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Bridged Oligonucleotides with Smoothed Hybridization Properties as a Tool for Analysis of Nucleotide Sequences

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Abstract

Bridged oligonucleotides that contain nonnucleotide inserts, i.e., diethylene glycol phosphate residues (DEG insert) have been studied. These oligonucleotide derivatives were shown to smooth the melting temperatures of their DNA duplexes of various nucleotide composition. The DEG insert has been shown to have almost no effect on the sequence specificity of modified oligonucleotides and regulate only their hybridization properties. It has been demonstrated that bridged oligonucleotides immobilized on microparticles can be successfully used to specifically and efficiently reveal DNA templates during the parallel solid-phase hybridization analysis. The use of bridged oligonucleotides along with DNA-dependent enzymes (Taq DNA polymerase and T4 DNA ligase) in this analysis has led to pronounced discrimination of wrong DNA molecules due to the covalent attachment of the label to the carrier, thus increasing the reliability of the hybridization analysis.

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REFERENCES

  1. 1

    SantaLucia, J. and Hicks, D., Annu. Rev. Biophys. Biomol. Struct., 2004, vol. 33, pp. 415–440.

  2. 2

    Kabilov, M.R. and Pyshnyi, D.V., JBPC, 2011, vol. 2, art. ID 5134.

  3. 3

    Matsuzaki, H., Loi, H., Dong, S., Tsai, Y.Y., Fang, J., Law, J., Di, X., Liu, W.M., Yang, G., Liu, G., Huang, J., Kennedy, G.C., Ryder, T.B., Marcus, G.A., Walsh, P.S., et al., Genome Res., 2004, vol. 14, pp. 414–425.

  4. 4

    Monia, B.P., Johnston, J.F., Eckers, D.J., Zounesn, M.A., Lima, W.F., and Freier, S.M., J. Biol. Chem., 1992, vol. 267, pp. 9954–19 962.

  5. 5

    Nguyen, H.-K., Fournier, O., Asseline, U., Dupret, D., and Thuong, N.T., Nucleic Acids Res., 1999, vol. 27, pp. 1492–1498.

  6. 6

    Rees, W.A., Yager, T.D., Korte, J., and von Hippel, P.H., Biochemistry, 1993, vol. 32, pp. 137–144.

  7. 7

    Pyshnyĭ, D.V., Krivenko, A.A., Lokhov, S.G., Ivanova, E.M., Dymshits, G.M., and Zarytova, V.F., Russ. J. Bioorg. Chem., 1998, vol. 24, pp. 32–37.

  8. 8

    Lee, A.H.F. and Kool, E.T., J. Am. Chem. Soc., 2005, vol. 127, pp. 3332–3338.

  9. 9

    Nguyen, H.-K., Bonfils, E., Auffray, P., Costaglioli, P., Schmitt, P., Asseline, U., Durand, M., Maurizot, J.-C., Dupret, D., and Thuong, N.T., Nucleic Acids Res., 1998, vol. 26, pp. 4249–4258.

  10. 10

    Winkler, J., Future Med Chem., 2015, vol. 7, pp. 1721–1731.

  11. 11

    Antsypovich, S.I., Oretskaya, T.S., Volkov, E.M., Romanova, E.A., Tashlitsky, V.N., Blumenfeld, M., and Shabarova, Z.A., Nucleosides Nucleotides, 1996, vol. 15, pp. 923–936.

  12. 12

    Berger, M., Wu, Y., Ogawa, A.K., McMinn, D.L., Schultz, P.G., and Romesberg, F.E., Nucleic Acids Res., 2000, vol. 28, pp. 2911–2914.

  13. 13

    Ahlborn, C., Siegmund, K., and Richert, C., J. Am. Chem. Soc., 2007, vol. 12949, pp. 15 218–15 232.

  14. 14

    Khomyakova, E.A., Zubin, E.M., Pavlova, L.V., Kazanova, E.V., Smirnov, I.P., Pozmogova, G.E., Muller, S., Dolinnaya, N.G., Kubareva, E.A., Hartmann, R.K., and Oretskaya, T.S., Russ. J. Bioorg. Chem., 2012, vol. 38, pp. 488–499.

  15. 15

    Mitsuoka, Y., Kodama, T., Ohnishi, R., Hari, Y., Imanishi, T., and Obika, S., Nucleic Acids Res., 2009, vol. 37, pp. 1225–1238.

  16. 16

    Fedotova, E.A., Yan, F., Kubareva, E.A., Romanova, E.A., Protsenko, A.S., Viryasov, M.B., Gianik, T., and Oretskaya, T.S., 2008, vol. 34, pp. 236–244.

  17. 17

    Kupryushkin, M.S., Pyshnyi, D.V., and Stetsenko, D.A., Acta Naturae, 2014, vol. 6, pp. 116–118.

  18. 18

    Walter, T.J. and Richert, C., Nucleic Acids Res., 2018, vol. 46, pp. 8069–8078.

  19. 19

    Summerton, J., Stein, D., Huang, S.B., Matthews, P., Weller, D., and Partridge, M., Antisense Nucleic Acid Drug Dev., 1997, vol. 7, pp. 63–70.

  20. 20

    Pyshnaya, I.A., Vinogradova, O.A., Kabilov, M.R., Ivanova, E.M., and Pyshnyi, D.V., Biokhimiya, 2009, vol. 74, pp. 1238–1251.

  21. 21

    Gao, H., Chidambaram, N., Chen, B.C., Pelham, D.E., Patel, R., Yang, M., Zhou, L., Cook, A., and Cohen, J.S., Biocojugate Chem., 1994, vol. 5, pp. 445–453.

  22. 22

    Rumney, S. and IV, KoolE.T., J. Am. Chem. Soc., 1995, vol. 117, pp. 5635–5646.

  23. 23

    Doktycz, M.J., Paner, T.M., and Benight, A.S., Biopolymers, 1993, vol. 33, pp. 1765–1777.

  24. 24

    Vo, T., Wang, S., and Kool, E.T., Nucleic Acids Res., 1995, vol. 23, pp. 2937–2944.

  25. 25

    Koroleva, O.N., Volkov, E.M., and Drutsa, V.L., Bioorg. Khim., 1994, vol. 20, pp. 420–432.

  26. 26

    Lomzov, A.A., Pyshnaya, I.A., Ivanova, E.M., and Pyshnyi, D.V., Dokl. Biochem. Biophys., 2006, vol. 409, pp. 211–215.

  27. 27

    Degtyarev, S.Kh., Belavin, P.A., Shiskina, I.G., Zarytova, V.F., Gavryuchenkova, L.P., and Morozov, S.M., Bioorg. Khim., 1989, vol. 15, pp. 358–362.

  28. 28

    Gallagher, S., Winston, S.E., Fuller, S.A., and Hurrell, J.G., Curr. Protoc. Cell Biol., 2011, vol. 52, pp. 6.2.1–6.2.28.

  29. 29

    Durand, M., Chevrie, K., Chassignol, M., Thuong, N.T., and Maurizot, J.C., Nucleic Acids Res., 1990, vol. 18, pp. 6353–6359.

  30. 30

    Pyshnyi, D.V., Skobel’tsyna, L.M., Gushchina, E.N., Pyshnaya, I.A., Shishkina, I.G., Dymshits, G.M., Zarytova, V.F., and Ivanova, E.M, Mol. Biol., 2000, vol. 34, pp. 984–999.

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ACKNOWLEDGMENTS

The authors would like to thank V.V. Koval (Center of the Collective Use, ICBFM, SB RAS) for recording mass spectra of bridged oligonucleotides.

FUNDING

The design of bridged oligonucleotides was supported by the State project no. А-0309-2016-0004. The study of modified oligonucleotides in the presence of DNA-dependent enzymes was supported by the grant no. 18-14-00357 from the Russian Scientific Foundation.

Author information

Correspondence to I. A. Pyshnaya.

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COMPLIANCE WITH ETHICAL STANDARDS

This article does not contain any studies with the use of humans and animals as objects of research.

Conflict of Interests

The authors state that there is no conflict of interests.

Additional information

Translated by A. Levina

Abbreviations: ODN, oligonucleotide (“deoxyribo” and prefix “d” for oligodeoxyribonucleotides are omitted); DEG insert, diethylene glycol phosphate residue; NA, nucleic acid; RT PCR, reverse transcription polymerase chain reaction; ou, optical unit; PB, phosphate buffer; TBEV, tick-borne encephalitis virus; 5'-UTR, 5'-untranslated region of the hepatitis C virus (HCV) genome; BCIP, 5-bromo-4-chloro-3-indolyl phosphate disodium salt; NBT, nitrotetrazolium blue; Tm, melting temperature of NA/NA complex.

Corresponding author: phone/fax: +7 (383) 363-51-35; e-mail: pyshnaya@niboch.nsc.ru.

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Pyshnaya, I.A., Lomzov, A.A. & Pyshnyi, D.V. Bridged Oligonucleotides with Smoothed Hybridization Properties as a Tool for Analysis of Nucleotide Sequences. Russ J Bioorg Chem 45, 677–683 (2019). https://doi.org/10.1134/S1068162019060335

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Keywords:

  • modified oligonucleotides
  • bridged oligonucleotides
  • nonnucleotide modifications
  • smoothing
  • hybridization properties
  • enzymatic labeling
  • melting temperature