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NMR Studies on RNA

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Experimental Approaches of NMR Spectroscopy

Abstract

Basic methods for NMR analysis of RNA are presented for researchers who recently joined or want to join this field. This chapter includes design of RNA sequences, sample preparation, NMR measurements and analysis as well as structure calculation. Some examples are also shown.

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References

  1. Varani, G., Aboul-ela, F., Allain, F.H.-T.: NMR investigation of RNA structure. Prog. NMR Spectrosc. 29, 51–127 (1996)

    Article  CAS  Google Scholar 

  2. Fürtig, B., Richter, C., Wöhnert, J., Schwalbe, H.: NMR spectroscopy of RNA. ChemBioChem 4, 936–962 (2003)

    Article  Google Scholar 

  3. Sato, K., Hamada, M., Asai, K., Mituyama, T.: CentroidFold: a web server for RNA secondary structure prediction. Nucleic Acids Res. 37, W277–W280 (2009)

    Article  CAS  Google Scholar 

  4. Dawson, W., Fujiwara, K., Kawai, G.: Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding. PLoS ONE 2, 905 (2007)

    Article  Google Scholar 

  5. Baba, S., Takahashi, K., Noguchi, S., Takaku, H., Koyanagi, Y., Yamamoto, N., Kawai, G.: Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J. Biochem. 138, 583–592 (2005)

    Article  CAS  Google Scholar 

  6. Milligan, J.F., Groebe, D.R., Witherell, W.G., Uhlenbeck, O.C.: Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783–8798 (1987)

    Article  CAS  Google Scholar 

  7. Ferré-D’Amaré, A.R., Doudna, J.A.: Use of cis- and trans-ribozymes to remove 5′ and 3′ heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res. 24, 977–978 (1996)

    Article  Google Scholar 

  8. Ohtsuki, T., Kawai, G., Watanabe, Y., Kita, K., Nishikawa, K., Watanabe, K.: Preparation of biologically active Ascaris suum mitochondrial tRNAMet with a TV-replacement loop by ligation of chemically synthesized RNA fragments. Nucleic Acids Res. 24, 662–667 (1996)

    Article  CAS  Google Scholar 

  9. Ohtsuki, T., Kawai, G., Watanabe, Y.: The minimal tRNA: unique structure of Ascaris suum mitochondrial tRNA SerUCU having a short T arm and lacking the entire D arm. FEBS Let. 514, 37–43 (2002)

    Article  CAS  Google Scholar 

  10. Someya, T., Ando, A., Kimoto, M., Hirao, I.: Site-specific labelling of RNA by combining genetic alphabet expansion transcription and copper-free click chemistry. Nucleic Acids Res. 43, 6665–6676 (2015)

    Article  CAS  Google Scholar 

  11. Xu, J., Lapham, J., Crothers, D.M.: Determining RNA solution structure by segmental isotopic labelling and NMR: application to Caenorhabditis elegans spliced leader RNA 1. Proc. Natl. Acad. Sci. USA 93, 44–48 (1996)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  14. Kawahara, I., Haruta, K., Ashihara, Y., Yamanaka, D., Kuriyama, M., Toki, N., Kondo, Y., Teruya, K., Ishikawa, J., Furuta, H., Ikawa, Y., Kojima, C., Tanaka, Y.: Site-specific isotope labelling of long RNA for structural and mechanistic studies. Nucleic Acids Res. 40, e7 (2012)

    Article  CAS  Google Scholar 

  15. Liu, Y., Holmstrom, E., Zhang, J., Yu, P., Wang, J., Dyba, M.A., Chen, D., Ying, J., Lockett, S., Nesbitt, D.J., Ferré-D’Amaré, A.R., Sousa, R., Stagno, J.R., Wang, Y.X.: Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature 522, 368–372 (2015)

    Article  CAS  Google Scholar 

  16. Longhini, A.P., LeBlanc, R.M., Becette, O., Salguero, C., Wunderlich, C.H., Johnson, B.A., D’Souza, V.M., Kreutz, C., Dayie, T.K.: Chemo-enzymatic synthesis of site-specific isotopically labelled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations. Nucleic Acids Res. 44, e52 (2016)

    Article  Google Scholar 

  17. Lukavsky, P.J., Puglisi, J.D.: Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides. RNA 10, 889–893 (2004)

    Article  CAS  Google Scholar 

  18. McKenna, S.A., Kim, I., Puglisi, E.V., Lindhout, D.A., Aitken, C.E., Marshall, R.A., Puglisi, J.D.: Purification and characterization of transcribed RNAs using gel filtration chromatography. Nat. Protoc. 2, 3270–3277 (2007)

    Article  CAS  Google Scholar 

  19. Plateau, P., Gueron, M.: Exchangeable proton NMR without base-line distorsion, using new strong-pulse sequences. J. Am. Chem. Soc. 104, 7310–7311 (1982)

    Article  CAS  Google Scholar 

  20. Piotto, M., Saudek, V., Sklenár, V.: Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR 2, 661–665 (1992)

    Article  CAS  Google Scholar 

  21. Dingley, A.J., Grzesiek, S.: Direct observation of hydrogen bonds in nucleic acid base pairs by internucleotide 2 J NN couplings. J. Am. Chem. Soc. 120, 8293–8297 (1998)

    Article  CAS  Google Scholar 

  22. 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)

    Article  CAS  Google Scholar 

  23. Hansen, M.R., Mueller, L., Pardi, A.: Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat. Struct. Biol. 5, 1065–1074 (1998)

    Article  CAS  Google Scholar 

  24. 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)

    Article  CAS  Google Scholar 

  25. Ottiger, M., Delaglio, F., Bax, A.: Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J. Magn. Reson. 131, 373–378 (1998)

    Article  CAS  Google Scholar 

  26. Pervushin, K., Riek, R., Wider, G., Wüthrich, K.: Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc. Natl. Acad. Sci. USA 94, 12366–123671 (1997)

    Article  CAS  Google Scholar 

  27. Bothe, J.R., Nikolova, E.N., Eichhorn, C.D., Chugh, J., Hansen, A.L., Al-Hashimi, H.M.: Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy. Nat. Methods 8, 919–931 (2011)

    Article  CAS  Google Scholar 

  28. Salmon, L., Yang, S., Al-Hashimi, H.M.: Advances in the determination of nucleic acid conformational ensembles. Annu. Rev. Phys. Chem. 65, 293–316 (2014)

    Article  CAS  Google Scholar 

  29. Nomura, Y., Tanaka, Y., Fukunaga, J., Fujiwara, K., Chiba, M., Iibuchi, I., Tanaka, T., Nakamura, Y., Kawai, G., Kozu, T., Sakamoto, T.: Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain. J. Biochem. 154, 513–519 (2013)

    Article  CAS  Google Scholar 

  30. Bermejo, G.A., Clore, M., Schwieters, C.D.: Improving NMR Structures of RNA. Structure 24, 806–815 (2016)

    Article  CAS  Google Scholar 

  31. Oguro, A., Yanagida, A., Fujieda, Y., Amano, R., Otsu, M., Sakamoto, T., Kawai, G., Matsufuji, S.: Two stems with different characteristics and an internal loop in an RNA aptamer contribute to spermine-binding. J. Biochem. 161, 197–206 (2016)

    Google Scholar 

  32. Okui, S., Kawai, g: In NMR tube transcription for rapid screening of RNA conformation. Nucleosides Nucleotides Nucleic Acids 34, 103–113 (2015)

    Article  CAS  Google Scholar 

  33. Helmling, C., Keyhani, S., Sochor, F., Fürtig, B., Hengesbach, M., Schwalbe, H.: Rapid NMR screening of RNA secondary structure and binding. J. Biomol. NMR 63, 67–76 (2015)

    Article  CAS  Google Scholar 

  34. Amano, R., Aoki, K., Miyakawa, S., Nakamura, Y., Kozu, T., Kawai, G., Sakamoto, T.: NMR monitoring of the SELEX process to confirm enrichment of structured RNA. Sci. Rep. 7, 283 (2017)

    Article  Google Scholar 

  35. Aeschbacher, T., Schmidt, E., Blatter, M., Maris, C., Duss, O., Allain, F.H.-T., Güntert, P., Schubert, M.: Automated and assisted RNA resonance assignment using NMR chemical shift statistics. Nucleic Acids Res. 41, e172 (2013)

    Article  CAS  Google Scholar 

  36. Bahrami, A., Clos II, L.J., Markley, J.L., Butcher, S.E., Eghbalnia, H.R.: RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts. J. Biomol. NMR 52, 289–302 (2012)

    Article  CAS  Google Scholar 

  37. Nakamura, S.: A novel virtual spectrometry: visualized regulatory motifs on ADM, rPolΒ and CD83 mRNAs in human-friendly manners. J. Biochem. 146, 251–261 (2009)

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Life and Environmental Sciences, Chiba Institute of Technology, Narashino, 275-0016, Chiba, Japan

    Taiichi Sakamoto, Maina Otsu & Gota Kawai

Authors
  1. Taiichi Sakamoto
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  2. Maina Otsu
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  3. Gota Kawai
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Corresponding author

Correspondence to Gota Kawai .

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Editors and Affiliations

  1. Kobe, Japan

    The Nuclear Magnetic Resonance Society of Japan

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Sakamoto, T., Otsu, M., Kawai, G. (2018). NMR Studies on RNA. In: The Nuclear Magnetic Resonance Society of Japan (eds) Experimental Approaches of NMR Spectroscopy. Springer, Singapore. https://doi.org/10.1007/978-981-10-5966-7_16

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