Preparation of large RNA oligonucleotides with complementary isotope-labeled segments for NMR structural studies


RNA structure determination by solution NMR spectroscopy is often restricted to small RNAs (<15 kDa) owing to the problem of chemical shift degeneracy. A fruitful coupling of novel NMR techniques with segmental RNA labeling methodologies could be a powerful tool to overcome the molecular mass limitation of RNA NMR spectroscopy. Herein, we describe a time- and cost-effective procedure to prepare and purify segmentally labeled large RNAs. Two sets of RNA fragments with complementary labeling schemes, such as one fragment 13C- and the other 15N-labeled, are prepared by in vitro transcription from a single plasmid DNA. The desired RNA fragments are excised from the primary transcript by two cis-acting hammerhead ribozymes, yielding the required engineered ends for subsequent, complementary ligation. The resulting RNA oligonucleotides display NMR spectra with greatly reduced resonance overlap and thus enable NMR studies of smaller labeled RNA segments within the native context of a large RNA. The procedure is expected to take 3–4 weeks to implement.

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Figure 1: Design of linked, cis-acting hammerhead ribozymes.
Figure 2: Cloning strategy to prepare plasmid template with linked cis-acting hammerhead ribozymes and products of in vitro transcription.
Figure 3: Complementary segmental labeling yields simplified NMR spectra.


  1. 1

    Varani, G., Aboul-Ela, F. & Allain, F. Prog. Nucl. Magn. Reson. Spectrosc. 29, 51–127 (1996).

  2. 2

    Furtig, B., Richter, C., Wohnert, J. & Schwalbe, H. NMR spectroscopy of RNA. ChemBioChem 4, 936–962 (2003).

  3. 3

    Latham, M.P., Brown, D.J., McCallum, S.A. & Pardi, A. NMR methods for studying the structure and dynamics of RNA. Chembiochem 6, 1492–1505 (2005).

  4. 4

    Tjandra, N. & Bax, A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278, 1111–1114 (1997).

  5. 5

    Zhou, H., Vermeulen, A., Jucker, F.M. & Pardi, A. Incorporating residual dipolar couplings into the NMR solution structure determination of nucleic acids. Biopolymers 52, 168–180 (1999).

  6. 6

    Hansen, M.R., Hanson, P. & Pardi, A. Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions. Methods Enzymol. 317, 220–240 (2000).

  7. 7

    Mollova, E.T. & Pardi, A. NMR solution structure determination of RNAs. Curr. Opin. Struct. Biol. 10, 298–302 (2000).

  8. 8

    Lukavsky, P.J. & Puglisi, J.D. Structure determination of large biological RNAs. Methods Enzymol. 394, 399–416 (2005).

  9. 9

    Lukavsky, P.J., Kim, I., Otto, G.A. & Puglisi, J.D. Structure of HCV IRES domain II determined by NMR. Nat. Struct. Biol. 10, 1033–1038 (2003).

  10. 10

    D'Souza, V., Dey, A., Habib, D. & Summers, M.F. NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus. J. Mol. Biol. 337, 427–442 (2004).

  11. 11

    Chen, Y. et al. Structure of stem-loop IV of Tetrahymena telomerase RNA. EMBO J. 25, 3156–3166 (2006).

  12. 12

    Kim, I., Lukavsky, P.J. & Puglisi, J.D. NMR study of 100 kDa HCV IRES RNA using segmental isotope labeling. J. Am. Chem. Soc. 124, 9338–9339 (2002).

  13. 13

    Tzakos, A.G., Easton, L.E. & Lukavsky, P.J. Complementary segmental labeling of large RNAs: economic preparation and simplified NMR spectra for measurement of more RDCs. J. Am. Chem. Soc. 128, 13344–13345 (2006).

  14. 14

    Ferbeyre, G., Bourdeau, V., Pageau, M., Miramontes, P. & Cedergren, R. Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank. Genome Res. 10, 1011–1019 (2000).

  15. 15

    Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415 (2003).

  16. 16

    Tiedge, H., Zhou, A., Thorn, N.A. & Brosius, J. Transport of BC1 RNA in hypothalamo-neurohypophyseal axons. J. Neurosci. 13, 4214–4219 (1993).

  17. 17

    Batey, R.T., Battiste, J.L. & Williamson, J.R. Preparation of isotopically enriched RNAs for heteronuclear NMR. Methods Enzymol. 261, 300–322 (1995).

  18. 18

    Li, Y., Wang, E. & Wang, Y. A modified procedure for fast purification of T7 RNA polymerase. Protein Expr. Purif. 16, 355–358 (1999).

  19. 19

    Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular Cloning: A Laboratory Manual 3rd edn. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2001).

  20. 20

    Ausubel, F.M. et al. (eds). Short Protocols in Molecular Biology: A Compedium of Methods. (John Wiley & Sons Inc., New York, 2002).

  21. 21

    Tanner, N.K. et al. A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses. Curr. Biol. 4, 488–498 (1994).

  22. 22

    Guo, H.C. & Collins, R.A. Efficient trans-cleavage of a stem–loop RNA substrate by a ribozyme derived from neurospora VS RNA. EMBO J. 14, 368–376 (1995).

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A.G.T. is grateful for an EMBO long-term fellowship.

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Correspondence to Peter J Lukavsky.

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Tzakos, A., Easton, L. & Lukavsky, P. Preparation of large RNA oligonucleotides with complementary isotope-labeled segments for NMR structural studies. Nat Protoc 2, 2139–2147 (2007) doi:10.1038/nprot.2007.306

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