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Definitions

• the invention relates to synthetic chemical compositions that are useful for modulation of Toll-Like Receptor (TLR)-mediated immune responses.
• TLR Toll-Like Receptor
• the invention relates to agonists of Toll-Like Receptor 9 (TLR9) that generate unique cytokine and chemokine profiles.
• TLRs Toll- like receptors
• these family consists of eleven proteins called TLRl to TLRl 1, which are known to recognize pathogen associated molecular patterns from bacteria, fungi, parasites, and viruses (Poltorak, a. et al. (1998) Science 282:2085-2088; Underhill, D.M., et al. (1999) Nature 401 :811-815; Hayashi, F. et. al (2001) Nature 410:1099-1103; Zhang, D. et al.
• TLRs are a key means by which vertebrates recognize and mount an immune response to foreign molecules and also provide a means by which the innate and adaptive immune responses are linked (Akira, S. et al. (2001) Nature Immunol. 2:675-680; Medzhitov, R. (2001) Nature Rev. Immunol. 1 : 135-145).
• Some TLRs are located on the cell surface to detect and initiate a response to extracellular pathogens and other TLRs are located inside the cell to detect and initiate a response to intracellular pathogens.
• TLR9 is known to recognize unmethylated CpG motifs in bacterial DNA and in synthetic oligonucleotides. (Hemmi, H. et al. (2000) Nature 408:740-745). Other modifications of CpG- containing phosphorothioate oligonucleotides can also affect their ability to act as modulators of immune response through TLR9 (see, e.g., Zhao et al, Biochem. Pharmacol. (1996) 51 :173-182; Zhao et al. (1996) Biochem Pharmacol. 52:1537-1544; Zhao et al. (1997) Antisense Nucleic Acid Drug Dev. 7:495-502; Zhao et al (1999) Bioorg. Med. Chem. Lett.
• TLR9 agonists have been shown to work synergistically with other known anti-tumor compounds (e.g. cetuximab, irinotecan) (Vincenzo, D., et al. (2006) Clin. Cancer Res. 12(2):577-583).
• TLR9 agonists are comprised of 3 '-3' linked DNA structures containing a core CpR dinucleotide, wherein the R is a modified guanosine (US Patent Application No. 10/279,684).
• R is a modified guanosine
• specific chemical modifications have allowed the preparation of specific oligonucleotide analogs that generate distinct modulations of the immuneresponse.
• structure activity relationship studies have allowed identification of synthetic motifs and novel DNA-based compounds that generate specific modulations of the immune response and these modulations are distinct from those generated by unmethylated CpG dinucleotides. (Kandimalla, E. et al. (2005) Proc. Natl. Acad. Sci. U S A 102:6925-6930.
• Kandimalla E. et al. (2003) Proc. Nat. Acad. Sci. U S A 100:14303-14308; Cong, Y. et al. (2003) Biochem Biophys Res. Commun.310:l 133-1139; Kandimalla, E. et al. (2003) Biochem. Biophys. Res. Commun. 306:948-953; Kandimalla, E. et al. (2003) Nucleic Acids Res. 31 :2393-2400; Yu, D. et al. (2003) Bioorg. Med. Chem.11 :459-464; Bhagat, L. et al. (2003) Biochem. Biophys. Res.
• the invention provides novel oligonucleotide-based compounds that individually provide distinct immune response profiles through their interactions as agonists with TLR9.
• the TLR9 agonists according to the invention are characterized by specific and unique chemical modifications, which provide their distinctive immune response activation profiles.
• the TLR9 agonists according to the invention induce immune responses in various cell types and in various in vitro and in vivo experimental models, with each agonist providing a distinct immune response profile. As such, they are useful as tools to study the immune system, as well as to compare the immune systems of various animal species, such as humans and mice.
• the TLR9 agonists according to the invention are also useful in the prevention and/or treatment of various diseases, either alone, in combination with other drugs, or as adjuvants for antigens used as vaccines.
• the invention provides oligonuceotide -based agonists of TLR9.
• the invention provides a composition comprising an oligonucleotide- based TLR9 agonist ("a compound”) according to the invention and a physiologically acceptable carrier.
• the invention provides a vaccine.
• Vaccines according to this aspect comprise a composition according to the invention, and further comprise an antigen.
• the invention provides methods for generating a TLR9- mediated immune response in a vertebrate, such methods comprising administering to the vertebrate a compound, composition or vaccine according to the invention.
• the invention provides methods for therapeutically treating a patient having a disease or disorder, such methods comprising administering to the patient a compound, composition or vaccine according to the invention.
• the invention provides methods for preventing a disease or disorder, such methods comprising administering to the patient a compound, composition or vaccine according to the invention.
• the invention provides novel oligonucleotide-based compounds that individually provide distinct immune response profiles through their interactions as agonists with TLR9.
• the TLR9 agonists according to the invention are characterized by unique chemical modifications, which provide their distinctive immune response activation profiles.
• the TLR9 agonists according to the invention induce immune responses in various cell types and in various in vivo and in vitro experimental models, with each agonist providing a distinct immune response profile. As such, they are useful as tools to study the immune system, as well as to compare the immune systems of various animal species, such as humans and mice.
• the TLR9 agonists according to the invention are also useful in the prevention and/or treatment of various diseases, either alone, in combination with other drugs, or as adjuvants for antigens used as vaccines.
• TLR9 agonists are shown in Table I below.
• the oligonucleotide-based TLR9 agonists have all phosphorothioate (PS) linkages, except where indicated. Except where indicated, all nucleotides are deoxyribonucleotides.
• PS phosphorothioate
• PO phosphodiester
• Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in HEK293 cells expressing TLR9, as described in Example 2.
• the results shown in Table II(a), II(b), II(c), and II(d) below demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides will alter their TLR9 mediated NF -kB activation profile 24 hours after administration. More generally, these data demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides can be used to increase or decrease NF -kB activation.
• Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the C57BL/6 mouse spleenocyte IL- 12 assay, as described in Example 3.
• the results shown in Table I ⁇ I(a), III(b) and III(c) below demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides will alter their TLR9 mediated IL- 12 activation profile in spleen cells 24 hours after administration and that this activation profile may be dose dependent depending on the chemical modification. More generally, these data demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides can be used to increase or decrease IL- 12 activation.
• Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the C57BL/6 mouse spleenocyte IL-6 assay, as described in Example 3.
• the results shown in Table IV(a), IV(b), and IV(c) below demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides will alter their TLR9 mediated IL-6 activation profile in spleen cells 24 hours after administration and that this activation profile may be dose dependent depending on the chemical modification. More generally, these data demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides can be used to increase or decrease IL-6 activation.
• Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the human B-cell proliferation assay, as described in Example 4.
• the results shown in Table V(a), V(b), V(c), V(d) and V(e) below demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides will alter their TLR9 mediated B-cell proliferation activity and that this activation profile may be dose dependent depending on the chemical modification. More generally, these data demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides can be used to regulate B-cell proliferation.
• Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the human PBMC and B-CeIl assays for IL-IRa, IL-6, IL-IO, and IL- 12, as described in Example 3.
• the results shown in Table VI(a), VI(b), VI(c), VI(d), VI(e), VI(f), VI(g), and VI(h) below demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides will alter their TLR9 mediated IL-lR ⁇ , IL-6, IL-IO, and/or IL-12 activation profile in human PBMCs. More generally, these data demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides can be used to increase or decrease IL-I Ra, IL-6, IL-IO, and IL-12 activation.
• Table VI(b) Human PBMC Assay for IL-I Ra, IL-6 and IL- 12
• Table VI(c) Human PBMC Assay for IL-6 (24 hours)
• TLR9 agonists from Table I were tested for immune stimulatory activity in the human PBMC assay for IFN- ⁇ , MIP-Ia and MlP- ⁇ , as described in Example 3.
• the results shown in Table V ⁇ I(a) and VII(b) below demonstrate that specific chemical modifications to 3'- 3' linked oligonucleotides will alter their TLR9 mediated IFN- ⁇ , MIP- l ⁇ , and/or MlP- ⁇ activation profile in human PBMCs. More generally, these data demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides can be used to increase or decrease IFN- ⁇ , MIP- l ⁇ , and MlP- ⁇ activation.
• Table V ⁇ I(a) Human PBMC Assay for IFN- ⁇ , MIP- l ⁇ and MlP- ⁇
• Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the human PBMC assay for MCP-I and IFN- ⁇ , as described in Example 3.
• the results shown in Table V ⁇ II(a) and V ⁇ II(b) below demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides will alter their TLR9 mediated MCP-I and/or IFN- ⁇ activation profile in human PBMCs. More generally, these data demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides can be used to increase or decrease MCP-I and IFN- ⁇ activation.
• Exemplar TLR9 agonists from Table I were tested for immune stimulatory activity in the human PBMC and pDC assays for IFN- ⁇ , IL6, and IL- 12, as described in Example 3.
• the results shown in Table IX(a), IX(b), IX(c), IX(d), IX(e), IX(f), and IX(g) below demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides will alter their TLR9 mediated IFN- ⁇ activation profile in human PBMCs and pDCs. More generally, these data demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides can be used to increase or decrease IFN- ⁇ , IL-6, and IL- 12 activation.
• Exemplar TLR9 agonists from Table I were tested for their induction of IL- 12 and IL-6 in mouse spleen cell cultures, as described in Example 3.
• the results shown in Table X(a) and X(b) below demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides will alter their TLR9 mediated IL-6 and/or IL- 12 activation profile in spleen cells and that this activation profile may be dose dependent depending on the chemical modification. More generally, these data demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides can be used to increase or decrease IL-6 and IL- 12 activation.
• Exemplar TLR9 agonists from Table I were tested for their induction of IL-IRa, IL-6 and IL-12p40p70 in human PBMC cultures, as described in Example 3.
• the results shown in Table XI below demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides will alter their TLR9 mediated IL-I Ra, IL-6, and IL-12p40p70 activation profile in human PBMCs. More generally, these data demonstrate that specific chemical modifications to 3 '-3' linked oligonucleotides can be used to increase or decrease IL-I Ra, IL-6, and IL-12p40p70 activation.
• the invention provides, in a first aspect, oligonucleotide-based synthetic agonists of TLR9. Based upon certain chemical modifications to the base, sugar, linkage, or linker, the agonists of TLR9 may possess increased stability when associated, duplexed, with other of the TLR9 agonist molecules, while retaining an accessible 5 '-end.
• the invention provides a composition comprising an oligonucleotide- based TLR9 agonist ("a compound") according to the invention and a physiologically acceptable carrier.
• a compound an oligonucleotide- based TLR9 agonist
• physiologically acceptable generally refers to a material that does not interfere with the effectiveness of the compound and that is compatible with a biological system such as a cell, cell culture, tissue, or organism.
• carrier encompasses any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, oil, lipid, lipid containing vesicle, microspheres, liposomal encapsulation, or other material well known in the art for use in physiologically acceptable formulations. It will be understood that the characteristics of the carrier, excipient, or diluent will depend on the route of administration for a particular application. The preparation of physiologically acceptable formulations containing these materials is described in, e.g. , Remington 's Pharmaceutical Sciences, 18th Edition, ed. A. Gennaro, Mack Publishing Co., Easton, PA, 1990.
• the active compound is included in the physiologically acceptable carrier or diluent in an amount sufficient to deliver to a patient a prophylactically or therapeutically effective amount without causing serious toxic effects in the patient treated.
• the term an "effective amount” or a “sufficient amount” generally refers to an amount sufficient to affect a desired biological effect, such as beneficial results. Thus, an "effective amount” or "sufficient amount” will depend upon the context in which it is being administered.
• the effective dosage range of the physiologically acceptable derivatives can be calculated based on the weight of the parent compound to be delivered. If the derivative exhibits activity in itself, the effective dosage can be estimated as above using the weight of the derivative, or by other means known to those skilled in the art.
• the invention provides a vaccine.
• Vaccines according to this aspect comprise a composition according to the invention, and further comprise an antigen.
• An antigen is a molecule that elicits a specific immune response.
• antigens include, without limitation, proteins, peptides, nucleic acids, carbohydrates and complexes or combinations of any of the same.
• Antigens may be natural or synthetic and generally induce an immune response that is specific for that antigen. Any such antigen may optionally be linked to an immunogenic protein, such as keyhole limpet hemocyanin (KLH), cholera toxin B subunit, or any other immunogenic carrier protein.
• KLH keyhole limpet hemocyanin
• Vaccines according to the invention may further include any of the plethora of known adjuvants, including, without limitation, Freund's complete adjuvant, KLH, monophosphoryl lipid A (MPL), alum, and saponins, including QS-21, imiquimod, R848, or combinations thereof.
• the invention provides methods for generating a TLR9- mediated immune response in a vertebrate, such methods comprising administering to the vertebrate a compound, composition or vaccine according to the invention.
• the vertebrate is a mammal.
• the term "mammal" is expressly intended to include humans and animals.
• the compound, composition or vaccine is administered to a vertebrate in need of immune stimulation.
• administration of a compound, composition or vaccine according to the invention can be by any suitable route, including, without limitation, parenteral, oral, intratumoral, sublingual, transdermal, topical, intranasal, aerosol, intraocular, intratracheal, intrarectal, mucosal, vaginal, by gene gun, dermal patch or in eye drop or mouthwash form.
• Administration of the compound, composition or vaccine 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 compound, composition or vaccine is preferably administered at a sufficient dosage to attain a blood level of a compound according to the invention from about 0.0001 micromolar to about 10 micromolar.
• a total dosage of a compound according to the invention ranges from about 0.001 mg per patient per day to about 200 mg per kg body weight per day. It may be 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.
• a compound, composition or vaccine according to the invention is administered in combination with another agent, including without limitation antibodies, cytotoxic agents, allergens, antibiotics, antisense oligonucleotides, SiRNA, aptamers, ribozymes, targeted therapies, peptides, proteins, gene therapy vectors, DNA vaccines, and/or adjuvants to enhance the specificity or magnitude of the immune response.
• another agent including without limitation antibodies, cytotoxic agents, allergens, antibiotics, antisense oligonucleotides, SiRNA, aptamers, ribozymes, targeted therapies, peptides, proteins, gene therapy vectors, DNA vaccines, and/or adjuvants to enhance the specificity or magnitude of the immune response.
• the term "in combination with” means in the course of treating a disease or disorder in a patient, administering the compound, composition or vaccine according to the invention and/or the other agent in any order, including simultaneous administration, as well as temporally spaced order of up to several hours, days or weeks apart.
• Such combination treatment may also include more than a single administration of the compound, composition or vaccine according to the invention, and/or the other agent.
• the administration of the compound, composition or vaccine according to the invention and/or the other agent may be by the same or different routes.
• the methods according to this aspect of the invention are useful for the prophylactic or therapeutic treatment of human or animal disease.
• the methods are useful for pediatric and veterinary vaccine applications.
• the methods are also useful for model studies of the immune system.
• the invention provides methods for therapeutically treating a patient having a disease or disorder, such methods comprising administering to the patient a compound, composition or vaccine according to the invention.
• the disease or disorder to be treated is cancer, an autoimmune disorder, infectious disease, airway inflammation, inflammatory disorders, allergy, asthma or a disease caused by a pathogen or allergen.
• Pathogens include for example bacteria, parasites, fungi, viruses, viroids, and prions.
• Administration is carried out as described for the fourth aspect of the invention.
• treatment generally refers to an approach intended to obtain a beneficial or desired results, which may include alleviation of symptoms, or delaying or ameliorating a disease progression.
• the term “allergy” generally refers to an inappropriate immune response characterized by inflammation and includes, without limitation, food allergies and respiratory allergies.
• airway inflammation includes, without limitation, asthma.
• autoimmune disorder refers to disorders in which "self components (e.g., proteins) undergo attack by the immune system. Such term includes autoimmune asthma.
• cancer includes, without limitation, any malignant growth or tumor caused by abnormal or uncontrolled cell proliferation and/or division. Cancers may occur in humans and/or animals and may arise in any and all tissues. Treating a patient having cancer with the invention may include administration of a compound, composition or vaccine according to the invention such that the abnormal or uncontrolled cell proliferation and/or division is affected.
• the invention provides methods for preventing a disease or disorder, such methods comprising administering to the patient a compound, composition or vaccine according to the invention.
• the disease or disorder to be prevented is cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, allergy, asthma or a disease caused by a pathogen.
• Pathogens include, without limitation, bacteria, parasites, fungi, viruses, viroids, and prions.
• Administration is carried out as described for the fourth aspect of the invention.
• the compound, composition or vaccine according to the invention can be administered in combination with any other agent useful for preventing or treating the disease or condition that does not diminish the immune stimulatory effect of the compound, composition or vaccine according to the invention.
• the agent useful for preventing or treating the disease or condition includes, but is not limited to, vaccines, antigens, antibodies, cytotoxic agents, allergens, antibiotics, antisense oligonucleotides, TLR agonist, peptides, proteins, gene therapy vectors, DNA vaccines and/or adjuvants to enhance the specificity or magnitude of the immune response, or co-stimulatory molecules such as cytokines, chemokines, protein ligands, trans- activating factors, peptides and peptides comprising modified amino acids.
• the compound, composition or vaccine according to the invention may be administered in combination with a chemotherapeutic compound or a monoclonal antibody.
• the agent can include DNA vectors encoding for antigen or allergen.
• the compound, composition or vaccine according to the invention can variously act as adjuvants and/or produce direct immunomodulatory effects.
• the linker derivatized CPG 5 was prepared by following the alternate approach which eliminates the need for making succinate 3 (Scheme 1).
• the CPG beads were activated by treating with 3% trichloroacetic acid (TCA) in dichloromethane (DCM) at room temperature (r.t.) to liberate maximum number of reactive amino groups on the surface of CPG.
• TCA 3% trichloroacetic acid
• DCM dichloromethane
• the activated CPG beads were then derivatized with succinic anhydride in the presence of DMAP to provide CPG beads 4.
• CPG derivatized linker 5 was obtained by condensation of 2 with carboxylic groups of CPG 4 in the presence of JV- ⁇ -dimethylaminopropyl)- ⁇ - ethylcarbodiimide hydrochloride (DEC)/DMAP. After derivatization, the residual carboxylic groups were eliminated by capping reaction with pentachlorophenol.
• 1,3,5-Pentanetriol linker derivatized CPG 10 and OligoPrep 11 were prepared starting from the commercially available diethyl 3-hydroxy glutarate 6 (Scheme 2). Reduction of 6 with LiAlH 4 yielded 1,3,5-pentanetriol 7 in quantitative yield.
• the triol 7 was then selectively protected with DMTCl in the presence of DMAP to afford bis-DMT protected alcohol 8, which was then successfully converted into succinate 9, which is ready to load on to the solid support, by treating with succinic anhydride in the presence of DMAP. Attachment of 9 to CPG was accomplished in quantitative loading yield in the presence of DIC/DMAP in pyridine/acetonitrile mixture (10).
• the C 5 linker functionalized supports 10 and 11 are ideal for making immunomers with identical sequences. Immunomers with unidentical sequences also exhibited potent immune stimulatory activity in our studies. Appropriately protected C5 linker, such as 14 (Scheme 3), is required in order to make immunomers with unidentical sequences.
• C5 linker 14 One of the hydroxyl groups of commercially available 1,5-pentanediol was selectively protected with DMT followed by phosphitylation with 2-cyanoethyl ⁇ /, ⁇ /-diisopropylchlorophos-phosphoramidite afforded the required C5 linker 14 (Scheme 3).
• CpG DNA dendrimers As potent synthetic immune modulatory motifs.
• appropriately protected linker phosphoramidites are essential.
• the C5 linker phosphramidites 15 and 16 were prepared from di-DMT alcohols 2 and 8, respectively, by phosphitylation with 2-cyanoethyl ⁇ /, ⁇ /-diisopropylchlorophosphosphoramidite as shown in Scheme 4.
• c ⁇ -Cyclohexanetriol linker derivatized with CPG 20 was accomplished as shown in Scheme 5.
• bis-DMT protected c ⁇ -l,3,5-cyclohexanetriol 18 was achieved from commercially available c ⁇ -l,3,5-cyclohexanetriol (17).
• the subsequent succinylation of the unprotected hydroxyl of 18 with succinic anhydride in the presence of DMAP afforded desired bis-DMT succinate 19 in 78% yield.
• Derivatization of CPG with succinate 19 was accomplished in quantitative loading yield (20, 40 ⁇ mol/g) in the presence of DIC/DMAP in pyridine/acetonitrile mixture.
• Reagents such as diethyl 3-hydroxy glutarate, lithium aluminum hydride (LiAlH 4 ), 4,4- dimethoxytrityl chloride (DMTCl), 4-dimethylaminopyridine (DMAP), succinic anhydride, O- (benzotriazol-l-yl)- ⁇ /, ⁇ /, ⁇ /"-tetramethyluronium tetrafluoroborate (TBTU), N 1 N'- diisopropylcarbodiimide (DIC), N-(3 -dimethylaminopropyl)- ⁇ /"-ethylcarbodiimide hydrochloride (DEC), trichloroacetic acid (TCA), N-methylimidazole (NMI), triethylamine (TEA), diisopropylethylamine (DIPEA) and solvents such as pyridine, dichloromethane (DCM) and tetrahydrofuran (THF) were obtained from Sigma-
• TLCs were run on silica gel 60 F 254 coated on aluminum sheets, and visualized by UV light or by a 5% phosphomolybdic acid (PMA) solution from Sigma-Aldrich (St. Louis, MO). Solvents such as ethyl acetate (EtOAc), hexanes, DCM, methanol, t-butyl methyl ether for chromatography were obtained from J. T. Baker and used without purification. Flash column chromatography was performed using silica gel 60 (mesh size 0.040 - 0.063 mm & 230 - 400 mesh ASTM) which was obtained from EMD Chemicals (Gibbstown, NJ). NMR spectra were performed on Varian 400MHz Unity Inova instrument.
• OligoPrep250 (100 g preswollen in acetonitrile) was taken in a peptide synthesis vessel and washed with anhydrous acetonitrile (3 x 100 mL). Succinate 9 (1.752 g, 2.125 mmol), DMAP (1.82 g, 14.87 mmol), TBTU (3.41 g, 10.62 mmol) and acetonitrile (100 mL) were added to OligoPrep250 and the slurry was shaken for 4 hrs.
• Pentanediol 12 (12.5 g, 120 mmol) and DMAP (14.6 g, 120 mmol) were dissolved in dry pyridine (100 mL), cooled to -10 0 C and maintained under argon atmosphere.
• DMTCl (37.3 g, 110 mmol, 0.92 equiv) in pyridine (150 mL) was added drop wise with vigorous stirring. The reaction mixture was allowed to slowly reach r.t. ( ⁇ 4 h) and continued stirring for overnight.
• the reaction mixture was diluted with another 500 mL of DCM and washed sequentially with saturated aqueous NaHCO 3 (1 x 500 mL), brine (2 x 500 mL) and water (1 x 500 mL).
• the organic layer dried over anhydrous MgSO 4 , filtered and rotoevaporated to dryness.
• the residue was purified on silica gel flash column chromatography using 3:1 hexane/EtOAc mixture containing 0.5% TEA to get 13 as a colorless viscous liquid (22.3 g, 74%).
• c/s-S ⁇ -U/s-dimethoxytrityloxy-cyclohexane-l-ol (18).
• c ⁇ -l,3,5-Cyclohexanetriol dehydrate (5.05 g, 30 mmol) was dissolved in pyridine (100 mL) and rotoevaporated to dryness and dried under high vacuum for 48 hrs to obtain anhydrous c ⁇ -l,3,5-cyclohexanetriol (4.05 g, 30.6 mmol).
• the above anhydrous cyclohexanetriol and DMAP (7.33 g, 60 mmol) were dissolved in dry pyridine (100 mL), cooled in ice bath and maintained under nitrogen atmosphere.
• Cap A (ABI, 80 mL) and Cap B (ABI, 90 mL) solutions were added to CPG support and shaken for 4 h. Solutions filtered off, CPG washed with acetonitrile containing 5% pyridine (2 x 100 mL) followed by acetonitrile (2 x 250 mL) and dried under high vacuum for 30 min. A solution of TBDMSCl (2.5 g) and imidazole (0.75 g) in acetonitrile containing 5% pyridine (100 mL) was added to CPG and shaken for 5 h.
• CPG was successively washed with acetonitrile containing 5% pyridine (3 x 100 mL) and DCM (4 x 100 mL) and dried under high vacuum in a desiccator for over night to get dry CPG support 20.
• Loading was determined by treating small portion of CPGwith 3% TCA in DCM and assayed DMT content 40 ⁇ mol/g) by measuring absorbance at 498 mm.
• Example 2 Cell Culture Conditions and Reagents,Cytokine induction by exemplar oligos from Table I in HEK293 cells expressing mouse TLR9
• HEK293 cells stably expressing mouse TLR9 (Invivogen, San Diego, CA) were cultured in 48-well plates in 250 ⁇ l/well DMEM supplemented with 10% heat-inactivated FBS in a 5% CO 2 incubator. At 80% confluence, cultures were transiently transfected with 400 ng/ml of SEAP (secreted form of human embryonic alkaline phosphatase) reporter plasmid (pNifty2- Seap) (Invivogen) in the presence of 4 ⁇ l/ml of lipofectamine (Invitrogen, Carlsbad, CA) in culture medium. Plasmid DNA and lipofectamine were diluted separately in serum-free medium and incubated at room temperature for 5 minutes.
• SEAP secreted form of human embryonic alkaline phosphatase reporter plasmid
• lipofectamine Invitrogen, Carlsbad, CA
• the diluted DNA and lipofectamine were mixed and the mixtures were incubated at room temperature for 20 minutes. Aliquots of 25 ⁇ l of the DNA/lipofectamine mixture containing 100 ng of plasmid DNA and 1 ⁇ l of lipofectamine were added to each well of the cell culture plate, and the cultures were continued for 4 hours.
• Example 3 Cytokine induction by exemplar oligos from Table I in human
• PBMCs PBMCs, pDCs, and mouse splenocytes Human PBMC isolation
• PBMCs Peripheral blood mononuclear cells from freshly drawn healthy volunteer blood (CBR Laboratories, Boston, MA) were isolated by Ficoll density gradient centrifugation method (Histopaque-1077, Sigma).
• Human pDC isolation pDCs were isolated from PBMCs by positive selection using the BDCA4 cell isolation kits (Miltenyi Biotec) according to the manufacturer's instructions.
• Spleen cells from 4-8 week old C57BL/6 mice were cultured in RPMI complete medium as described by Zhao, Q., et al (Biochem Pharmacol. 51 : 173-182 (1996)) and Branda, R.F., et al (Biochem. Pharmacol 45: 2037-2043 (1993)). All other culture reagents were purchased from Mediatech (Gaithersburg, MD).
• Human PBMCs or mouse splenocytes were plated in 48-well plates using 5x10 6 cells/ml.
• Human pDCs were plated in 96-well dishes using IXlO 6 cells/ml.
• the exemplar oligos from Table I dissolved in DPBS (pH 7.4; Mediatech) were added to the cell cultures.
• the cells were then incubated at 37 0 C for 24 hr and the supernatants were collected for luminex multiplex or ELISA assays.
• the levels of IFN- ⁇ , IL-6, and/or IL-12 were measured by sandwich ELISA.
• the required reagents, including cytokine antibodies and standards, were purchased from PharMingen.
• IL-I Ra the levels of IL-I Ra, IL-6, IL-IO, IL- 12, IFN-a, IFN- ⁇ , MIP-Ia, MlP- ⁇ , MCP-I, and IL-12p40p70 in culture supernatants were measured by Luminex multiplex assays, which were performed using Biosource human multiplex cytokine assay kits on Luminex 100 instrument and the data were analyzed using StarStation software supplied by Applied Cytometry Systems (Sacramento, CA).
• Human B cell proliferation assay in the presence of exemplar oligos from Table I Human B cells were isolated from PBMCs by positive selection using the CD 19 Cell
• the culture medium used for the assay consisted of RPMI 1640 medium supplemented with 1.5 mM glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 50 ⁇ M 2- mercaptoethanol, 100 IU/ml penicillin-streptomycin mix and 10% heat-inactivated fetal bovine serum.
• ICi 37 GBq; Perkin Elmer Life Sciences

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