Skip to main content
SpringerLink
Log in

Two- and three-dimensional 31P-driven NMR procedures for complete assignment of backbone resonances in oligodeoxyribonucleotides

  • Research Paper
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Summary

We describe a strategy for sequential assignment of 31P and deoxyribose 1H NMR resonances in oligodeoxyribonucleotides. The approach is based on 31P−1H J-cross-polarization (hetero TOCSY) experiments, recently demonstrated for the assignment of resonances in RNA [Kellogg, G.W. (1992) J. Magn. Reson., 98, 176; Kellogg, G.W. et al. (1992) J. Am. Chem. Soc., 114, 2727]. Two-dimensional hetero TOCSY and hetero TOCSY-NOESY experiments are used to connect proton spin systems from adjacent nucleotides in the dodecamer d(CGCGAATTCGCG)2 entirely on the basis of through-bond scalar connectivities. All phosphorus resonances of the dodecamer are assigned by this method, and many deoxyribose 1H resonances can be assigned as well. A new three-dimensional hetero TOCSY-NOESY experiment is used for backbone proton 4′, 5′ and 5″ resonance assignments, completing assignments begun on this molecule in 1983 [Hare, D.R. et al. (1983) J. Mol. Biol., 171, 319]. Numerical simulations of the time dependence of coherence transfer aid in the interpretation of hetero TOCSY spectra of oligonucleotides and address the dependence of hetero TOCSY and related spectra on structural features of nucleic acids. The possibility of a generalized backbone-driven 1H and 31P resonance-assignment strategy for oligonucleotides is discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Altona, C. (1982) Recl. Trav. Chim. Pays-Bas, 101, 412–433.

    Google Scholar 

  • Arnott, S., Chandrasekeharan, R., Birdsall, D.L., Leslie, A.G.W. and Ratcliffe, R.L. (1980) Nature, 283, 743–745.

    Google Scholar 

  • Artemov, D.Y. (1991) J. Magn. Reson., 91, 405–407.

    Google Scholar 

  • Bax, A. and Davis, D.G. (1985) J. Magn. Reson., 65, 355–360.

    Google Scholar 

  • Bax, A. and Lerner, L. (1988) J. Magn. Reson., 79, 429–438.

    Google Scholar 

  • Bax, A., Sparks, S.W. and Torchia, D.A. (1989) Methods Enzymol., 176, 134–150.

    Google Scholar 

  • Bearden, D.W. and Brown, L.R. (1989) Chem. Phys. Lett., 163, 432–436.

    Google Scholar 

  • Braunschweiler, L. and Ernst, R.R. (1983) J. Magn. Reson., 53, 521–528.

    Google Scholar 

  • Byrd, R.A., Summers, M.F., Zon, G., Fouts, C.S. and Marzilli, L.G. (1986) J. Am. Chem. Soc., 108, 504–505.

    Google Scholar 

  • Cavanagh, J., Chazin, W.W. and Rance, M. (1990) J. Magn. Reson., 87, 110–131.

    Google Scholar 

  • Chary, K.V.R., Hosur, R.V. and Govil, G. (1989) Biochemistry, 27, 3858–3867.

    Google Scholar 

  • Clore, G.M. and Gronenborn, A.M. (1985) FEBS Lett., 199, 187–198.

    Google Scholar 

  • Connolly, B.A. and Eckstein, F. (1984) Biochemistry, 23, 5523–5527.

    Google Scholar 

  • Feigon, J., Leupin, W., Denny, W.A. and Kearns, D.R. (1983) Biochemistry, 22, 5943–5951.

    Google Scholar 

  • Fesik, S.W. and Zuiderweg, E.R.P. (1988) J. Magn. Reson., 78, 588–593.

    Google Scholar 

  • Field, L.D. and Messerle, B.A. (1985) J. Magn. Reson., 62, 453–460.

    Google Scholar 

  • Field, L.D. and Messerle, B.A. (1986) J. Magn. Reson., 66, 483–490.

    Google Scholar 

  • Fu, J.M., Schroeder, S.A., Jones, C.R., Santini, R. and Gorenstein, D.G. (1988) J. Magn. Reson., 77, 577–582.

    Google Scholar 

  • Glaser, S.J., Remerowski, M.L. and Drobny, G.P. (1989) Biochemistry, 28, 1483–1492.

    Google Scholar 

  • Gochin, M., Zon, G. and James, T.L. (1990) Biochemistry, 29, 11161–11171.

    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 

  • Hare, D.R., Wemmer, D.E., Chou, S., Drobny, G. and Reid, B.R. (1983) J. Mol. Biol., 171, 319–336.

    Google Scholar 

  • Haasnoot, C.A.G., De Leeuw, F.A.A.M. and Altona, C. (1980) Tetrahedron, 36, 2783–2792.

    Google Scholar 

  • Hiroaki, H. and Uesugi, S. (1989) FEBS Lett., 244, 43–46.

    Google Scholar 

  • Hosur, R.V., Ravikumar, M., Chary, K.V.R., Sheth, A., Govil, G., Zu-Kun, T. and Miles, H.R. (1986) FEBS Lett., 205, 71–76.

    Google Scholar 

  • Jones, C.R., Schroeder, S.A. and Gorenstein, D.G. (1988) J. Magn. Reson., 80, 370–374.

    Google Scholar 

  • Kellogg, G.W. (1992a) J. Magn. Reson., 98, 176–182.

    Google Scholar 

  • Kellogg, G.W. (1992b) J. Magn. Reson., 97, 623–627.

    Google Scholar 

  • Kellogg, G.W., Szewczak, A.A. and Moore, P.B. (1992) J. Am. Chem. Soc., 114, 2727–2728.

    Google Scholar 

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

    Google Scholar 

  • Marion, D. and Lancelot, G. (1984) Biochem. Biophys. Res. Commun., 124, 774–783.

    Google Scholar 

  • Marion, D. and Wüthrich, K. (1983) Biochem. Biophys. Res. Commun., 113, 967–974.

    Google Scholar 

  • Marion, D., Kay, L.E., Sparks, S., Torchia, D. and Bax, A. (1989) J. Am. Chem. Soc., 111, 1515.

    Google Scholar 

  • Metzler, W.J., Wang, C., Kitchen, D., Levy, R.M. and Pardi, A. (1990) J. Mol. Biol., 214, 711–736.

    Google Scholar 

  • Mooren, M.M.W., Hilbers, C.W., Van der Marel, G.A. and Van Boom, J.H. (1991) J. Magn. Reson., 94, 101–111.

    Google Scholar 

  • Morris, G.A. and Gibbs, A. (1991) J. Magn. Reson., 91, 444–449.

    Google Scholar 

  • Müller, L. and Ernst, R.R. (1979) Mol. Phys., 38, 963–992.

    Google Scholar 

  • Nerdal, W., Hare, D.R. and Reid, B.R. (1989) Biochemistry, 28, 10008–10021.

    Google Scholar 

  • Nikonowicz, E.P. and Pardi, A. (1992a) J. Am. Chem. Soc., 114, 1082–1083.

    Google Scholar 

  • Nikonowicz, E.P. and Pardi, A. (1992b) Nature, 355, 184–186.

    Google Scholar 

  • Nilges, M., Clore, G.M., Gronenborn, A.M., Brunger, A.T., Karplus, M. and Nilsson, L. (1987) Biochemistry, 26, 3718–3733.

    Google Scholar 

  • Ott, J. and Eckstein, F. (1985) Biochemistry, 24, 2530–2535.

    Google Scholar 

  • Otting, G., Widmer, H., Wagner, G. and Wüthrich, K. (1985) J. Magn. Reson., 66, 187–193.

    Google Scholar 

  • Pardi, A., Walker, R., Rapoport, H., Wider, G. and Wüthrich, K. (1983) J. Am. Chem. Soc., 105, 1652.

    Google Scholar 

  • Pardi, A. and Nikonowicz, E.P. (1992) J. Am. Chem. Soc., 114, 9202–9203.

    Google Scholar 

  • Piotto, M.E. and Gorenstein, D.G. (1991) J. Am. Chem. Soc., 113, 1438–1440.

    Google Scholar 

  • Reid, B.R. (1987) Quart. Rev. Biophys., 20, 1–34.

    Google Scholar 

  • Rinkel, L.J. and Altona, C. (1987) J. Biomol. Struct. Dyn., 4, 621–649.

    Google Scholar 

  • Roongta, V.A., Jones, C.R. and Gorenstein, D.G. (1990) Biochemistry, 29, 5245–5258.

    Google Scholar 

  • Schroeder, S.A., Fu, J.M., Jones, C.R. and Gorenstein, D.G. (1987) Biochemistry, 26, 3812–3821.

    Google Scholar 

  • Shaka, A.J. (1988) J. Magn. Reson., 77, 274–280.

    Google Scholar 

  • Scheek, R.M., Boelens, R., Russo, N., Van Boom, J.H. and Kaptein, R. (1984) Biochemistry, 23, 1371–1376.

    Google Scholar 

  • Sklenar, V., Miyashiro, H., Zon, G., Miles, H.T. and Bax, A. (1986) FEBS Lett., 208, 94–98.

    Google Scholar 

  • Sklenar, V. and Bax, A. (1987) J. Am. Chem. Soc., 109, 7525–7526.

    Google Scholar 

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

    Google Scholar 

  • Van de Ven, F.J.M. and Hilbers, C.W. (1988) Eur. J. Biochem., 178, 1–38.

    Google Scholar 

  • Van Wijk, J., Huckriede, B.D., Ippel, J.H. and Altona, C. (1992) Methods Enzymol., 211, 286–306.

    Google Scholar 

  • Varani, G. and TinocoJr., I. (1991) Quart. Rev. Biophys., 24, 479–532.

    Google Scholar 

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

    Google Scholar 

  • Zagorski, M.G. and Norman, D.G. (1989) J. Magn. Reson., 83, 167–172.

    Google Scholar 

  • Zuiderweg, E.R.P. (1990) J. Magn. Reson., 89, 533–542.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Molecular Biophysics and Biochemistry, Yale University, 06510-8064, New Haven, CT, U.S.A.

    Gregory W. Kellogg

  2. Department of Chemistry, Yale University, 06510-8064, New Haven, CT, U.S.A.

    Gregory W. Kellogg

  3. Department of Pediatrics, Yale University, School of Medicine, 333 Ceder Street, 06510-8064, New Haven, CT, U.S.A.

    Barry I. Schweitzer

Authors
  1. Gregory W. Kellogg
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Barry I. Schweitzer
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

To whom correspondence should be addressed.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kellogg, G.W., Schweitzer, B.I. Two- and three-dimensional 31P-driven NMR procedures for complete assignment of backbone resonances in oligodeoxyribonucleotides. J Biomol NMR 3, 577–595 (1993). https://doi.org/10.1007/BF00174611

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00174611

Keywords

Search

Navigation