inv. chim.) 56.8
  • Hybll2 inv. hyb. 72.1 Hybl22 (chimeric) 60.5
  • Hybll3 (inv. hyb.) 74.3 Hybl23 (chimeric) 59.0
  • Hybll4 (inv. hyb.) 71.3 Hybl24 (chimeric) not detect.

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