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Protocols for Oligonucleotides and Analogs pp 315–353Cite as

Oligonucleotide Analogs with Dimethylenesulfide, -sulfoxide, and -sulfone Groups Replacing Phosphodiester Linkages

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 20))

Abstract

As demonstrated by this volume, analogs of oligonucleotides retaining the molecular recognition properties of natural oligonucleotides, but having altered physical, chemical, and biological properties are synthetic targets of some interest. Much of the interest comes from the possibility that such analogs might allow the sequence-specific control of the expression of encoded genetic information in vivo using what has come to be known as the “antisense” strategy (1–5).

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References

  1. Hirashima, A. and Inouye, M. (1973) Specific biosynthesis of an envelope protein of Escherichia coli. Nature 242,405–407.

    Article  CAS  Google Scholar 

  2. Green, P. J., Pines, O., and Inouye M. (1986) The role of antisense RNA in gene regulation. Ann. Rev. Biochem. 55, 569–597.

    Article  CAS  Google Scholar 

  3. Inouye, M. (1988) Antisense RNA: Its functions and applications in gene regulation—A review. Gene 72, 25–34.

    Article  CAS  Google Scholar 

  4. Paterson, B. M., Roberts, B. E., and Kuff, E. L. (1977) Structural gene identification and mapping by DNA-mRNA hybrid-arrested cell-free translation. Proc. Natl. Acad. Sci. USA 74,4370–4374.

    Article  CAS  Google Scholar 

  5. Stephenson, M. L. and Zamecnik, P. C. (1978) Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide. Proc. Natl. Acad. Sci. USA 75, 285–288.

    Article  CAS  Google Scholar 

  6. Rich, A. (1962) On the problems of evolution and biochemical information transfer, in Horizons in Biochemistry (Kasha, M. and Pullman, B., eds.), Academic, New York, pp. 103–126.

    Google Scholar 

  7. Letsinger, R. L., Bach, S. A., and Eadie J. S. (1986) Effects of pendant groups at phosphorus on binding properties of δ-ApA analogues. Nucl. Acids Res. 14, 3487–3499.

    Article  CAS  Google Scholar 

  8. Ts’o, P. O. P. and Miller, P. S. (1984) Nonionic nucleic acid alkyl and aryl phosphonates and processes for manufacture and use thereof. US Patent number 4,469,863, Sept. 4.

    Google Scholar 

  9. Miller, P. S., Agris, C. H., Aurelian, L., Blake K. R., Murakami A., Reddy M. P., Spitz S. A., and Ts’o P. O. P. (1985) Biochimie 67, 769–776.

    Article  CAS  Google Scholar 

  10. Miller, P. S., McParland, K. B., Jayaraman, K., and Ts’o, P. O. P. (1981) Biochemical and biological effects of nonionic nucleic acid methylphosphonates. Biochemistry 20, 1874–1880.

    Article  CAS  Google Scholar 

  11. Murakami, A., Blake, K. R., and Miller, P. S. (1985) Characterization of sequence-specific oligodeoxyribonucleoside methylphosphonates and their interaction with rabbit globin mRNA. Biochemistry 24,4041–4046.

    Article  CAS  Google Scholar 

  12. Johnsson, K., Allemann, R. K., and Benner, S. A. (1990) Designed enzymes: new peptides that fold in aqueous solution and catalyze reactions, in Molecular Mechanisms in Bioorganic Processes (Bleasdale, C. and Golding, B. T., eds.), Royal Society of Chemistry, Cambridge, UK, pp. 166–187.

    Google Scholar 

  13. Benner, S. A. and Allemann, R. K. (1989) The return of pancreatic ribonucleases. Trends Biochem. Sci. 14, 396,397.

    Article  CAS  Google Scholar 

  14. Gonnet G. H. and Benner S. A. (1991) Computational biochemistry research at ETH, Technical Report 154, Departement Informatik, March 1991.

    Google Scholar 

  15. Moody, H. M., Quaedflieg, P. J. L. M., Koole, L. H., van Genderen, M. H. P., Buck, H. M., Smit, L., Jurrianns, S., Geelen, J. L. M. C., and Goudsmit, J. (1990) Inhibition of HIV-1 infectivity by phosphate-methylated DNA: retraction. Science 250, 125,pp126.

    Article  CAS  Google Scholar 

  16. Nambiar, K. P., Stackhouse, J., Stauffer, D. M., Kennedy, W. P., Eldredge, J. K., and Benner, S. A. (1984) Total synthesis and cloning of a gene coding for the ribonuclease S protein. Science 223, 1299–1301.

    Article  CAS  Google Scholar 

  17. Schaller, H., Weimann, G., Lerch, B., and Khorana, H. G. (1963) Studies on polynucleotides XXIV. J. Am. Chem. Soc. 85, 3821–3827.

    Article  CAS  Google Scholar 

  18. Schneider, K. C. and Benner, S. A. (1990) Building blocks for oligonucleotide analogs with dimethylene-sulfide,-sulfoxide, and-sulfone groups replacing phosphodiester linkages. Tetrahedron Lett. 31, 335–338.

    Article  CAS  Google Scholar 

  19. Huang, Z., Schneider, K. C., and Benner, S. A. (1991) Building blocks for analogs of ribo-and deoxyribonucleotides with dimethylene-sulfide,-sulfoxide, and-sulfone groups replacing phosphodiester linkages. J. Org. Chem. 56, 3869–3882.

    Article  CAS  Google Scholar 

  20. Blancou, H. and Casadevall, E. (1976) Reaction d’elimination-1,3 action du n-butyl lithium sur les iodomethyl-2 tosyloxy-1 cyclohexanes (enes) cis et trans, stereochimie et mecanisme. Tetrahedron 32, 2907–2913.

    Article  CAS  Google Scholar 

  21. Mitsunobu, O. (1981) The use of diethyl azodicarboxylate and triphenylphos-phine in synthesis and transformation of natural products. Synthesis 13, 1–28.

    Article  Google Scholar 

  22. Volante, R. P. (1981) A new highly efficient method for the conversion of alcohols to thiolesters and thiols. Tetrahedron Lett. 22, 3119–3122.

    Article  CAS  Google Scholar 

  23. Mazur, A., Tropp, B. E., and Engel R. (1984) Isosteres of natural phosphates. 11. Synthesis of a phosphonic acid analog of an oligonucleotide. Tetrahedron 40, 3949–3956.

    Article  CAS  Google Scholar 

  24. Gurjar, M. K., Patil, V. J., and Pawar, S. M. (1987) Sythesis of (1R, rR)-2,6-dioxabicyclo [3.3.0] octan-3-one from D-glucose. Carbohydrate Res. 165, 313–317.

    Article  CAS  Google Scholar 

  25. Saito, I., Ikehira, H., Kasatani, R., Watanabe, M., and Matsuura, T. (1986) Selective deoxygenation of secondary alcohols by photosensitized electron-transfer reaction. A general procedure for deoxygenation of ribonucleosides. J. Am. Chem. Soc. 108, 3115–3117.

    Article  CAS  Google Scholar 

  26. Boland, W, Niedermeyer, U., and Jaenicke, L. (1985) Enantioselective syntheses and absolute configurations of viridiene and aucantene, two constituents of algae pheromone bouquets. Helv. Chim. Acta 68, 2062–2073.

    Article  CAS  Google Scholar 

  27. Gais, H. J. and Lukas, K. L. (1984) Enantioselektive und enantiokonvergente Synthese von Bausteinen zur Totalsynthese cyclopentanoida Naturstoffe. Angew. Chem. 96, 140, 141.

    Article  CAS  Google Scholar 

  28. Schneider, M., Engel, N., Honicke, P., Hdnemann, G., and Görisch, H. (1984) Enzymatische Synthesen chiraler Bausteine aus prochiralen) meso-Substraten: Herstellung von Methyl(hydrogen)-1,2-cycloalkandicarboxylaten. Angew. Chem. 96, 55,56.

    Article  CAS  Google Scholar 

  29. Wilson, W. K., Baca, S. B., Barber, Y. J., Scallen, T. J., and Morrow, C. J. (1983) Enantioselective hydrolysis of 3-hydroxy-3-methylalkanoic acid esters with pig liver esterase. J. Org. Chem. 48, 3960–3966.

    Article  CAS  Google Scholar 

  30. Mohr, P., Waespe-Sarcevic, N., and Tamm, C. (1983) A study of stereoselective hydrolysis of symmetrical diesters with pig liver esterase. Helv. Chim. Acta 66,2501–2511.

    Article  CAS  Google Scholar 

  31. Huang, F. C., Lee, L. F. H., Mittal, R. S. D., Ravikumar, P. R., Chan, J. A., Sih, C. J., Caspi, E., and Eck, C. R. (1975) Synthesis and characterization of the fluxional species H2OS3(CO)10L. The crystal structure of H2OS3(CO)11. J. Am. Chem. Soc. 97,4144,4145.

    Article  CAS  Google Scholar 

  32. Barton, D. H. R. and McCombie, S. W. (1975) A new method for the deoxy-genation of secondary alcohols. J. C. S. Perkin I 1574–1585.

    Google Scholar 

  33. Cambou, B. and Klibanov, A. M. (1984) Preparative production of optically active esters and alcohols using esterase-catalyzed stereospecific transesteri-fication in organic media. J. Am. Chem. Soc. 106, 2687–2692.

    Article  CAS  Google Scholar 

  34. Jones, J. B. and Mehes, M. M. (1979) Effects of organic cosolvents on enzyme stereospecificity. The enantiomeric specificity of α-chymotypsin is reduced by high organic solvent concentrations. Can. J. Chem. 57, 2245–2248.

    Article  CAS  Google Scholar 

  35. Ellison, R. A., Lukenbach, E. R., and Chiu, C.-W. (1975) Cyclopentenone synthesis via aldol condensation. Synthesis of a key prostaglandin intermediate. Tetrahedron Lett. 16,499–502.

    Article  Google Scholar 

  36. Vorbruggen, H., Bennua, B., and Su, T.S. (1981) Nucleoside von 3,6-dihydro-2H-l,2,6-thiadiazindioxiden. Chem. Ber. 114, 1269–1286.

    Article  Google Scholar 

  37. Watanabe, K. A., Hollenberg, D. H., and Fox, J. J. (1974) Mechanisms of nucleoside synthesis by condensation reactions. J. Carbohydr. Nucleosides Nucleotides 1, 1–37.

    CAS  Google Scholar 

  38. Johnson, T. B. and Hilbert, G. E. (1929) The synthesis of pyrimidine—Nucleosides. Science 69, 579,580.

    Article  CAS  Google Scholar 

  39. Wittenburg, E. (1986) Synthese von Thymin-nucleosiden ueber Silyl-pyrimidin-Verbindungen3. Chem. Ber. 101, 1095–1114.

    Article  Google Scholar 

  40. Niedballa, U. and Vorbruggen, H. (1976) A general synthesis of N-Glycosides. 6. On the mechanism of the stannic chloride catalyzed Silyl Hilbert-Johnson reaction. J. Org. Chem. 41, 2084–2086.

    Article  CAS  Google Scholar 

  41. Hubbard, A. J., Jones, A. S., and Walker R. T. (1984) An investigation by HNM spectroscopy into the factors determining the b:a ratio of the product in 2′-deoxynucleoside synthesis. Nucl. Acids Res. 12, 6827–6837.

    Article  CAS  Google Scholar 

  42. Tocik, Z., Earl, R. A., and Beranek, J. (1986) The use of iodotrimethylsilane in nucleosidation procedures, in Nucleic Acid Chemistry (Townsend, L.B. and Tipson, R. S., eds.), Section III, New York, pp 105–111.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Laboratory for Organic Chemistry, Zurich, Switzerland

    Zhen Huang, K. Christian Schneider & Steven A. Benner

Authors
  1. Zhen Huang
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  2. K. Christian Schneider
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  3. Steven A. Benner
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Editor information

Editors and Affiliations

  1. Worcester Foundation for Experimental Biology, Shrewsbury, Massachusetts

    Sudhir Agrawal

Additional information

This contribution is dedicated to Frank H. Westheimer, on the occasion of his 80th birthday.

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© 1993 Humana Press Inc., Totowa, NJ

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Huang, Z., Schneider, K.C., Benner, S.A. (1993). Oligonucleotide Analogs with Dimethylenesulfide, -sulfoxide, and -sulfone Groups Replacing Phosphodiester Linkages. In: Agrawal, S. (eds) Protocols for Oligonucleotides and Analogs. Methods in Molecular Biology, vol 20. Humana Press. https://doi.org/10.1385/0-89603-281-7:315

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  • DOI: https://doi.org/10.1385/0-89603-281-7:315

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-281-1

  • Online ISBN: 978-1-59259-507-5

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