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NMR structure of the chimeric hybrid duplex r(gcaguggc)⋅r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription

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Abstract

A high-quality NMR solution structure of the chimeric hybrid duplex r(gcaguggc)⋅r(gcca)d(CTGC) was determined using the program DYANA with its recently implemented new module FOUND, which performs exhaustive conformational grid searches for dinucleotides. To ensure conservative data interpretation, the use of 1H-1H lower distance limit constraints was avoided. The duplex comprises the tRNA–DNA junction formed during the initiation of HIV-1 reverse transcription. It forms an A-type double helix that exhibits distinct structural deviations from a standard A-conformation. In particular, the minor groove is remarkably narrow, and its width decreases from about 7.5 Å in the RNA/RNA stem to about 4.5 Å in the RNA/DNA segment. This is unexpected, since minor groove widths for A-RNA and RNA/DNA hybrid duplexes of ∼11 Å and ∼8.5 Å, respectively, were previously reported. The present, new structure supports that reverse transcriptase-associated RNaseH specificity is related primarily to conformational adaptability of the nucleic acid in 'induced-fit'-type interactions, rather than the minor groove width of a predominantly static nucleic acid duplex.

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References

  • Anil Kumar, Ernst, R.R. and Wüthrich, K. (1980) Biochem. Biophys. Res. Commun., 95, 1–6.

    Google Scholar 

  • Arnott, S., Chandrasekaran, R., Millane, R.P. and Park, H.-S. (1986) J. Mol. Biol., 188, 631–640.

    Google Scholar 

  • Babcock, M.S., Pednault, E.P.D. and Olson, W.K. (1994) J. Mol. Biol., 237, 125–156.

    Google Scholar 

  • Bachelin, M., Hessler, G., Kurz, G., Hacia, J.G., Dervan, P.B. and Kessler, H. (1998) Nat. Struct. Biol., 5, 271–275.

    Google Scholar 

  • Baltimore, D. (1970) Nature, 226, 1209–1211.

    Google Scholar 

  • Ban, C., Ramakrishnan, B. and Sundaralingam, M. (1992) Curr. Opin. Struct. Biol., 5, 282–295.

    Google Scholar 

  • Bartels, C., Xia, T., Billeter, M., Güntert, P. and Wüthrich, K. (1995) J. Biomol. NMR, 6, 1–10.

    Google Scholar 

  • Bebenek, K., Beard, W. A., Darden, T. A., Li, L., Prasard, R., Luton, B.A., Gorenstein, D.A., Wilson, S.H. and Kunkel, T.A. (1997) Nat. Struct. Biol., 4, 194–197.

    Google Scholar 

  • Blain, S.W. and Goff, S.P. (1993) J. Biol. Chem., 268, 23585–23592.

    Google Scholar 

  • Cheatham, T.E. and Kollman, P.A. (1996) J. Am. Chem. Soc., 119, 4805–4825.

    Google Scholar 

  • Chuprina, V.P., Fedoroff, O.Y. and Reid, B.R. (1991a) Biochemistry, 30, 561–568.

    Google Scholar 

  • Chuprina, V.P., Lipanov, A.A., Fedoroff, O.Y., Kim, S.-G., Kintanar, A. and Reid, B.R. (1991b) Proc. Natl. Acad. Sci. USA, 88, 9087–9091.

    Google Scholar 

  • Davies, J.F., Hostomska, Z., Hostomsky, Z., Jordan, S.R. and Matthews, D.A. (1991) Science, 252, 88–95.

    Google Scholar 

  • DeMesmaeker, A., Altmann, K.-H., Waldner, A. and Wendeborn, S. (1995) Curr. Opin. Struct. Biol., 5, 343–355.

    Google Scholar 

  • Dickerson, R.E. (1992) Methods Enzymol., 211, 67–111.

    Google Scholar 

  • Ding, J., Jacobo-Molina, A., Tantillo, C., Lu, X., Nanni, R.C. and Arnold, E. (1994) J. Mol. Recogn., 7, 157–161.

    Google Scholar 

  • Dock-Bregeon, A.C., Chevrier, B., Podjarny, A., Johnson, J., de-Bear, J.S., Gough, G.R., Gilham, P.T. and Moras, D. (1989) J. Mol. Biol., 209, 459–474.

    Google Scholar 

  • Egli, M., Usman, N., Zhang, S. and Rich, A. (1992) Proc. Natl. Acad. Sci. USA, 89, 534–538.

    Google Scholar 

  • Egli, M., Usman, N. and Rich, A. (1993) Biochemistry, 32, 3221–3273.

    Google Scholar 

  • Egli, M., Portmann, S. and Usman, N. (1996) Biochemistry, 35, 8489–8494.

    Google Scholar 

  • Fedoroff, O.Y., Salazar, M. and Reid, B.R. (1993) J. Mol. Biol., 233, 509–523.

    Google Scholar 

  • Fedoroff, O.Y., Salazar, M. and Reid, B.R. (1996) Biochemistry, 35, 11070–11080.

    Google Scholar 

  • Fedoroff, O.Y., Ge, Y. and Reid, B.R. (1997) J. Mol. Biol., 269, 225–239.

    Google Scholar 

  • Fernández, C., Szyperski, T., Bruyére, T., Ramage, P., Mösinger, E. and Wüthrich, K. (1997) J. Mol. Biol., 266, 576–593.

    Google Scholar 

  • Furfine, E.S. and Reardon, J.E. (1991) Biochemistry, 30, 7041–7046.

    Google Scholar 

  • González, C., Stec, W., Kobylanska, A., Hogrefe, R.I., Reynolds, M. and James, T.L. (1994) Biochemistry, 33, 11062–11072.

    Google Scholar 

  • Gorenstein, D.G., Schroeder, S.A., Fu, J.M., Metz, J.T., Roongta, V. and Jones, C.R. (1988) Biochemistry, 27, 7223–7237.

    Google Scholar 

  • Götte, M., Fackler, S., Hermann, T., Perola, E., Cellai, L., Gross, H.J., Le Grice, S.F.J. and Heumann, H. (1995) EMBO J., 14, 833–841.

    Google Scholar 

  • Griesinger, C., Sørensen, O. and Ernst, R.R. (1985) J. Am. Chem. Soc., 107, 6394–6396.

    Google Scholar 

  • Griesinger, C., Otting, G., Wüthrich, K. and Ernst, R.R. (1988) J. Am. Chem. Soc., 110, 7870–7872.

    Google Scholar 

  • Guéron, M. and Leroy, J.L. (1995) Methods Enzymol., 261, 383–413.

    Google Scholar 

  • Güntert, P., Braun, W. and Wüthrich, K. (1991) J. Mol. Biol., 217, 517–530.

    Google Scholar 

  • Güntert, P., Dötsch, V., Wider, G. and Wüthrich, K. (1992) J. Biomol. NMR, 2, 619–629.

    Google Scholar 

  • Güntert, P., Mumenthaler, C. and Wüthrich, K. (1997) J. Mol. Biol., 273, 283–298.

    Google Scholar 

  • Güntert, P., Billeter, M., Ohlenschläger, O., Brown, L.R. and Wüthrich, K. (1998) J. Biomol. NMR, 12, 543–548.

    Google Scholar 

  • Han, G.W., Kopka, M.L., Cascio, D., Grzeskowiak, K. and Dickerson, R.E. (1997) J. Mol. Biol., 269, 811–826.

    Google Scholar 

  • Hartmann, B. and Lavery, R. (1996) Q. Rev. Biophys., 29, 309–368.

    Google Scholar 

  • Horton, N.C. and Finzel, B.C. (1996) J. Mol. Biol., 264, 521–533.

    Google Scholar 

  • Hostomsky, Z., Hughes, S.H., Goff, S.P. and Le Grice, S.F.J. (1994) J. Virol., 68, 1970–1971.

    Google Scholar 

  • Isel, C., Landry, J.M., LeGrice, S.F., Ehresmann, C., Ehresmann, B. and Marquet, R. (1996) EMBO J., 15, 917–924.

    Google Scholar 

  • Jacobo-Molina, A., Ding, J., Nanni, R.G., Clark, A.D., Lu, X., Tantillo, C., Williams, R.L., Kamer, G., Ferris, A.L., Clark, P., Hizi, A., Hughes, S.H. and Arnold, E. (1993) Proc. Natl. Acad. Sci. USA, 90, 6320–6324.

    Google Scholar 

  • Kanaya, E. and Kanaya, S. (1995) Eur. J. Biochem., 231, 557–562.

    Google Scholar 

  • Kennard, O. and Hunter, W.N. (1991) Angew. Chem. Int. Ed. Engl., 30, 1254–1277.

    Google Scholar 

  • Kiefer, J.R., Mao, C., Braman, J.C. and Beese, L.S. (1998) Nature, 391, 304–307.

    Google Scholar 

  • Kim, S.-G., Lin, L.-J. and Reid, B.R. (1992) Biochemistry, 31, 3564–3574.

    Google Scholar 

  • Klinck, R., Sprules, T. and Gehring, K. (1997) Nucleic Acid Res., 25, 2120–2137.

    Google Scholar 

  • Koradi, R., Billeter, M. and Wüthrich, K. (1996) J. Mol. Graph., 14, 51–55.

    Google Scholar 

  • Lanchy, J.-M., Ehresmann, C., Le Grice, S.F.J., Ehresmann, B. and Marquet, R. (1996) EMBO J., 15, 7178–7187.

    Google Scholar 

  • Lane, A.N., Ebel, S. and Brown, T. (1993) Eur. J. Biochem., 215, 297–306.

    Google Scholar 

  • Liepinsh, E., Otting, G. and Wüthrich, K. (1992) Nucleic Acid Res., 20, 6549–6553.

    Google Scholar 

  • Luginbühl, P., Güntert, P., Billeter, M. and Wüthrich, K. (1996) J. Biomol. NMR, 8, 136–146.

    Google Scholar 

  • Mak, J. and Kleiman, L. (1997) J. Virol., 71, 8087–8095.

    Google Scholar 

  • Mandel, A.M., Akke, M. and Palmer III, A.G. (1995) J. Mol. Biol., 246, 144–162.

    Google Scholar 

  • Marino, J.P., Schwalbe, H., Glaser, S.J. and Griesinger, C. (1996) J. Am. Chem. Soc., 118, 4388–4395.

    Google Scholar 

  • Marquet, R., Isel, C., Ehresmann, C. and Ehresmann, B. (1995) Biochimie, 77, 113–124.

    Google Scholar 

  • Müller, U., Maier, G., Onori, A.M., Cellai, L., Heumann, H. and Heinemann, U. (1998) Biochemistry, 37, 12005–12011.

    Google Scholar 

  • Nakamura, H., Oda, Y., Iwai, S., Inoue, H., Ohtsuka, E., Kanaya, S., Kimura, S., Katsuda, C., Katayanagi, K., Morikawa, K., Miyashiro, H. and Ikehara, M. (1991) Proc. Natl. Acad. Sci. USA, 88, 11535–11539.

    Google Scholar 

  • Nelson, H.C.M., Finch, J.T., Bonaventura, F.L. and Klug, A. (1986) Nature, 330, 221–226.

    Google Scholar 

  • Nishizaki, T., Iwai, S., Ohkubo, T., Kojima, C., Nakamura, H., Kyogoku, Y. and Ohtsuka, E. (1995) Biochemistry, 34, 4016–4025.

    Google Scholar 

  • Otting, G., Orbons, L.P.M. and Wüthrich, K. (1990) J. Magn. Reson., 89, 423–430.

    Google Scholar 

  • Piotto, M., Saudek, V. and Sklenář, V. (1992) J. Biomol. NMR, 2, 661–665.

    Google Scholar 

  • Rance, M., Sørensen, O.W., Bodenhausen, G., Wagner, G., Ernst, R.R. and Wüthrich, K. (1983) Biochem. Biophys. Res. Commun., 117, 479–485.

    Google Scholar 

  • Ravishankar, G., Swaminathan, S., Beveridge, D.L., Lavery, R. and Sklenar, H. (1988) J. Biomol. Struct. Dyn., 6, 669–699.

    Google Scholar 

  • Salazar, M., Fedoroff, O.Y., Zhu, L. and Reid, B.R. (1994) J. Mol. Biol., 241, 440–455.

    Google Scholar 

  • Salazar, M., Fedoroff, O.Y. and Reid, B.R. (1996) Biochemistry, 35, 8126–8135.

    Google Scholar 

  • Sklénař, V. and Bax, A. (1987) J. Magn. Reson., 74, 469–474.

    Google Scholar 

  • Smith, J.S. and Roth, M.J. (1992) J. Biol. Chem., 267, 15071–15079.

    Google Scholar 

  • Szyperski, T., Güntert, P., Otting, G. and Wüthrich, K. (1992) J. Magn. Reson., 99, 552–560.

    Google Scholar 

  • Szyperski, T., Fernández, C., Ono, A., Kainosho, M. and Wüthrich, K. (1998) J. Am. Chem. Soc., 120, 821–822.

    Google Scholar 

  • Telesnitsky, A. and Goff, S.P. (1997) Retroviruses (Eds, Coffin, J.M., Hughes, S.H. and Varmus, H.E.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, U.S.A., pp. 21–160.

    Google Scholar 

  • Temin, H.M. and Mizutani, S. (1970) Nature, 226, 1211–1213.

    Google Scholar 

  • Varani, G. and Tinoco Jr., I. (1991) Q. Rev. Biophys., 24, 479–532.

    Google Scholar 

  • Wahl, M.C. and Sundaralingam, M. (1995) Curr. Opin. Struct. Biol., 5, 282–295.

    Google Scholar 

  • Wang, A.C., Kim, S.G., Flynn, P.F., Chou, S.-H., Orba, J. and Reid, B.R. (1992) Biochemistry, 31, 3940–3946.

    Google Scholar 

  • Weiner, S.J., Kollman, P.A., Nguyen, D.T. and Case, D.A. (1986) J. Comput. Chem., 7, 230–252.

    Google Scholar 

  • Wijmenga, S.S., Mooren, M.M.W. and Hilbers, C. (1993) In NMR of Macromolecules. A Practical Approach (Ed., Roberts, G.C.K.), Oxford University Press, Oxford, U.K., pp. 217–283.

    Google Scholar 

  • Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York, NY, U.S.A.

    Google Scholar 

  • Zhu, L., Salazar, M. and Reid, B.R. (1995) Biochemistry, 34, 2372–2380.

    Google Scholar 

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Authors and Affiliations

  1. Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg, CH-8093, Zürich, Switzerland

    Thomas Szyperski, Martin Billeter & Kurt Wüthrich

  2. Max-Planck-Institut für Biochemie, D-82152, Martinsried, Germany

    Matthias Götte & Hermann Heumann

  3. Istituto di Strutturistica Chimica, CNR, P.O. Box 10, I-00016, Monterotondo Stazione, Rome, Italy

    Emanuele Perola & Luciano Cellai

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  1. Thomas Szyperski
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Szyperski, T., Götte, M., Billeter, M. et al. NMR structure of the chimeric hybrid duplex r(gcaguggc)⋅r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription. J Biomol NMR 13, 343–355 (1999). https://doi.org/10.1023/A:1008350604637

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