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The invention provides immunostimulatory oligonucleotides having at least one CpG dinucleotide and a secondary structure at the 5′- or 3′-end. These oligonucleotides have either reduced or improved immunostimulatory properties. The invention establishes that 5′-terminal secondary structures affect i

The invention provides immunostimulatory oligonucleotides having at least one CpG dinucleotide and a secondary structure at the 5′- or 3′-end. These oligonucleotides have either reduced or improved immunostimulatory properties. The invention establishes that 5′-terminal secondary structures affect immunostimulatory activity significantly more than those at the 3′-end. The invention also provides methods for increasing or decreasing the immunostimulatory activity of a CpG-containing nucleic acid.

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1. A method for treating cancer, infection, inflammatory disease or autoimmune disease comprising administering to a patient an immunostimulatory nucleic acid, having secondary structure formed by intermolecular hydrogen bonding between two oligonucleotide compounds, wherein each of the oligonucleot

1. A method for treating cancer, infection, inflammatory disease or autoimmune disease comprising administering to a patient an immunostimulatory nucleic acid, having secondary structure formed by intermolecular hydrogen bonding between two oligonucleotide compounds, wherein each of the oligonucleotide compounds comprise the general structure of: Domain A-Domain B-Domain C,  (I) wherein Domain A is 5′-3′ DNA not having a palindromic or self-complementary domain and containing at least one dinucleotide selected from the group consisting of CpG, C*pG, C*pG* and CpG*, wherein C is cytidine or 2′-deoxycitidine, G is guanosine or 2′-deoxyguanosine, C* is 2′-deoxythymidine, 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine, 2′ dideoxy-5-halocytosine, 2′-dideoxy-5-nitrocytosine, arabinocytidine, 2′-deoxy-2′-substitutedarabinocytidine, 2′-O-substituted arabinocytidine, 2′-deoxy-5-hydroxycytidine, 2′-deoxy-N4-alkyl-cytidine, 2′-deoxy-4-thiouridine, or other non-natural pyrimidine nucleosides, G*is 2′ deoxy-7-deazaguanosine, 2′-deoxy-6-thioguanosine, arabinoguanosine, 2′-deoxy-2′-substituted-arabinoguanosine, 2′-O-substituted-arabinoguanosine, 2′-deoxyinosine, or other non-natural purine nucleoside, and p is an internucleoside linkage selected from the group consisting of phosphodiester, phosphorothioate, and phosphorodithioate, wherein Domain B is a non-nucleoside linker joining Domain A and Domain C, wherein Domain C is 3′-5′ DNA or RNA having a palindromic or self-complementary domain allowing for intermolecular hydrogen bonding, and which can or cannot have a dinucleotide selected from the group consisting of CpG, C*pG, C*pG* and CpG*, wherein C is cytidine or 2′deoxycitidine, G is guanosine or 2′ deoxyguanosine, C* is 2′-deoxythymidine, 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine, 2′-dideoxy-5-halocytosine, 2′-dideoxy-5-nitrocytosine, arabinocytidine, 2′-deoxy-2′-substituted arabinocytidine, 2′-O-substituted arabinocytidine, 2′-deoxy-5-hydroxycytidine, 2′-deoxy-N4-alkyl-cytidine, 2′-deoxy-4-thiouridine, or other non-natural pyrimidine nucleosides, G* is 2′ deoxy-7-deazaguanosine, 2′-deoxy-6-thioguanosine, arabinoguanosine, 2′-deoxy-2′substituted-arabinoguanosine, 2′-O-substituted-arabinoguanosine, 2′-deoxyinosine, or other non-natural purine nucleoside, p is an internucleoside linkage selected from the group consisting of phosphodiester and phosphorothioate, and wherein each oligonucleotide compound comprises from about 12 to about 50 nucleotides in length. 2. The method according to claim 1, wherein Domain A contains at least one dinucleotide selected from the group consisting of C*pG, C*pG* and CpG*. 3. The method according to claim 1, wherein Domain C contains at least one dinucleotide selected from the group consisting of CpG, C*pG, C*pG* and CpG*. 4. The method according to claim 1, wherein each oligonucleotide compound comprises from about 12 to about 26 nucleotides in length. 5. The method according to claim 1, wherein the immunostimulatory nucleic acid has the structure: 6. A method for treating cancer, infection, inflammatory disease or autoimmune disease comprising administering to a patient an immunostimulatory nucleic acid, having secondary structure formed by intermolecular hydrogen bonding between at least two oligonucleotide compounds, wherein each of the oligonucleotide compounds comprise the general structure of: Domain A-Domain B-Domain C,  (I) wherein Domain A is 5′-3′ DNA having a palindromic or self-complementary domain allowing for intermolecular hydrogen bonding and containing or not containing at least one dinucleotide selected from the group consisting of CpG, C*pG, C*pG* and CpG*, wherein C is cytidine or 2′-deoxycitidine, G is guanosine or 2′-deoxyguanosine, C* is 2′-deoxythymidine, 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine, 2′ dideoxy-5-halocytosine, 2′-dideoxy-5-nitrocytosine, arabinocytidine, 2′-deoxy-2′-substitutedarabinocytidine, 2′-O-substituted arabinocytidine, 2′-deoxy-5-hydroxycytidine, 2′-deoxy-N4-alkyl-cytidine, 2′-deoxy-4-thiouridine, or other non-natural pyrimidine nucleosides, G*is 2′ deoxy-7-deazaguanosine, 2′-deoxy-6-thioguanosine, arabinoguanosine, 2′-deoxy-2′-substituted-arabinoguanosine, 2′-O-substituted-arabinoguanosine, 2′-deoxyinosine, or other non-natural purine nucleoside, and p is an internucleoside linkage selected from the group consisting of phosphodiester, phosphorothioate, and phosphorodithioate, wherein Domain B is a-non-nucleoside linker joining Domain A and Domain C, wherein Domain C is 3′-5′ DNA or RNA having a palindromic or self-complementary domain allowing for intermolecular hydrogen bonding and containing or not containing at least one dinucleotide selected from the group consisting of CpG, C*pG, C*pG* and CpG*, wherein C is cytidine or 2′deoxycitidine, G is guanosine or 2′ deoxyguanosine, C* is 2′-deoxythymidine, 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine, 2′-dideoxy-5-halocytosine, 2′-dideoxy-5-nitrocytosine, arabinocytidine, 2′-deoxy-2′-substituted arabinocytidine, 2′-O-substituted arabinocytidine, 2′-deoxy-5-hydroxycytidine, 2′-deoxy-N4-alkyl-cytidine, 2′-deoxy-4-thiouridine, or other non-natural pyrimidine nucleosides, G* is 2′ deoxy-7-deazaguanosine, 2′-deoxy-6-thioguanosine, arabinoguanosine, 2′-deoxy-2′substituted-arabinoguanosine, 2′-O-substituted-arabinoguanosine, 2′-deoxyinosine, or other non-natural purine nucleoside, p is an internucleoside linkage selected from the group consisting of phosphodiester and phosphorothioate; provided that Domain A or Domain C has at least one dinucleotide selected from the group consisting of CpG, C*pG, C*pG* and CpG*, and wherein each oligonucleotide compound comprises from about 12 to about 50 nucleotides in length. 7. The method according to claim 6, wherein each oligonucleotide compound comprises from about 12 to about 26 nucleotides. 8. The method according to claim 6, wherein the immunostimulatory nucleic acid has the structure: 9. The method according to claim 6, wherein Domain A contains at least one dinucleotide selected from the group consisting of CpG, C*pG, C*pG* and CpG*. 10. The method according to claim 6, wherein Domain C contains at least one dinucleotide selected from the group consisting of CpG, C*pG, C*pG* and CpG*. 11. The method according to claim 6, wherein Domain A and Domain C contain at least one dinucleotide selected from the group consisting of CpG, C*pG, C*pG* and CpG*. 12. The method according to claim 1, wherein the infection is a viral infection. 13. The method according to claim 1, wherein the infection is a bacterial infection. 14. The method according to claim 1, wherein the inflammatory disease is asthma. 15. The method according to claim 1, wherein the inflammatory disease is allergy. 16. The method according to claim 1, further comprising administering a vaccine, antigen or an antisense oligonucleotide. 17. Then method according to claim 16, wherein the vaccine is a cancer vaccine. 18. The method according to claim 17, wherein the cancer vaccine is selected from the group consisting of EFG, Anti-idiotypic cancer vaccines, Gp75 antigen, GMK melanoma vaccine, MGV ganglioside conjugate vaccine, Her2/new, Ovarex, M-Vax, O-Vax, L-Vax, STn-KHL theratope, BLP25 (MUC-1), liposomal idiotypic vaccine, Melacine, peptide antigen vaccines, toxin/antigen vaccines, MVA-vased vaccine, PACIS, BCG vaccine, TA-HPV, TA-CIN, DISC-virus and ImmunCyst/TheraCys. 19. The method according to claim 6, wherein the infection is a viral infection. 20. The method according to claim 6, wherein the infection is a bacterial infection. 21. The method according to claim 6, wherein the inflammatory disease is asthma. 22. The method according to claim 6, wherein the inflammatory disease is allergy. 23. The method according to claim 6, further comprising administering a vaccine, antigen or an antisense oligonucleotide. 24. Then method according to claim 23, wherein the vaccine is a cancer vaccine. 25. The method according to claim 24, wherein the cancer vaccine is selected from the group consisting of EFG, Anti-idiotypic cancer vaccines, Gp75 antigen, GMK melanoma vaccine, MGV ganglioside conjugate vaccine, Her2/new, Ovarex, M-Vax, O-Vax, L-Vax, STn-KHL theratope, BLP25 (MUC-1), liposomal idiotypic vaccine, Melacine, peptide antigen vaccines, toxin/antigen vaccines, MVA-vased vaccine, PACIS, BCG vaccine, TA-HPV, TA-CIN, DISC-virus and ImmunCyst/TheraCys.