Skip to main content
SpringerLink
Log in

Therapeutic Oligonucleotides

  • Protocol
  • First Online:
Therapeutic Oligonucleotides

Part of the book series: Methods in Molecular Biology ((MIMB,volume 764))

Abstract

A brief historical introduction describes early attempts to silence specific genes using the antisense oligonucleotides that flourished in the 1980s. Early aspirations for therapeutic applications were almost extinguished by the unexpected complexity of oligonucleotide pharmacology. Once the biochemistry and molecular biology behind some of the pharmacology was worked out, new approaches became apparent for using oligonucleotides to treat disease. The biochemistry of small nucleic acids is outlined in Section 2. Various approaches employing oligonucleotides to control cellular functions are reviewed in Section 3. These include antisense oligonucleotides and siRNA that bind to RNA, antigene oligonucleotides that bind to DNA, and aptamers, decoys, and CpG oligonucleotides that bind to proteins.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Zamecnik, P. C., & Stephenson, M. L. (1978) Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. Proceedings of the National Academy of Sciences USA 75, 280–284.

    Article  CAS  Google Scholar 

  2. Stephenson, M. L., & Zamecnik, P. C. (1978) Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxynucleotide. Proceedings of the National Academy of Sciences USA 75, 285–288.

    Article  CAS  Google Scholar 

  3. Zamecnik, P., Goodchild, J., Taguchi, Y., & Sarin, P. S. (1986) Inhibition of replication and expression of human T-cell lymphotropic virus type III in cultured cells by exogenous synthetic oligonucleotides complementary to viral RNA. Proceedings of the National Academy of Sciences USA 83, 4143–4146.

    Article  CAS  Google Scholar 

  4. Wilson, T. J., & Lilley, D. M. (2009) The evolution of ribozyme chemistry. Science 232, 1436–1438.

    Article  Google Scholar 

  5. Breaker, R. R. (2008) Complex riboswitches. Science 319, 1795–1797.

    Article  PubMed  CAS  Google Scholar 

  6. Ghildiyal, M., & Zamore, P. D. (2009) Small silencing RNAs: An expanding universe. Nature Reviews Genetics 10, 94–108.

    Article  PubMed  CAS  Google Scholar 

  7. Lewis, B. P., Burge, C. B., & Bartel, D. P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20.

    Article  PubMed  CAS  Google Scholar 

  8. Moazed, D. (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature 457, 413–420.

    Article  PubMed  CAS  Google Scholar 

  9. Carthew, R. W., & Sontheimer, E. J. (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642–655.

    Article  PubMed  CAS  Google Scholar 

  10. Vasudevan, S., Tong, Y., & Steitz, J. A. (2007) Switching from repression to activation: MicroRNAs can up-regulate translation. Science 318, 1931–1934.

    Article  PubMed  CAS  Google Scholar 

  11. Dolgin, E. (2009) Now showing: RNA activation. The Scientist 23, 34–39.

    Google Scholar 

  12. Farazi, T. A., Juranek, S. A., & Tuschl, T. (2008) The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 135, 1201–1214.

    Article  PubMed  CAS  Google Scholar 

  13. Olejniczak, M., Galka, P., & Krzyzosiak, W. J. (2010) Sequence-non-specific effects of RNA interference triggers and microRNA regulators. Nucleic Acids Research 38, 1–16.

    Article  PubMed  CAS  Google Scholar 

  14. Lee, H.-C., et al. (2009) qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 459, 274–277.

    Article  PubMed  CAS  Google Scholar 

  15. Ku, G., & McManus, M. T. (2008) Behind the scenes of a small RNA gene-silencing pathway. Human Gene Therapy 19, 17–26.

    Article  PubMed  CAS  Google Scholar 

  16. Marquez, R. T., & McCaffrey, A. P. (2008) Advances in MicroRNAs: Implications for gene therapists. Human Gene Therapy 19, 27–38.

    Article  PubMed  CAS  Google Scholar 

  17. Bonauer, A., et al. (2009) MicroRNA-92a controls angiogenesis and functional recovery of ischemic tissues in mice. Science 324, 1710–1713.

    Article  PubMed  CAS  Google Scholar 

  18. Williams, A. H., et al. (2009) MicroRNA-206 delays ALS progression and promotes regeneration of neuromuscular synapses in mice. Science 326, 1549–1554.

    Article  PubMed  CAS  Google Scholar 

  19. Amaral, P. P., Dinger, M. E., Mercer, T. R., & Mattick, J. S. (2008) The eukaryotic genome as an RNA machine. Science 319, 1787–1789.

    Article  PubMed  CAS  Google Scholar 

  20. Pennisi, E. (2009) Some RNA may play key role in repressing genes, slowing cancer. Science 324, 1252–1253.

    Article  PubMed  CAS  Google Scholar 

  21. Morris, K. V. (2009) RNA-directed transcriptional gene silencing and activation in human cells. Oligonucleotides 19, 299–305.

    Article  PubMed  CAS  Google Scholar 

  22. Hawkins, P. G., Santoso, S., Adams, C., Anest, V., & Morris, K. V. (2009) Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells. Nucleic Acids Research 37, 2984–2995.

    Article  PubMed  CAS  Google Scholar 

  23. Schwartz, J., et al. (2008) Antisense transcripts are targets for activating small RNAs. Nature Structural & Molecular Biology 15, 842–848.

    Article  CAS  Google Scholar 

  24. Panter, G., Kužnik, A., & Jerala, R. (2009) Therapeutic applications of nucleic acids as ligands for toll-like receptors. Current Opinion Molecular Therapeutics 11, 133–145.

    CAS  Google Scholar 

  25. Juliano, R., Alam, M. R., Dixit, V., & Kang, H. (2008) Mechanisms and strategies for effective delivery of antisense and siRNA oligonucleotides. Nucleic Acids Research 36, 4158–4171.

    Article  PubMed  CAS  Google Scholar 

  26. Juliano, R., Bauman, J., Kang, H., & Ming, X. (2009) Biological barriers to therapy with antisense and siRNA oligonucleotides. Molecular Pharmaceutics 6, 686–695.

    Article  PubMed  CAS  Google Scholar 

  27. Stein, C. A., et al. (2010) Efficient gene silencing by delivery of locked nucleic acid antisense oligonucleotides, unassisted by transfection reagents. Nucleic Acids Research 38, e3.

    Article  PubMed  CAS  Google Scholar 

  28. Rudnick, S. I., Swaminathan, J., Sumaroka, M., Liebhaber, S., & Gewirtz, A. M. (2008) Effects of local mRNA structure on posttranscriptional gene silencing. Proceedings of the National Academy of Sciences 105, 13787–13792.

    Article  CAS  Google Scholar 

  29. Ichihara, M., et al. (2007) Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Nucleic Acids Research 35, e123.

    Article  PubMed  Google Scholar 

  30. Kauffmann, A. D., Campagna, R. J., Bartels, C. B., & Childs-Disney, J. L. (2009) Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides. Nucleic Acids Research 37, e121.

    Article  PubMed  Google Scholar 

  31. Li, Z., Fortin, Y., & Shen, S.-H. (2009) Forward and robust selection of the most potent and noncellular toxic siRNAs from RNAi libraries. Nucleic Acids Research 37, e8.

    Article  PubMed  Google Scholar 

  32. Gifford, L. K., et al. (2005) Identification of antisense nucleic acid hybridization sites in mRNA molecules with self-quenching fluorescent reporter molecules. Nucleic Acids Research 33, e28.

    Article  PubMed  Google Scholar 

  33. Perkel, J. M. (2009) RNAi therapeutics: A two-year update. Science 326, 454–456.

    Article  Google Scholar 

  34. Lanford, R. E., et al. (2010) Therapeutic silencing of MicroRNA-122 in primates with chronic hepatitis C virus infection. Science 327, 198–201.

    Article  PubMed  CAS  Google Scholar 

  35. Hashizume, R., et al. (2008) New therapeutic approach for brain tumors: Intranasal delivery of telomerase inhibitor GRN163. Neuro-oncol 10, 112–120.

    Article  PubMed  CAS  Google Scholar 

  36. Lu, Y., et al. (2009) A single anti-microRNA antisense oligodeoxyribonucleotide (AMO) targeting multiple microRNAs offers an improved approach for microRNA interference. Nucleic Acids Research 37, e24.

    Article  PubMed  Google Scholar 

  37. Medina, P. P., & Slack, F. J. (2009) Inhibiting microRNA function in vivo. Nature Methods 6, 37–38.

    Article  PubMed  CAS  Google Scholar 

  38. Horwich, M. D., & Zamore, P. D. (2008) Design and delivery of antisense oligonucleotides to block microRNA function in cultured drosophila and human cells. Nature Protocols 3, 1537–1549.

    Article  PubMed  CAS  Google Scholar 

  39. Trang, P., et al. (2009) Regression of murine lung tumors by the let-7 microRNA. Oncogene 29, 1580–1587.

    Article  PubMed  Google Scholar 

  40. Koizumi, M. (2006) ENA® oligonucleotides as therapeutics. Current Opinion Molecular Therapeutics 8, 144–149.

    CAS  Google Scholar 

  41. Mitsuoka, Y., et al. (2009) A bridged nucleic acid, 2',4'-BNACOC: Synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2',4'-BNACOC monomers and RNA-selective nucleic-acid recognition. Nucleic Acids Research 37, 1225–1238.

    Article  PubMed  CAS  Google Scholar 

  42. Ørum, H., & Wengel, J. (2001) Locked nucleic acids: A promising molecular family for gene-function analysis and antisense drug development. Current Opinion Molecular Therapeutics 3, 239–243.

    Google Scholar 

  43. Rottman, F., Dunlap, B. E., & Friderici, K. H. (1971) 2'-O-methyl polynucleotides as templates for cell-free amino acid incorporation. Biochemistry 10, 2581–2587.

    Article  PubMed  CAS  Google Scholar 

  44. Iversen, P. L., & Newbry, S. (2005) Manipulation of zebrafish embryogenesis by phosphorodiamidate morpholino oligomers indicates minimal non-specific teratogenesis. Current Opinion Molecular Therapeutics 7, 104–108.

    CAS  Google Scholar 

  45. Boutimah-Hamoudi, F., et al. (2007) Cellular antisense activity of peptide nucleic acid (PNAs) targeted to HIV-1 polypurine tract (PPT) containing RNA. Nucleic Acids Research 35, 3907–3917.

    Article  PubMed  CAS  Google Scholar 

  46. Bramsen, J. B., et al. (2009) A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity. Nucleic Acids Research 37, 2867–2881.

    Article  PubMed  CAS  Google Scholar 

  47. Thiel, K. W., & Giangrande, P. H. (2009) Therapeutic applications of DNA and RNA aptamers. Oligonucleotides 19, 209–222.

    Article  PubMed  CAS  Google Scholar 

  48. Collingwood, M. A., et al. (2008) Chemical modification patterns compatible with high potency dicer-substrate small interfering RNAs. Oligonucleotides 18, 187–200.

    Article  PubMed  CAS  Google Scholar 

  49. Hickerson, R. P., et al. (2008) Stability study of unmodified siRNA and relevance to clinical use. Oligonucleotides 18, 345–354.

    Article  PubMed  CAS  Google Scholar 

  50. Querbes, W., et al. (2009) Direct CNS delivery of siRNA mediates robust silencing in oligodendrocytes. Oligonucleotides 19, 23–29.

    Article  PubMed  CAS  Google Scholar 

  51. Kalluri, R., & Kanasaki, K. (2008) Generic block on angiogenesis. Nature 452, 543–544.

    Article  PubMed  CAS  Google Scholar 

  52. Robbins, M., Judge, A., & MacLachlan, I. (2009) siRNA and innate immunity. Oligonucleotides 19, 89–101.

    Article  PubMed  CAS  Google Scholar 

  53. Kenworthy, R., et al. (2009) Short-hairpin RNAs delivered by lentiviral vector transduction trigger RIG-I-mediated IFN activation. Nucleic Acids Research 37, 6587–6599.

    Article  PubMed  CAS  Google Scholar 

  54. Olejniczak, M., Galka, P., & Krzyzosiak, W. J. (2009) Sequence-non-specific effects of RNA interference triggers and microRNA regulators. Nucleic Acids Research 38, 1–16.

    Article  PubMed  Google Scholar 

  55. Kleinman, M. E., et al. (2008) Sequence- and target-independent angiogenesis suppression by siRNA via TLR3. Nature 452, 591–597.

    Article  PubMed  CAS  Google Scholar 

  56. Khan, A. A., et al. (2009) Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nature Biotechnology 27, 549–555.

    Article  PubMed  CAS  Google Scholar 

  57. Grimm, D., et al. (2006) Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 441, 537–541.

    Article  PubMed  CAS  Google Scholar 

  58. Goodchild, J. (2000) Hammerhead ribozymes: Biochemical and chemical considerations. Current Opinion Molecular Therapeutics 2, 272–281.

    CAS  Google Scholar 

  59. Müller-Kuller, T., Capalbo, G., Klebba, C., Engels, J. W., & Klein, S. A. (2009) Identification and characterization of a highly efficient anti-HIV pol hammerhead ribozyme. Oligonucleotides 19, 265–271.

    Article  PubMed  Google Scholar 

  60. Schlosser, K., & Li, Y. (2009) Biologically inspired synthetic enzymes made from DNA. Chemistry & Biology 16, 311–322.

    Article  CAS  Google Scholar 

  61. Schlosser, K., & Li, Y. (2009) DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides. Nucleic Acids Research 37, 413–420.

    Article  PubMed  CAS  Google Scholar 

  62. Reyes-Gutiérrez, P., & Alvarez-Salas, L. M. (2009) Cleavage of HPV-16 E6/E7 mRNA mediated by modified 10-23 deoxyribozymes. Oligonucleotides 19, 233–242.

    Article  PubMed  Google Scholar 

  63. Beane, R., Gabillet, S., Montaillier, C., Arar, K., & Corey, D. (2008) Recognition of chromosomal DNA inside cells by locked nucleic acids. Biochemistry 57, 13147–13149.

    Article  Google Scholar 

  64. Beane, R., et al. (2007) Inhibiting gene expression with locked nucleic acids (LNAs) that target chromosomal DNA. Biochemistry 46, 7572–7580.

    Article  PubMed  CAS  Google Scholar 

  65. Hu, J., & Corey, D. R. (2007) Inhibiting gene expression with peptide nucleic acid (PNA)–peptide conjugates that target chromosomal DNA. Biochemistry 46, 7581–7589.

    Article  PubMed  CAS  Google Scholar 

  66. Duca, M., Vekhoff, P., Oussedik, K., Halby, L., & Arimondo, P. B. (2008) The triple helix: 50 years later, the outcome. Nucleic Acids Research 36, 5123–5138.

    Article  PubMed  CAS  Google Scholar 

  67. Liu, Y., Nairn, R. S., & Vasquez, K. M. (2009) Targeted gene conversion induced by triplex-directed psoralen interstrand crosslinks in mammalian cells. Nucleic Acids Research 37, 6378–6388.

    Article  PubMed  CAS  Google Scholar 

  68. Fraunfelder, F. W. (2005) Pegaptanib for wet macular degeneration. Drugs of Today 41, 703–709.

    Article  PubMed  CAS  Google Scholar 

  69. Blake, C. M., Sullenger, B. A., Lawrence, D. A., & Fortenberry, Y. M. (2009) Antimetastatic potential of PAI-1–Specific RNA aptamers. Oligonucleotides 19, 117–128.

    Article  PubMed  CAS  Google Scholar 

  70. Huang, Y.-F., et al. (2009) Molecular assembly of an aptamer-drug conjugate for targeted drug delivery to tumor cells. ChemBioChem 10, 862–868.

    Article  PubMed  CAS  Google Scholar 

  71. Mallikaratchy, P., Tang, Z. W., & Tan, W. H. (2008) Cell specific aptamer-photosensitizer conjugates as a molecular tool in photodynamic therapy. ChemMedChem 3, 425–428.

    Article  PubMed  CAS  Google Scholar 

  72. Cao, Z., et al. (2009) Reversible cell-specific drug delivery with aptamer-functionalized liposomes. Angewandte Chemie International Edition English 48, 6494–6498.

    Article  CAS  Google Scholar 

  73. Levy-Nissenbaum, E., Radovic-Moreno, A. F., Wang, A. Z., Langer, R., & Farokhzad, O. C. (2008) Nanotechnology and aptamers: Applications in drug delivery. Trends in Biotechnology 26, 442–449.

    Article  PubMed  CAS  Google Scholar 

  74. Zhou, J., et al. (2009) Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of dicer substrate siRNAs into HIV infected cells. Nucleic Acids Research 37, 3094–3109.

    Article  PubMed  CAS  Google Scholar 

  75. Hunsicker, A., et al. (2009) An RNA aptamer that induces transcription. Chemistry & Biology 16, 173–180.

    Article  CAS  Google Scholar 

  76. Kang, J., Lee, M. S., Copland, J. A., Luxon, B. A., & Gorenstein, D. G. (2008) Combinatorial selection of a single standed DNA thioaptamer from whole cell selection. Chemistry – A European Journal 14, 1769–1775.

    Article  Google Scholar 

  77. Tomita, N., Morishita, R., Tomita, T., & Ogihara, T. (2002) Potential therapeutic applications of decoy oligonucleotides. Current Opinion Molecular Therapeutics 4, 166–170.

    CAS  Google Scholar 

  78. Tomita, N., et al. (2003) Development of novel decoy oligonucleotides: Advantages of circular dumb-bell decoy. Current Opinion Molecular Therapeutics 5, 107–112.

    CAS  Google Scholar 

  79. Crinelli, R., Bianchi, M., Gentilini, L., Palma, L., & Magnani, M. (2004) Locked Nucleic Acids (LNA): Versatile tools for designing oligonucleotide decoys with high stability and affinity. Current Drug Targets 5, 745–52.

    Article  PubMed  CAS  Google Scholar 

  80. Warncke, S., Gégout, A., & Carell, T. (2009) Phosphorothioation of oligonucleotides strongly influences the inhibition of bacterial (M.HhaI) and human (Dnmt1) DNA methyltransferases. ChemBioChem 10, 728–734.

    Article  PubMed  CAS  Google Scholar 

  81. Krieg, A. M. (2006) Therapeutic potential of toll-like receptor 9 activation. Nature Reviews Drug Discovery 5, 471–484.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry, Worcester State University, Worcester, MA, 01602-2597, USA

    John Goodchild

Authors
  1. John Goodchild
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to John Goodchild .

Editor information

Editors and Affiliations

  1. Dept. Chemistry, Worcester State College, Chandler St. 486, Worcester, 01602, Massachusetts, USA

    John Goodchild

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Goodchild, J. (2011). Therapeutic Oligonucleotides. In: Goodchild, J. (eds) Therapeutic Oligonucleotides. Methods in Molecular Biology, vol 764. Humana Press. https://doi.org/10.1007/978-1-61779-188-8_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-188-8_1

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-187-1

  • Online ISBN: 978-1-61779-188-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation