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Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
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Putative Secondary Structure of Human Hepatitis B Viral X mRNA

  • Kim, Ha-Dong (Department of Chemistry, Seoul National University) ;
  • Choi, Yoon-Chul (Department of Chemistry, Seoul National University) ;
  • Lee, Bum-Yong (Mogam Biotechnology Research Institute) ;
  • Junn, Eun-Sung (Department of Biological Sciences, Korea Advanced Institute of Science and Technology) ;
  • Ahn, Jeong-Keun (Department of Microbiology, Choongnam National University) ;
  • Kang, Chang-Won (Department of Biological Sciences, Korea Advanced Institute of Science and Technology) ;
  • Park, In-Won (Department of Chemistry, Seoul National University)
  • Received : 1995.07.06
  • Published : 1995.11.30
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Abstract

A putative secondary structure of the mRNA for the human hepatitis B virus (HBV) X gene is proposed based on not only chemical and enzymatic determination of its single- and double-stranded regions but also selection by the computer program MFOLD for energy minimum conformation under the constraints that the experimentally determined nucleotides were forced or prohibited to base pair. An RNA of 536 nucleotides including the 461-nucleotide HBV X mRNA sequence was synthesized in vitro by the phage T7 RNA polymerase transcription. The thermally renatured transcripts were subjected to chemical modifications with dimethylsulfate and kethoxal and enzymatic hydrolysis with single strand-specific RNase T1 and double strand-specific RNase V1, separately. The sites of modification and cleavage were detected by reverse transcriptase extension of 4 different primers. Many nucleotides could be assigned with high confidence, twenty in double-stranded and thirty-seven in Single-stranded regions. These nucleotides were forced and prohibited, respectively, to base pair in running the recursive RNA folding program MFOLD. The results suggest that 6 different regions (5 within X mRNA) of 14~23 nucleotides are Single-stranded. This putative structure provides a good working model and suggests potential target sites for antisense and ribozyme inhibitors and hybridization probes for the HBV X mRNA.

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References

  1. EMBO J. v.9 Aufiero, B.;Schneider, R.J.
  2. Proc. Natl. Acad. Sci. USA v.83 Buzayan, J.M.;Gerlach, W.L.;Bruening, G.B. https://doi.org/10.1073/pnas.83.23.8859
  3. Critical Review in Eucaryotic Gene Expression v.2 Castanotto, D.;Rossi, J.J.;Deshler, J.D.
  4. J. Virol. v.63 Colgrove, R.;Simon, G.;Ganem, D.
  5. Cell v.50 Forster, A.C.;Symons, R.H. https://doi.org/10.1016/0092-8674(87)90657-X
  6. Biochemie v.67 Gouy, M.;Marliere, P.;Papanicolaou, C.;Ninio, J. https://doi.org/10.1016/S0300-9084(85)80272-8
  7. Nature v.334 Haseloff, J.;Gerlach, W.L. https://doi.org/10.1038/334585a0
  8. Nucleic Acids Res. v.20 Hendry, P.;McCall, M.J.;Santiago, F.S.;Jennings, P.A. https://doi.org/10.1093/nar/20.21.5737
  9. EMBO J. v.9 Hohne, M.;Schaefer, S.;Seifer, M.;Feitelson, M.A.;Paul, M.A.;Gerlich, W.H.
  10. Nucleic Acids Res. v.14 Hutchins, C.J.;Rathjen, P.O.;Forster, A.C.;Symons, R.H. https://doi.org/10.1093/nar/14.9.3627
  11. Cell v.36 Izant, J.G.;Weintraub, H. https://doi.org/10.1016/0092-8674(84)90050-3
  12. Proc. Natl. Acad. Sci. USA v.86 Jaeger, J.A.;Turner, D.H.;Zuker, M. https://doi.org/10.1073/pnas.86.20.7706
  13. Methods Enzymol. v.183 Jaeger, J.A.;Turner, D.H.;Zuker, M.
  14. Nature v.351 Kim, C.M.;Koike, K.;Saitoh, I.;Miyamura, T.;Jay, G. https://doi.org/10.1038/351017a0
  15. Korean Biochem. J. v.22 Kim, C.S.;Yu, M.H.
  16. Lee, B.Y.
  17. Nucleic Acids Res. v.12 Melton, D.A.;Krieg, P.A.;Rebagliati, M.R.;Maniatis, T.;Zin, K.;Green, M.R. https://doi.org/10.1093/nar/12.18.7035
  18. Methods Enzymol. v.152 Mierendorf, R.C.;Pfeffer, D.
  19. SIAM (Soci. Ind. Appl. Math.) J. Appl. Math. v.35 Nussinov, R.;Pieczenik, G.;Griggs, J.R.;Kleitman, D.J. https://doi.org/10.1137/0135006
  20. Proc. Natl. Acad. Sci. USA v.72 Pipas, J.M.;McMahon, J.E. https://doi.org/10.1073/pnas.72.6.2017
  21. Science v.231 Prody, G.A.;Bakos, J.J.;Buzayan, J.M.;Schneider, T.R.;Bruening, G.B. https://doi.org/10.1126/science.231.4745.1577
  22. Biochemistry v.29 Ruffner, D.E.;Stormo, G.D.;Uhlenbeck, O.C. https://doi.org/10.1021/bi00499a018
  23. Proc. Natl. Acad. Sci. USA v.74 Sanger, F.;Nicklen, S.;Coulson, A.R. https://doi.org/10.1073/pnas.74.12.5463
  24. Nature v.344 Seto, E.;Mitchell, P.J.;Yen, T.B.S. https://doi.org/10.1038/344072a0
  25. J. Virol. v.62 Spandau, D.F.;Lee, C.H.
  26. Methods Enzymol. v.164 Stern, S.;Moazed, D.;Noller, H.F.
  27. Proc. Natl. Acad. Sci. USA v.86 Twu, J.S.;Robinson, W.S. https://doi.org/10.1073/pnas.86.6.2046
  28. J. Virol. v.61 Twu, J.S.;Schloemer, R.H.
  29. Nature v.328 Uhlenbeck, O.C. https://doi.org/10.1038/328596a0
  30. Oncogene v.3 Wollerscheim, M.;Debelka, U.;Hofschneider, P.H.
  31. Cell v.63 Wu, J.Y.;Zhou, Z.Y.;Judd, A.;Cartwright, C.A.;Robinson, W.S. https://doi.org/10.1016/0092-8674(90)90135-2
  32. Oncogene v.3 Zahm, P.;Hofschneider, P.H.;Koshy, R.
  33. Science v.244 Zuker, M. https://doi.org/10.1126/science.2468181