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Hybrid-hybrid matrix structural refinement of a DNA three-way junction from 3D NOESY-NOESY

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Abstract

Homonuclear 3D NOESY-NOESY has shown great promise for the structural refinement of large biomolecules. A computationally efficient hybrid-hybrid relaxation matrix refinement methodology, using 3D NOESY-NOESY data, was used to refine the structure of a DNA three-way junction having two unpaired bases at the branch point of the junction. The NMR data and the relaxation matrix refinement confirm that the DNA three-way junction exists in a folded conformation with two of the helical stems stacked upon each other. The third unstacked stem extends away from the junction, forming an acute angle (∼60° ) with the stacked stems. The two unpaired bases are stacked upon each other and are exposed to the solvent. Helical parameters for the bases in all three strands show slight deviations from typical values expected for right-handed B-form DNA. Inter-nucleotide imino-imino NOEs between the bases at the branch point of the junction show that the junction region is well defined. The helical stems show mobility (± 20° ) indicating dynamic processes around the junction region. The unstacked helical stem adjacent to the unpaired bases shows greater mobility compared to the other two stems. The results from this study indicate that the 3D hybrid-hybrid matrix MORASS refinement methodology, by combining the spectral dispersion of 3D NOESY-NOESY and the computational efficiency of 2D refinement programs, provides an accurate and robust means for structure determination of large biomolecules. Our results also indicate that the 3D MORASS method gives higher quality structures compared to the 2D complete relaxation matrix refinement method.

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References

  • Altona, C., Pikkemaat, J.A. and Overmars, F.J.J. (1996) Curr. Opin. Struct. Biol., 6, 305–316.

    Google Scholar 

  • Anderson, R.J., Galatowicz, G., Macdonald, I.D., Lowdell, M.W., Corbett, T.J. and Prentice, H.C. (1997) Exp. Hematology, 25, 256–262.

    Google Scholar 

  • Belague, C., Kalla, M. and Zhang, W. (1997) J. Virology, 71, 3299–3306.

    Google Scholar 

  • Berg, J.N., Boelens, R., Vuister, G.W. and Kaptein, R. (1990) J. Magn. Reson., 87, 646–651.

    Google Scholar 

  • Bernks, K.I. and Bohenzky, R.A. (1987) Adv. Virus Res., 32, 243–306.

    Google Scholar 

  • Bernstein, R., Ross, A., Cieslar, C. and Holak, T.A. (1993) J. Magn. Reson., B101, 185.

    Google Scholar 

  • Birikh, K.R., Heaton, P.A. and Eckstein, F. (1997) Eur. J. Biochem., 245, 1–16.

    Google Scholar 

  • Boelens, R., Vuister, G.W., Koning, T.M.G. and Kaptein, R. (1989a) J. Am. Chem. Soc., 111, 8525–8526.

    Google Scholar 

  • Boelens, R., Koning, T.M.G., van der Marel, G.A., van Boom, J.H. and Kaptein, R. (1989b) J. Magn. Reson., 82, 290–308.

    Google Scholar 

  • Bonvin, A.M.J.J., Boelens, R. and Kaptein, R. (1991) J. Magn. Reson., 95, 626–631.

    Google Scholar 

  • Bothner-By, A.A. and Noggle, J.H. (1979) J. Am. Chem. Soc., 101, 5152–5155.

    Google Scholar 

  • Brünger, A.T. (1993) X-PLOR, version 3.1. A System for X-Ray Crystallography and NMR, Yale University Press, London.

  • Case, D.A., Pearlman, J.W., Caldwell, T.E., Chetham III, T.E., Ross, W.S., Simmerling, C.L., Darden, T., Merz, K.M., Stanton, A.L., Cheng, J.J., Vincent, M., Crowley, M., Ferguson, D.M., Radmer, R.J., Seibel, G.L., Singh, U.C., Weiner, P.K. and Kollman, P.A. (1997) AMBER 5, University of California, San Francisco, CA.

    Google Scholar 

  • Cheatham III, T.E. (1996) http://www.amber.ucsf.edu/amber/tutorial/ polyA-polyT/

  • Chastain, P.D. and Sinden, R.R. (1998) J. Mol. Biol., 275, 405–411.

    Google Scholar 

  • Donne, D.G., Gozansky, E.K. and Gorenstein, D.G. (1995) J. Magn. Reson., 106, 156–163.

    Google Scholar 

  • Duckett, D.R. and Lilley, D.M. (1990) EMBO J., 9, 1659–1664.

    Google Scholar 

  • Essman, U., Perera, M.L., Berkowitz, M.L., Darden, T., Lee, H. and Pedersen, L. (1995) J. Chem. Phys., b103, 8577–8593.

    Google Scholar 

  • Ewald, P. (1921) Ann. Phys. (Leipzig), 64, 253.

    Google Scholar 

  • Felden, B., Florentz, C., Ciege, R. and Westhof, E. (1996) RNA, 2, 201–212.

    Google Scholar 

  • Gorenstein, D. (1994) Chem. Rev., 94, 1315–1338.

    Google Scholar 

  • Guntert, P. and Wüthrich, K. (1992) J. Magn. Reson., 96, 403–407.

    Google Scholar 

  • Guo, Q., Lu, M., Seeman, N.C. and Kallenbach, N.R. (1990) Biochemistry, 29, 570–578.

    Google Scholar 

  • Habazettl, J., Ross, A., Oschkinat, H. and Holak, T.A. (1992a) J. Magn. Reson., 97, 511–521.

    Google Scholar 

  • Habazettl, J., Schleicher, M., Otlewski, J. and Holak, T.A. (1992b) J. Mol. Biol., 228, 156–169.

    Google Scholar 

  • Jensch, F. and Kemper, B. (1986) EMBO J., 5, 181–189.

    Google Scholar 

  • Keepers, J. and James, T.L. (1984) J. Magn. Reson., 57, 404–426.

    Google Scholar 

  • Kessler, H., Seip, S. and Saulitis, J. (1991) J. Biomol. NMR, 1, 83–92.

    Google Scholar 

  • Ladbury, J.E., Sturtevant, J.M. and Leontis, N.B. (1994) Biochemistry, 33, 6828–6833.

    Google Scholar 

  • Lai, X., Chen, C. and Anderson, J. (1993) J. Magn. Reson., B101, 271–288.

    Google Scholar 

  • Leontis, N.B., Kwok, W. and Newman, J.S. (1991) Nucleic Acids Res., 19, 759–766.

    Google Scholar 

  • Leontis, N.B., Hills, M.T., Piotto, M., Malhotra, A., Nussbaum, J. and Gorenstein, D.G. (1993) J. Biomol. Struct. Dyn., 11, 215–223.

    Google Scholar 

  • Leontis, N.B., Hills, M.T., Piotto, M., Ouporov, I.V., Malhotra, A. and Gorenstein, D.G. (1995) Biophys. J., 68, 251–274.

    Google Scholar 

  • Luxon, B.A. and Gorenstein, D.G. (1995) Methods Enzymol., 261, 45–73.

    Google Scholar 

  • Ma, R.-I., Kallenbach, N.R., Sheardy, R.D., Petrillo, M.L. and Seeman, N.C. (1986) Nucleic Acids Res., 14, 9745–9753.

    Google Scholar 

  • Macura, S. and Ernst, R.R. (1980) Mol. Phys., 41, 95–117.

    Google Scholar 

  • Meadows, R., Post, C.B., Luxon, B.A. and Gorenstein, D.G. (1996) MORASS Program, University of Texas Medical Branch, Galveston, TX.

    Google Scholar 

  • Mujeeb, A., Kerwin, S.M., Kenyon, G.L. and James, T.L. (1993) Biochemistry, 32, 13419–13431.

    Google Scholar 

  • Nussbaum, J.M., Newport, M.E.A., Mackie, M. and Leontis, N.B. (1994) Photochem. Photobiol., 59, 515–528.

    Google Scholar 

  • Ouporov, I.V. and Leontis, N.B. (1995) Biophys. J., 68, 266–274.

    Google Scholar 

  • Overmars, F.J.J., Pikkemaat, J.A., Van den Elst, H., Van Boom, J.H. and Altona, C. (1996) J. Mol. Biol., 255, 702–713.

    Google Scholar 

  • Pley, H.W., Flaherty, K.M. and McKay, D.B. (1994) Nature, 372, 111–113.

    Google Scholar 

  • Post, C.B., Meadows, R.P. and Gorenstein, D.G. (1990) J. Am. Chem. Soc., 112, 6796–6803.

    Google Scholar 

  • Puglisi, J.D. and Tinoco, I., Jr. (1989) Methods Enzymol., 180, 304–325.

    Google Scholar 

  • Rosen, M.A. and Patel, D.J. (1993a) Biochemistry, 32, 6563–6575.

    Google Scholar 

  • Rosen, M.A. and Patel, D.J. (1993b) Biochemistry, 32, 6576–6587.

    Google Scholar 

  • Ross, W.S. (1995) CARNAL, University of California, San Francisco, CA.

    Google Scholar 

  • Schafmeister, C.E.A.F., Ross, W.S. and Romanovski, V. (1995) LEaP (version 1.0) University of California, San Francisco, CA.

    Google Scholar 

  • Shen, Z. and Hagerman, P.J. (1994) J. Mol. Biol., 241, 415–430.

    Google Scholar 

  • Scott, W.G., Murray, J.B., Arnold, J.R.P., Stoddard, B.L. and Klug, A. (1996) Science, 274, 2065–2069.

    Google Scholar 

  • Shlyakhtenko, L.S., Rekesh, D., Lindsay, S.M., Kutyavin, I., Appella, E., Harrington, R.E. and Lyubchenko, Y.L. (1994) J. Biomol. Struct. Dyn., 11, 1175–1189.

    Google Scholar 

  • States, D.J., Haberkorn, R.A. and Ruben, D.J. (1982) J. Magn. Reson., 48, 286–292.

    Google Scholar 

  • Stuhmeier, F., Welch, J.B., Murchie, A.I.H., Lilley, D.M.J. and Clegg, R.M. (1997a) Biochemistry, 36, 13530–13538.

    Google Scholar 

  • Stuhmeier, F., Lilley, D.M.J. and Clegg, R.M. (1997b) Biochemistry, 36, 13539–13551.

    Google Scholar 

  • Thomas, P.D., Basus, V.J. and James, T.L. (1991) Proc. Natl. Acad. Sci. USA, 88, 1237–1241.

    Google Scholar 

  • Welch, J.B., Duckett, D.R. and Lilley, D.M.J. (1993) Nucleic Acids Res., 21, 4548–4555.

    Google Scholar 

  • Welch, J.B., Walter, F. and Lilley, D.M.J. (1995) J. Mol. Biol., 251, 507–519.

    Google Scholar 

  • Yang, M. and Miller, D.P. (1996) Biochemistry, 35, 7959–7967.

    Google Scholar 

  • Yip, P. and Case, D.A. (1989) J. Magn. Reson., 83, 643–648.

    Google Scholar 

  • Yip, P. (1993) J. Biomol. NMR, 3, 361–365.

    Google Scholar 

  • Zhang, Q., Chen, J., Gozansky, E.K., Zhu, F., Jackson, P.L. and Gorenstein, D.G. (1995) J. Magn. Reson., B106, 164–169.

    Google Scholar 

  • Zhong, M., Rashes, M.S., Leontis, N.B. and Kallenbach, N.R. (1994) Biochemistry, 33, 3660–3667.

    Google Scholar 

  • Zhu, F.Q., Donne, D.G., Gozansky, E.K., Luxon, B.A. and Gorenstein, D.G. (1996) Magn. Reson. Chem., 34, 125–135.

    Google Scholar 

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Authors and Affiliations

  1. Sealy Center for Structural Biology & Department of Human Biological Chemistry & Genetics, University of Texas Medical Branch, Galveston, TX, 77555-1157, U.S.A.

    Varatharasa Thiviyanathan, Bruce A. Luxon, Nishantha Illangasekare, David G. Donne & David G. Gorenstein

  2. Department of Chemistry, Bowling Green State University, Bowling Green, OH, 43403-0213, U.S.A.

    Neocles B. Leontis

Authors
  1. Varatharasa Thiviyanathan
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  2. Bruce A. Luxon
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  3. Neocles B. Leontis
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  4. Nishantha Illangasekare
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  5. David G. Donne
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  6. David G. Gorenstein
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Thiviyanathan, V., Luxon, B.A., Leontis, N.B. et al. Hybrid-hybrid matrix structural refinement of a DNA three-way junction from 3D NOESY-NOESY. J Biomol NMR 14, 209–221 (1999). https://doi.org/10.1023/A:1008330011425

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