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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Reese, C. B. (2005) Oligo- and poly-nucleotides: 50 years of chemical synthesis. Org. Biomol. Chem. 3, 3851–3868.
Nair, V. (2003) Novel inhibitors of HIV integrase: The discovery of potential anti-HIV therapeutic agents. Curr. Pharm. Des. 9, 2553–2565.
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.
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.
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.
Verma, S., and Eckstein, F. (1998) Modified oligonucleotides: Synthesis and strategy for users. Annu. Rev. Biochem. 67, 99–134.
Eckstein, F. (2000) Phosphorothioate oligodeoxynucleotides: What is their origin and what is unique about them? Antisense Nucleic Acid Drug Dev. 10, 117–121.
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.
Cosstick, R., and Gaynor, J. W. (2008) Synthesis, properties and application of nucleic acids containing phosphorothiolate linkages. Curr. Org. Chem. 12, 291–308.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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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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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