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Dinucleotides Containing 3′-S-Phosphorothiolate Linkages

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

Abstract

The 3′-S-phosphorothiolate (3′-SP) linkage has proven to be a very useful analogue of the phosphodiester group in nucleic acid derivatives; it is achiral and also shows good resistance to nucleases. Whilst oligonucleotides containing a 3′-SP linkage are best prepared using phosphoramidite chemistry, the corresponding dinucleotides are most efficiently synthesised using a Michaelis–Arbuzov reaction between a nucleoside 5′-phosphite and a nucleoside 3′-S-disulphide. The method described here is for a thymidine dinucleotide and is based on the use of a silyl phosphite, which is more reactive than simple alkyl phosphites and also simplifies the deprotection strategy. Full experimental details and spectroscopic data for the synthetic intermediates and the target dinucleotide are provided.

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References

  1. Reese, C. B. (2005) Oligo- and poly-nucleotides: 50 years of chemical synthesis. Org. Biomol. Chem. 3, 3851–3868.

    Article  PubMed  CAS  Google Scholar 

  2. Nair, V. (2003) Novel inhibitors of HIV integrase: The discovery of potential anti-HIV therapeutic agents. Curr. Pharm. Des. 9, 2553–2565.

    Article  PubMed  CAS  Google Scholar 

  3. Aubert, Y., Chassignol, M., Roig, V., Mbemba, G., Weiss, J., Meudal, H., Mouscadet, J.-F., and Asseline, U. (2009) Synthesis and anti-HIV-1 integrase activity of modified dinucleotides. Eur. J. Med. Chem. 44, 5029–5044.

    Article  PubMed  CAS  Google Scholar 

  4. Iyer, R. P., Jin, Y., Roland., A., Morrey, J. D., Mounir, S., and Korba, B. (2004) Phosphorothioate di-and trinucleotides as a novel class of anti-hepatitis B virus agents. Antimicrob. Agents Chemother. 48, 2199–2205.

    Article  PubMed  CAS  Google Scholar 

  5. Iyer, R. P., Roland, A., Jin, Y., Mounir, S., Korba, B., Julander, J. G., and Morrey, J. D. (2004) Anti-hepatitis B virus activity of ORI-9020, a novel phosphorothioate dinucleotide, in a transgenic mouse model. Antimicrob. Agents Chemother. 48, 2318–2320.

    Article  PubMed  CAS  Google Scholar 

  6. Verma, S., and Eckstein, F. (1998) Modified oligonucleotides: Synthesis and strategy for users. Annu. Rev. Biochem. 67, 99–134.

    Article  PubMed  CAS  Google Scholar 

  7. Eckstein, F. (2000) Phosphorothioate oligodeoxynucleotides: What is their origin and what is unique about them? Antisense Nucleic Acid Drug Dev. 10, 117–121.

    Article  PubMed  CAS  Google Scholar 

  8. Oka, N., Yamamoto, M., Sato, T., and Wada, T. (2008) Solid-phase synthesis of stereoregular oligodeoxyribonucleoside phosphorothioates using bicyclic oxazaphospholidine derivatives as monomer units. J. Am. Chem. Soc. 130, 16031–16037.

    Article  PubMed  CAS  Google Scholar 

  9. Cosstick, R., and Gaynor, J. W. (2008) Synthesis, properties and application of nucleic acids containing phosphorothiolate linkages. Curr. Org. Chem. 12, 291–308.

    Article  Google Scholar 

  10. Jahn-Hofmann, K., and Engels, J. W. (2004) Efficient solid phase synthesis of cleavable oligodeoxynucleotides based on a novel strategy for the synthesis of 5′-S-(4,4′-dimethoxytrityl)-2′-deoxy-5′-thionucleoside phosphoramidites. Helv. Chim. Acta 87, 2812–2828.

    Article  CAS  Google Scholar 

  11. Beevers, A. P. G., Witch, E. M., Jones, B., Cosstick, R., Arnold, J. R. P., and Fisher, J. (1999) Conformational analysis of 3′-S-PO3-linked ribo- and deoxyribodinucleoside monophosphates. Magn. Reson. Chem. 37, 814–820.

    Article  CAS  Google Scholar 

  12. Beevers, A. P. G., Fettes, K. J., O’Neil, I. A., Roberts, S. M., Arnold, J. R. P., Cosstick, R., and Fisher, J. (2002) Probing the effect of a 3′-S-phosphorothiolate link on the conformation of a DNA:RNA hybrid; implications for antisense drug design. Chem. Commun. 1458–1459.

    Google Scholar 

  13. Bentley, J., Brazier, J. A., Fisher, J., and Cosstick, R. (2007) Duplex stability of DNA:DNA and DNA:RNA duplexes containing 3′-S-phosphorothiolate linkages. Org. Biomol. Chem. 5, 3698–3702.

    Article  PubMed  CAS  Google Scholar 

  14. Li, X., Scott, G. K., Baxter, A. D., Taylor, R. J., Vyle, J. S., and Cosstick, R. (1994) Application of the michaelis-arbusov reaction to the synthesis of internucleoside 3'-S-phosphorothiolate linkages. J. Chem. Soc. Perkin Trans. 1, 2123–2129.

    Article  Google Scholar 

  15. Higson, A. P., Scott, G. K., Earnshaw, D. J., Baxter, A. D., Taylor, R. A., and Cosstick, R. (1996) Synthesis and structure of S-nucleosidyl S-aryl disulfides and their reaction with phosphites. Tetrahedron 52, 1027–1034.

    Article  CAS  Google Scholar 

  16. Sabbagh, G., Fettes, K. J., Gossain, R., O’Neil, I. A., and Cosstick, R. (2004) Synthesis of phosphorothioamidites derived from 3′-thio-3′-deoxythymidine and 3′-thio-2′,3′-dideoxycytidine and the automated synthesis of oligodeoxy-nucleotides containing a 3′-S-phosphorothiolate linkage. Nucleic Acids Res. 32, 495–501.

    Article  PubMed  CAS  Google Scholar 

  17. Gaynor, J. W., Piperakis, M. W., Fisher, J., and Cosstick, R. (2010) Reverse-direction (5′→3′) synthesis of oligonucleotides containing a3′-S-phosphorothiolate linkage and 3′-terminal 3′-thionucleosides. Org. Biomol. Chem. 8, 1463–1470.

    Google Scholar 

  18. Gaynor, J. W., Bentley, J., and Cosstick, R. (2007) Synthesis of the 3′-thionucleosides and subsequent automated synthesis of oligodeoxynucleotides containing a 3′-S-phosphorothiolate linkage. Nat. Protoc. 2, 3122–3135.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

JWG was supported by the EPSRC (EP/F011938). The authors would like to thank AP Higson, X Li, GK Scott and JS Vyle who originally worked on the Michaelis–Arbuzov approach.

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Correspondence to Richard Cosstick .

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Gaynor, J.W., Cosstick, R. (2011). Dinucleotides Containing 3′-S-Phosphorothiolate Linkages. In: Goodchild, J. (eds) Therapeutic Oligonucleotides. Methods in Molecular Biology, vol 764. Humana Press. https://doi.org/10.1007/978-1-61779-188-8_2

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  • DOI: https://doi.org/10.1007/978-1-61779-188-8_2

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-187-1

  • Online ISBN: 978-1-61779-188-8

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