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Detection of Single-Base Substitutions in Amplified Fragments via Ligation of a Tandem of Short Oligonucleotides in Solution and on a Solid Carrier

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Abstract

Ligation of a tandem of short oligonucleotides was proposed for detecting single-base substitutions in amplified DNA fragments. An octamer–tetramer–octamer tandem was ligated on a 20-mer template with T4 DNA ligase. As shown with radiolabeled oligonucleotides, the efficiency and selectivity of ligation did not change with an octamer linked to a water-soluble carrier based on polyethylene glycol (MPEG), while ligation was somewhat lower with the octamer immobilized on methacrylate beads (DMEG). In both cases, polymer attachment improved the discrimination of 20-mer templates with single-base substitutions in the binding site for the tetramer or for the immobilized octamer. Tandems with a radiolabeled or biotinylated component were also efficiently ligated on amplified DNA fragments. The data obtained with DNA fragments of HIV-1 strains bru and rf demonstrate the possibility of reliable detection of single-base substitutions via ligation of a tandem and colorimetric detection of the immobilized ligation product with the streptavidin–alkaline phosphatase technique.

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REFERENCES

  1. Wu, D.Y. and Wallance, B.R., Gene, 1989, vol. 76, pp. 245–254.

    PubMed  Google Scholar 

  2. Landegren, U., Kaiser, R., Sanders, J., and Hood, L., Science, 1988, vol. 241, pp. 1077–1080.

    PubMed  Google Scholar 

  3. Harada, K. and Orgel, L.E., Nucleic Acids Res., 1993, vol. 21, pp. 2287–2291.

    PubMed  Google Scholar 

  4. Wu, D.Y. and Wallace, R.B., Genomics, 1989, vol. 4, pp. 560–569.

    PubMed  Google Scholar 

  5. James, K.D., Boles, A.R., Henke, D., and Ellington, A.D., Nucleic Acids Res., 1998, vol. 26, pp. 5203–5211.

    PubMed  Google Scholar 

  6. Bi, W. and Stambrook, P.J., Nucleic Acids Res., 1997, vol. 25, pp. 2949–2951.

    PubMed  Google Scholar 

  7. Khanna, M., Park, P., Zirvi, M., et al., Oncogene, 1999, vol. 18, pp. 27–38.

    PubMed  Google Scholar 

  8. Edelstein, R.V., Nickerson, D.A., Tobe, V.O., et al., J. Clin. Microbiol., 1998, vol. 36, pp. 569–572.

    PubMed  Google Scholar 

  9. Drmanac, R., Labat, I., Brukner, I., and Crkvenjakov, R., Genomics, 1989, vol. 4, pp. 114–128.

    PubMed  Google Scholar 

  10. Khrapko, K.P., Ivanov, I.B., Lysov, Yu.P., et al., FEBS Lett., 1989, vol. 256, pp. 118–122.

    PubMed  Google Scholar 

  11. Gerry, N.P., Witowski, N.E., Day, J., et al., J. Mol. Biol., 1999, vol. 292, pp. 251–262.

    PubMed  Google Scholar 

  12. Hacia, J.G., Sun, B., Hunt, N., et al., Genome Res., 1988, vol. 8, pp. 1245–1258.

    Google Scholar 

  13. Pastinen, T., Kurg, A., Metspalu, A., et al., Genome Res., 1997, vol. 7, pp. 606–614.

    PubMed  Google Scholar 

  14. Beier, M. and Hoheisel, J.D., Nucleic Acid Res., 2000, vol. 28, E11, i-vi.

    Google Scholar 

  15. Cho, J.R., Fromont-Racine, M., Wodicka, L., et al., Proc. Natl. Acad. Sci. USA, 1998, vol. 95, pp. 3752–3757.

    PubMed  Google Scholar 

  16. Nickerson, D.A., Kaiser, R., Lappin, S., et al., Proc. Natl. Acad. Sci. USA, 1990, vol. 87, pp. 8923–8927.

    PubMed  Google Scholar 

  17. Barany, F., Proc. Natl. Acad. Sci. USA, 1991, vol. 88, pp. 189–193.

    PubMed  Google Scholar 

  18. Chen, X., Livak, K.J., and Kwok, P.-Y., Genome Res., 1998, vol. 8, pp. 549–556.

    PubMed  Google Scholar 

  19. Dubiley, S., Kirillov, E., Lysov, Yu., and Mirzabekov, A., Nucleic Acids Res., 1997, vol. 25, pp. 2259–2265.

    PubMed  Google Scholar 

  20. Gerry, N.P., Witowski, N.E., Day, J., et al., J. Mol. Biol., 1999, vol. 292, pp. 251–262.

    PubMed  Google Scholar 

  21. Gunderson, K.L., Huang, X.C., Morris, M.S., et al., Genome Res., 1998, vol. 8, pp. 1142–1153.

    PubMed  Google Scholar 

  22. Thitovich, A.V., Dolinnaya, N.G., and Shabarova, Z.A., Mol. Biol., 1988, vol. 22, pp. 690–699.

    Google Scholar 

  23. Pritchard, C.E. and Southern, E.M., Nucleic Acids Res., 1997, vol. 25, pp. 3403–3407.

    PubMed  Google Scholar 

  24. Housby, J.N., Thorbjarnardottir, S.H., Jonsson, Z.O., and Southern, E.M., Nucleic Acid Res., 2000, vol. 28, E10, i-v.

    Google Scholar 

  25. Pyshnyi, D.V., Krivenko, A.A., Lokhov, S.G., et al., Bioorgan. Khim., 1998, vol. 24, pp. 32–37.

    Google Scholar 

  26. Skobeltsyna, L.M., Pyshnyi, D.V., Shishkina, I.G., et al., Mol. Biol., 2000, vol. 34, pp. 378–385.

    Google Scholar 

  27. Zarytova, V.F., Ivanova, E.M., and Romanenko, V.P., Bioorgan. Khim., 1983, vol. 9, pp. 516–521.

    Google Scholar 

  28. Brown, T. and Brown, D.J.S., Oligonucleotides and Analogues, Eckstein, F., Ed., New York: IRL, 1991, pp. 1–24.

    Google Scholar 

  29. Gorozhankin, A.V., Ivanova, E.M., and Kobets, N.D., Bioorgan. Khim., 1993, vol. 19, pp. 81–85.

    Google Scholar 

  30. Pyshnyi, D.V., Krivenko, A.A., Lokhov, S.G., et al., Bioorgan. Khim., 1998, vol. 24, pp. 25–31.

    Google Scholar 

  31. Zarytova, V.F., Ivanova, E.M., and Chasovskikh, M.N., Bioorgan. Khim., 1990, vol. 16, pp. 610–616.

    Google Scholar 

  32. Handbook of Biochemistry and Molecular Biology: Nucleic Acids, Fasman, G.D., Ed., Cleveland: CRC, 1975, vol. 1, p. 589.

    Google Scholar 

  33. Haralambidis, J., Chai, M., and Tregear, G.W., Nucleic Acids Res., 1987, vol. 15, pp. 4857–4876.

    PubMed  Google Scholar 

  34. Berkner, K.L. and Folk, W.R., Biol. Chem., 1977, vol. 252, pp. 3176–3184.

    Google Scholar 

  35. Degtyarev, S.Kh., Belavin, P.A., Shishkina, I.G., et al., Bioorgan. Khim., 1989, vol. 15, pp. 358–362.

    Google Scholar 

  36. New England Biolabs: A Catalog, 1990–1991, New England Biolabs, p. 51.

  37. Bonora, G.M., Ivanova, E., Zarytova, V., et al., Bioconjugate Chem., 1997, vol. 8, pp. 793–797.

    Google Scholar 

  38. Southern, E., Mir, K., and Shchepilov, M., Nat. Genet., 1999, vol. 21, pp. 5–9.

    PubMed  Google Scholar 

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Authors and Affiliations

  1. Novosibirsk Institute of Bioorganic Chemistry, Siberian Division, Russian Academy of Sciences, Novosibirsk, 630090, Russia

    D. V. Pyshnyi, E. N. Gushchina, I. A. Pyshnaya, V. F. Zarytova & E. M. Ivanova

  2. Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk, 630090, Russia

    L. M. Skobeltsyna, I. G. Shishkina & G. M. Dymshits

Authors
  1. D. V. Pyshnyi
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  2. L. M. Skobeltsyna
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  3. E. N. Gushchina
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  4. I. A. Pyshnaya
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  5. I. G. Shishkina
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  6. G. M. Dymshits
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  7. V. F. Zarytova
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  8. E. M. Ivanova
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Pyshnyi, D.V., Skobeltsyna, L.M., Gushchina, E.N. et al. Detection of Single-Base Substitutions in Amplified Fragments via Ligation of a Tandem of Short Oligonucleotides in Solution and on a Solid Carrier. Molecular Biology 34, 840–851 (2000). https://doi.org/10.1023/A:1026623708863

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