Skip to main content
SpringerLink
Log in

Assignment methodology for larger RNA oligonucleotides: Application to an ATP-binding RNA aptamer

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

Abstract

The use of uniform 13C,15N labeling in the NMR spectroscopic study of RNA structures hasgreatly facilitated the assignment process in small RNA oligonucleotides. For ribose spinsystem assignments, exploitation of these labels has followed previously developed methodsfor the study of proteins. However, for sequential assignment of the exchangeable andnonexchangeable protons of the nucleotides, it has been necessary to develop a variety of newNMR experiments. Even these are of limited utility in the unambiguous assignment of largerRNAs due to the short carbon relaxation times and extensive spectral overlap for all nuclei.These problems can largely be overcome by the additional use of base-type selectively13C,15N-labeled RNA in combination with a judicious use of related RNAs with basesubstitutions. We report the application of this approach to a 36-nucleotide ATP-binding RNAaptamer in complex with AMP. Complete sequential 1H assignments, as well as the majorityof 13C and 15N assignments, were obtained.

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

  • Allain, F. and Varani, G. (1995) J. Mol. Biol., 250, 333–353.

    Google Scholar 

  • Batey, R.T., Inada, M., Kujawinski, E., Puglisi, J.D. and Williamson, J.R. (1992) Nucleic Acids Res., 20, 4515–4523.

    Google Scholar 

  • Battiste, J.L., Tan, R., Frankel, A.D. and Williamson, J.R. (1995) J. Biomol. NMR, 6, 375–389.

    Google Scholar 

  • Bax, A., Clore, G.M., Driscoll, P.C., Gronenborn, A.M., Ikura, M. and Kay, L.E. (1990) J. Magn. Reson., 87, 620–627.

    Google Scholar 

  • Cavanagh, J., Fairbrother, W.J., Palmer, A.G.I. and Skelton, N.J. (1996) Protein NMR Spectroscopy: Principles and Practice, Academic Press, San Diego, CA, U.S.A.

    Google Scholar 

  • Cheong, C., Varani, G. and Tinoco Jr., I. (1990) Nature, 346, 680–682.

    Google Scholar 

  • Clore, G.M., Bax, A., Driscoll, P.C., Wingfield, P.T. and Gronenborn, A.M. (1990) Biochemistry, 29, 8172–8184.

    Google Scholar 

  • Clore, G.M. and Gronenborn, A.M. (1993) NMR of Proteins, CRC Press, Boca Raton, FL, U.S.A.

    Google Scholar 

  • Dieckmann, T. and Feigon, J. (1994) Curr. Opin. Struct. Biol., 4, 745–749.

    Google Scholar 

  • Dieckmann, T., Suzuki, E., Nakamura, G.K. and Feigon, J. (1996) RNA, 2, 628–640.

    Google Scholar 

  • Ellington, A.D. and Szostak, J.W. (1990) Nature, 346, 818–822.

    Google Scholar 

  • Farmer II, B.T., Müller, L., Nikonowicz, E.P. and Pardi, A. (1993) J. Am. Chem. Soc., 115, 11040–11041.

    Google Scholar 

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

    Google Scholar 

  • Feigon, J., Sklenář, V., Wang, E., Gilbert, D.E., Macaya, R.F. and Schultze, P. (1992) Methods Enzymol., 211, 235–254.

    Google Scholar 

  • Feigon, J., Dieckmann, T. and Smith, F.W. (1996) Chem. Biol., 3, 611–617.

    Google Scholar 

  • Fiala, R., Jiang, F. and Patel, D.J. (1996) J. Am. Chem. Soc., 118, 689–690.

    Google Scholar 

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

    Google Scholar 

  • Heus, H.A., Wijmenga, S.S., Van de Ven, F.J.M. and Hilbers, C.W. (1994) J. Am. Chem. Soc., 116, 4983–4984.

    Google Scholar 

  • Jiang, F., Kumar, R.A., Jones, R.A. and Patel, D.J. (1996) Nature, 382, 183–186.

    Google Scholar 

  • Legault, P., Farmer II, B.T., Müller, L. and Pardi, A. (1994) J. Am. Chem. Soc., 116, 2203–2204.

    Google Scholar 

  • Marino, J.P., Prestegard, J.H. and Crothers, D.M. (1994a) J. Am. Chem. Soc., 116, 2205–2206.

    Google Scholar 

  • Marino, J.P., Schwalbe, H., Anklin, C., Bermel, W., Crothers, D.M. and Griesinger, C. (1994b) J. Am. Chem. Soc., 116, 6472–6473.

    Google Scholar 

  • Marino, J.P., Schwalbe, H., Anklin, C., Bermel, W., Crothers, D.M. and Griesinger, C. (1995) J. Biomol. NMR, 5, 87–92.

    Google Scholar 

  • Marion, D., Kay, L.E., Sparks, S.W., Torchia, D.A. and Bax, A. (1989) J. Am. Chem. Soc., 111, 1515–1517.

    Google Scholar 

  • Michnicka, M.J., Harper, J.W. and King, G.C. (1993) Biochemistry, 32, 395–400.

    Google Scholar 

  • Milligan, J.F., Groebe, D.R., Witherell, G.W. and Uhlenbeck, O.C. (1987) Nucleic Acids Res., 15, 8783–8798.

    Google Scholar 

  • Moore, P.B. (1993) Curr. Opin. Struct. Biol., 3, 340–344.

    Google Scholar 

  • Müller, L., Nikonowicz, E.P., Farmer II, B.T. and Pardi, A. (1994) J. Biomol. NMR, 4, 129–133.

    Google Scholar 

  • Nikonowicz, E.P., Sirr, A., Legault, P., Jucker, F.M., Baer, L.M. and Pardi, A. (1992) Nucleic Acids Res., 20, 4507–4513.

    Google Scholar 

  • Nikonowicz, E.P. and Pardi, A. (1993) J. Mol. Biol., 232, 1141–1156.

    Google Scholar 

  • Otting, G., Qian, Y.Q., Billeter, M., Müller, M., Affolter, M., Gehring, W.J. and Wüthrich, K. (1990) EMBO J., 9, 3085–3092.

    Google Scholar 

  • Otting, G. and Wüthrich, K. (1990) Q. Rev. Biophys., 23, 39–96.

    Google Scholar 

  • Pardi, A. (1995) Methods Enzymol., 261, 350–380.

    Google Scholar 

  • Peterson, R.D., Bartel, D.P., Szostak, J.W., Horvath, S.J. and Feigon, J. (1994) Biochemistry, 33, 5357–5366.

    Google Scholar 

  • Piantini, U., Sørensen, O.W. and Ernst, R.R. (1982) J. Am. Chem. Soc., 104, 6800–6801.

    Google Scholar 

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

    Google Scholar 

  • Santoro, J. and King, G. (1992) J. Magn. Reson., 97, 202–207.

    Google Scholar 

  • Sassanfar, M. and Szostak, J.W. (1993) Nature, 364, 550–553.

    Google Scholar 

  • Scheek, R.M., Russo, N., Boelens, R. and Kaptein, R. (1983) J. Am. Chem. Soc., 105, 2914–2916.

    Google Scholar 

  • Simorre, J.-P., Zimmermann, G.R., Pardi, A., Farmer II, B.T. and Müller, L. (1995) J. Biomol. NMR, 4, 427–432.

    Google Scholar 

  • Simorre, J.-P., Zimmermann, G.R., Müller, L. and Pardi, A. (1996a) J. Biomol. NMR, 7, 153–156.

    Google Scholar 

  • Simorre, J.-P., Zimmermann, G.R., Müller, L. and Pardi, A. (1996b) J. Am. Chem. Soc., 118, 5316–5317.

    Google Scholar 

  • Sklenář, V. and Bax, A. (1987) J. Magn. Reson., 74, 469–479.

    Google Scholar 

  • Sklenář, V., Peterson, R.D., Rejante, M.R. and Feigon, J. (1993a) J. Biomol. NMR, 3, 721–727.

    Google Scholar 

  • Sklenář, V., Peterson, R.D., Rejante, M.R., Wang, E. and Feigon, J. (1993b) J. Am. Chem. Soc., 115, 12181–12182.

    Google Scholar 

  • Sklenář, V., Piotto, M., Leppik, R. and Saudek, V. (1993c) J. Magn. Reson., A102, 241–245.

    Google Scholar 

  • Sklenář, V., Peterson, R.D., Rejante, M.R. and Feigon, J. (1994) J. Biomol. NMR, 4, 117–122.

    Google Scholar 

  • Sklenář, V., Dieckmann, T., Butcher, S.E. and Feigon, J. (1996) J. Biomol. NMR, 7, 83–87.

    Google Scholar 

  • Tate, S.-I., Ono, A. and Kainosho, M. (1994) J. Am. Chem. Soc., 116, 5977–5978.

    Google Scholar 

  • Tolbert, T.J. and Williamson, J.R. (1996) J. Am. Chem. Soc., 118, 7929–7940.

    Google Scholar 

  • Tuerk, C. and Gold, L. (1990) Science, 249, 505–510.

    Google Scholar 

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

    Google Scholar 

  • Varani, G., Aboul-ela, F. and Allain, F.H.T. (1996) Prog. NMR Spectrosc., 29, 51–127.

    Google Scholar 

  • Vuister, G.W. and Bax, A. (1992) J. Magn. Reson., 98, 428–435.

    Google Scholar 

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

    Google Scholar 

  • Zuiderweg, E.R.P., McIntosh, L.P., Dahlquist, F.W. and Fesik, S.W. (1990) J. Magn. Reson., 86, 210–216.

    Google Scholar 

  • Zuiderweg, E.R.P., Petros, A.M., Fesik, S.W. and Olejniczak, E.T. (1991) J. Am. Chem. Soc., 113, 370–372.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, P.O. Box 951569, Los Angeles, CA, 90095-1569, U.S.A

    Thorsten Dieckmann & Juli Feigon

Authors
  1. Thorsten Dieckmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Juli Feigon
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Dieckmann, T., Feigon, J. Assignment methodology for larger RNA oligonucleotides: Application to an ATP-binding RNA aptamer. J Biomol NMR 9, 259–272 (1997). https://doi.org/10.1023/A:1018622708674

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1018622708674

Search

Navigation