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Nucleic Acids Res. Sep 11, 1995; 23(17): 3578–3584.
PMCID: PMC307240

Design, biochemical, biophysical and biological properties of cooperative antisense oligonucleotides.

Abstract

Short oligonucleotides that can bind to adjacent sites on target mRNA sequences are designed and evaluated for their binding affinity and biological activity. Sequence-specific binding of short tandem oligonucleotides is compared with a full-length single oligonucleotide (21mer) that binds to the same target sequence. Two short oligonucleotides that bind without a base separation between their binding sites on the target bind cooperatively, while oligonucleotides that have a one or two base separation between the binding oligonucleotides do not. The binding affinity of the tandem oligonucleotides is improved by extending the ends of the two oligonucleotides with complementary sequences. These extended sequences form a duplex stem when both oligonucleotides bind to the target, resulting in a stable ternary complex. RNase H studies reveal that the cooperative oligonucleotides bind to the target RNA with sequence specificity. A short oligonucleotide (9mer) with one or two mismatches does not bind at the intended site, while longer oligonucleotides (21mers) with one or two mismatches still bind to the same site, as does a perfectly matched 21mer, and evoke RNase H activity. HIV-1 inhibition studies reveal an increase in activity of the cooperative oligonucleotide combinations as the length of the dimerization domain increases.

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Selected References

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  • Padmapriya AA, Tang J, Agrawal S. Large-scale synthesis, purification, and analysis of oligodeoxynucleotide phosphorothioates. Antisense Res Dev. 1994 Fall;4(3):185–199. [PubMed]
  • Zhang R, Yan J, Shahinian HK, Shahinian H, Amin G, Lu Z, Liu T, Saag MS, Jiang Z, Temsamani J, et al. Pharmacokinetics of an anti-human immunodeficiency virus antisense oligodeoxynucleotide phosphorothioate (GEM 91) in HIV-infected subjects. Clin Pharmacol Ther. 1995 Jul;58(1):44–53. [PubMed]
  • Crooke ST, Grillone LR, Tendolkar A, Garrett A, Fratkin MJ, Leeds J, Barr WH. A pharmacokinetic evaluation of 14C-labeled afovirsen sodium in patients with genital warts. Clin Pharmacol Ther. 1994 Dec;56(6 Pt 1):641–646. [PubMed]
  • Bayever E, Iversen PL, Bishop MR, Sharp JG, Tewary HK, Arneson MA, Pirruccello SJ, Ruddon RW, Kessinger A, Zon G, et al. Systemic administration of a phosphorothioate oligonucleotide with a sequence complementary to p53 for acute myelogenous leukemia and myelodysplastic syndrome: initial results of a phase I trial. Antisense Res Dev. 1993 Winter;3(4):383–390. [PubMed]
  • Stephenson ML, Zamecnik PC. Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide. Proc Natl Acad Sci U S A. 1978 Jan;75(1):285–288. [PMC free article] [PubMed]
  • Woolf TM, Melton DA, Jennings CG. Specificity of antisense oligonucleotides in vivo. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7305–7309. [PMC free article] [PubMed]
  • Herschlag D. Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: more isn't always better. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):6921–6925. [PMC free article] [PubMed]
  • Stein CA, Cheng YC. Antisense oligonucleotides as therapeutic agents--is the bullet really magical? Science. 1993 Aug 20;261(5124):1004–1012. [PubMed]
  • Asseline U, Delarue M, Lancelot G, Toulmé F, Thuong NT, Montenay-Garestier T, Hélène C. Nucleic acid-binding molecules with high affinity and base sequence specificity: intercalating agents covalently linked to oligodeoxynucleotides. Proc Natl Acad Sci U S A. 1984 Jun;81(11):3297–3301. [PMC free article] [PubMed]
  • Maher LJ, 3rd, Dolnick BJ. Comparative hybrid arrest by tandem antisense oligodeoxyribonucleotides or oligodeoxyribonucleoside methylphosphonates in a cell-free system. Nucleic Acids Res. 1988 Apr 25;16(8):3341–3358. [PMC free article] [PubMed]
  • Gryaznov SM, Lloyd DH. Modulation of oligonucleotide duplex and triplex stability via hydrophobic interactions. Nucleic Acids Res. 1993 Dec 25;21(25):5909–5915. [PMC free article] [PubMed]
  • Maher LJ, 3rd, Dolnick BJ. Specific hybridization arrest of dihydrofolate reductase mRNA in vitro using anti-sense RNA or anti-sense oligonucleotides. Arch Biochem Biophys. 1987 Feb 15;253(1):214–220. [PubMed]
  • Agrawal S, Tang JY. GEM 91--an antisense oligonucleotide phosphorothioate as a therapeutic agent for AIDS. Antisense Res Dev. 1992 Winter;2(4):261–266. [PubMed]
  • Clever J, Sassetti C, Parslow TG. RNA secondary structure and binding sites for gag gene products in the 5' packaging signal of human immunodeficiency virus type 1. J Virol. 1995 Apr;69(4):2101–2109. [PMC free article] [PubMed]
  • Baudin F, Marquet R, Isel C, Darlix JL, Ehresmann B, Ehresmann C. Functional sites in the 5' region of human immunodeficiency virus type 1 RNA form defined structural domains. J Mol Biol. 1993 Jan 20;229(2):382–397. [PubMed]
  • Sundquist WI, Heaphy S. Evidence for interstrand quadruplex formation in the dimerization of human immunodeficiency virus 1 genomic RNA. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3393–3397. [PMC free article] [PubMed]
  • Awang G, Sen D. Mode of dimerization of HIV-1 genomic RNA. Biochemistry. 1993 Oct 26;32(42):11453–11457. [PubMed]
  • Posner MR, Hideshima T, Cannon T, Mukherjee M, Mayer KH, Byrn RA. An IgG human monoclonal antibody that reacts with HIV-1/GP120, inhibits virus binding to cells, and neutralizes infection. J Immunol. 1991 Jun 15;146(12):4325–4332. [PubMed]
  • Pauwels R, Balzarini J, Baba M, Snoeck R, Schols D, Herdewijn P, Desmyter J, De Clercq E. Rapid and automated tetrazolium-based colorimetric assay for the detection of anti-HIV compounds. J Virol Methods. 1988 Aug;20(4):309–321. [PubMed]
  • Mosmann T. Rapid colorimetric assay for cellular growth and survival: application to proliferation and cytotoxicity assays. J Immunol Methods. 1983 Dec 16;65(1-2):55–63. [PubMed]
  • Harada S, Koyanagi Y, Yamamoto N. Infection of HTLV-III/LAV in HTLV-I-carrying cells MT-2 and MT-4 and application in a plaque assay. Science. 1985 Aug 9;229(4713):563–566. [PubMed]
  • Popovic M, Sarngadharan MG, Read E, Gallo RC. Detection, isolation, and continuous production of cytopathic retroviruses (HTLV-III) from patients with AIDS and pre-AIDS. Science. 1984 May 4;224(4648):497–500. [PubMed]
  • Gazdar AF, Carney DN, Bunn PA, Russell EK, Jaffe ES, Schechter GP, Guccion JG. Mitogen requirements for the in vitro propagation of cutaneous T-cell lymphomas. Blood. 1980 Mar;55(3):409–417. [PubMed]
  • Vujcic LK, Shepp DH, Klutch M, Wells MA, Hendry RM, Wittek AE, Krilov L, Quinnan GV., Jr Use of a sensitive neutralization assay to measure the prevalence of antibodies to the human immunodeficiency virus. J Infect Dis. 1988 May;157(5):1047–1050. [PubMed]
  • HERSKOVITS TT. Nonaqueous solutions of DNA; denaturation by urea and its methyl derivatives. Biochemistry. 1963 Mar-Apr;2:335–340. [PubMed]
  • Young S, Wagner RW. Hybridization and dissociation rates of phosphodiester or modified oligodeoxynucleotides with RNA at near-physiological conditions. Nucleic Acids Res. 1991 May 11;19(9):2463–2470. [PMC free article] [PubMed]
  • Cedergren R, Grosjean H. RNA design by in vitro RNA recombination and synthesis. Biochem Cell Biol. 1987 Aug;65(8):677–692. [PubMed]
  • Krämer A, Keller W, Appel B, Lührmann R. The 5' terminus of the RNA moiety of U1 small nuclear ribonucleoprotein particles is required for the splicing of messenger RNA precursors. Cell. 1984 Aug;38(1):299–307. [PubMed]
  • Crum C, Johnson JD, Nelson A, Roth D. Complementary oligodeoxynucleotide mediated inhibition of tobacco mosaic virus RNA translation in vitro. Nucleic Acids Res. 1988 May 25;16(10):4569–4581. [PMC free article] [PubMed]
  • Galbraith WM, Hobson WC, Giclas PC, Schechter PJ, Agrawal S. Complement activation and hemodynamic changes following intravenous administration of phosphorothioate oligonucleotides in the monkey. Antisense Res Dev. 1994 Fall;4(3):201–206. [PubMed]

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