Skip to main content

Incorporation of Modified Bases into Oligonucleotides

  • Protocol
Book cover Protocols for Oligonucleotide Conjugates

Part of the book series: Methods in Molecular Biology ((MIMB,volume 26))

Abstract

Nucleobases with attached side chains have been incorporated into oligodeoxynucleotides (ODNs) to achieve a number of goals. The functionalized side chains have been used to attach reporter groups (protein ligands as well as fluorescent moieties) and metal-chelating groups. Electrophilic and photochemical alkylating functions have been attached to react with the other strand(s) in a duplex (or triplex).

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight 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. Meyer, R. B., Jr., Tabone, J. C, Hurst, G, Smith, T M, and Gamper H. (1989) Efficient, specific crosslinking and cleavage of DNA by stable, synthetic comple mentary oligodeoxynucleotides. J. Am. Chem Soc 111, 8517–8519.

    Article  CAS  Google Scholar 

  2. Haralambidis, J, Chai, M., and Tregear, G W (1987) Preparation of base-modified nucleosides suitable for non-radioactive label attachment and their incorporation into synthetic oligodeoxyribonucleotides. Nucleic Acids Res. 15, 4856–4876

    Article  Google Scholar 

  3. Gibson, K. J. and Benkovic, S. J. (1987) Synthesis and application of derivatiz-able oligonucleotides. Nucleic Acids Res 15, 6455–6467

    Article  CAS  Google Scholar 

  4. Dreyer, G. B. and Dervan, P. B. (1985) Sequence-specific cleavage of single-stranded DNA: oligodeoxynucleotide-EDTA-Fe(II). Proc. Natl. Acad. Sci. USA 82, 968–972.

    Article  CAS  Google Scholar 

  5. Horn, T. and Urdea, M. S. (1989) Forks and combs and DNA: the synthesis of branched oligodeoxyribonucleotides Nucleic Acids Res. 17, 6959–6967.

    Article  CAS  Google Scholar 

  6. Sanghvi, Y. S., Hoke, G. D., Zounes, M, Chan, H., Acevedo, O, Ecker, D. J., Mirabelli, C. K., Crooke, S. T., and Cook, P. D. (1991) Synthesis and biological evaluation of antisense oligonucleotides containing modified pyrrolidines Nucleosides Nucleotides 10, 345.

    Article  CAS  Google Scholar 

  7. Ramasamy, K., Springer, R. S, Martin, J F., Freier, S. M., Hoke, G. D, Bruice, T. W., and Cook, P. D. (1991) Synthesis and biophysical evaluation of N1-substituted guanine and adenine modified oligonucleotides as catalytic cleavers of RNA. International Union of Biochemistry Conference on Nucleic Acid Therapeutics, Clearwater Beach, FL, No. 82.

    Google Scholar 

  8. Petrie, C. R., Adams, A D, Stamm, M., Van Ness, J., Watanabe, S. M., and Meyer, R. B., Jr. (1991) A novel biotinylated adenylate analog derived from pyrazolo[3,4-J]pynmidine for labeling DNA probes. Bioconj. Chem. 2, 441–446

    Article  CAS  Google Scholar 

  9. Still, W C, Kahn, M, and Mitra, A. (1978) Rapid chromatographic technique for preparative separations with moderate resolution. Org. Chem. 43, 2923–2925.

    Article  CAS  Google Scholar 

  10. Maxam, A. M. and Gilbert, W. (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Meth. Enzymol. 65, 499–560.

    Article  CAS  Google Scholar 

  11. Sambrook, J, Fntsch, E F II, and Mamatas, T (1989) Molecular Cloning A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

    Google Scholar 

  12. Eur. pat. appl. 87305848-l/01.07.87.87

    Google Scholar 

  13. Kazimierczuk, Z., Cottam, H. B., Revankar, G. R, and Robins, R. K. (1984) Synthesis of 2′-deoxytubercidin, 2′-deoxyadenosine, and related 2′-deoxynucleosides via a novel direct stereospecific sodium salt glycosylation procedure. J. Am. Chem. Soc. 106, 6379–6382.

    Article  CAS  Google Scholar 

  14. McLaughlin, L. W. (1984) in Gait, M. J. (ed.), Oligonucleotide Synthesis-A Practical Approach, IRL, Oxford, UK.

    Google Scholar 

  15. Van Ness, J., Kalbfleisch, S., Petrie, C. R., Reed, M. W., Tabone, J. C, and Vermeulen, N. M J. (1991) A versatile solid support system for oligonucleotide probe-based hybridization assays. Nucleic Acids Res. 19, 3345–3350.

    Article  Google Scholar 

  16. Hobbs, F. W., Jr. (1989) Palladium-catalyzed synthesis of alkynylamino nucleosides. A universal linker for nucleic acids. J. Org. Chem. 54, 3420–3422.

    Article  CAS  Google Scholar 

  17. Mitsunobu, O. (1981) The use of diethyl azodicarboxylate and triphenylphos-phine in synthesis and transformation of natural products. Synthesis 1–23.

    Google Scholar 

  18. Jones, R. A. (1984) In Oligonucleotide Synthesis (Gait, M. J., ed.), IRL, Washington, DC, Chapter 2.

    Google Scholar 

  19. Germann, M. W., Pon, R. T., and van de Sande, J. H. (1987) A general method for the purification of synthetic oligodeoxyribonucleotides containing strong secondary structure by reversed-phase high-performance liquid chromatography on PRP-1 resin. Anal. Biochem. 165, 399–405.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

Copyright information

© 1994 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

Meyer, R.B. (1994). Incorporation of Modified Bases into Oligonucleotides. In: Protocols for Oligonucleotide Conjugates. Methods in Molecular Biology, vol 26. Humana Press. https://doi.org/10.1007/978-1-59259-513-6_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-59259-513-6_2

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-252-1

  • Online ISBN: 978-1-59259-513-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics