Analyses of RNA Structure and Dynamics

  • Gota KawaiEmail author
Reference work entry


In this chapter, some examples of recent applications of NMR on RNA structure and dynamics were shown, including the residual dipolar coupling (RDC), the paramagnetic relaxation enhancement (PRE), and the relaxation dispersion (RD). Targets of NMR study on RNA became larger. Some examples for the NMR analysis of the long RNA were also shown.


RNA Residual dipolar coupling Relaxation dispersion Paramagnetic relaxation enhancement 


  1. 1.
    Kawai G. Conformational analysis of DNA and RNA. In: Webb GA, editor. Modern magnetic resonance. Dordrecht: Springer; 2006. p. 667–72.Google Scholar
  2. 2.
    Keane SC, Van V, Frank HM, Sciandra CA, McCowin S, Santos J, Heng X, Summers MF. NMR detection of intermolecular interaction sites in the dimeric 5′-leader of the HIV-1 genome. Proc Natl Acad Sci. 2016;113:13033–8.CrossRefGoogle Scholar
  3. 3.
    Tjandra N, Bax A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science. 1997;278:1111–4.CrossRefGoogle Scholar
  4. 4.
    Hansen MR, Mueller L, Pardi A. Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat Struct Biol. 1998;5:1065–74.CrossRefGoogle Scholar
  5. 5.
    Hansen MR, Hansen P, Pardi A. Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions. Methods Enzymol. 2000;317:220–40.CrossRefGoogle Scholar
  6. 6.
    Lukavsky PJ, Kim I, Otto GA, Puglisi JD. Structure of HCV IRES domain II determined by NMR. Nat Struct Biol. 2003;10:1033–8.CrossRefGoogle Scholar
  7. 7.
    Bondensgaard K, Mollova ET, Pardi A. The global conformation of the hammerhead ribozyme determined using residual dipolar couplings. Biochemist. 2002;41:11532–42.CrossRefGoogle Scholar
  8. 8.
    Tjandra N, Omichinski JG, Gronenborn AM, Close GM, Bax A. Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat Struct Biol. 1997;4:732–8.CrossRefGoogle Scholar
  9. 9.
    Bayer P, Varani L, Varani G. Refinement of the structure of protein-RNA complexes by residual dipolar coupling analysis. J Biomol NMR. 1999;14:149–55.CrossRefGoogle Scholar
  10. 10.
    Varani G, Chen Y, Leeper TC. NMR studies of protein-nucleic acid interactions. Methods Mol Biol. 2004;278:289–312.Google Scholar
  11. 11.
    Ottiger M, Bax A. Characterization of magnetically oriented phospholipid micelles for measurement of dipolar couplings in macromolecules. J Biomol NMR. 1998;12:361–72.CrossRefGoogle Scholar
  12. 12.
    Ying J, Grishaev A, Latham MP, Pardi A, Bax A. Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field. J Biomol NMR. 2007;39:91–6.CrossRefGoogle Scholar
  13. 13.
    Fitzkee NC, Bax A. Facile measurement of 1H-15N residual dipolar couplings in larger perdeuterated proteins. J Biomol NMR. 2010;48:65–70.CrossRefGoogle Scholar
  14. 14.
    Ying J, Wang J, Grishaev A, Yu P, Wang Y-X, Bax A. Measurement of 1H-15N and 1H-13C residual dipolar couplings in nucleic acids from TROSY intensities. J Biomol NMR. 2011;51:89.CrossRefGoogle Scholar
  15. 15.
    Latham MP, Hanson P, Brown DJ, Pardi A. Comparison of alignment tensors generated for native tRNAVal using magnetic fields and liquid crystalline media. J Biomol NMR. 2008;40:83.CrossRefGoogle Scholar
  16. 16.
    Salmon L, Bascom G, Andricioaei I, Al-Hashimi HM. A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: The basis for interhelical motions revealed. J Am Chem Soc. 2013;135:5457–66.CrossRefGoogle Scholar
  17. 17.
    Salmon L, Giambaşu GM, Nikolova EN, Petzold K, Bhattacharya A, Case DA, Al-Hashimi HM. Modulating RNA alignment using directional dynamic kinks: application in determining an atomic-resolution ensemble for a hairpin using NMR residual dipolar couplings. J Am Chem Soc. 2015;137:12954–65.CrossRefGoogle Scholar
  18. 18.
    Grishaev A, Ying J, Canny MD, Pardi A, Bax A. Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data. J Biomol NMR. 2008;42:99.CrossRefGoogle Scholar
  19. 19.
    Clore GM, Kuszewski J. Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation. J Am Chem Soc. 2003;125:1518.CrossRefGoogle Scholar
  20. 20.
    Wunderlich CH, Huber RG, Spitzer R, Liedl KR, Kloiber K, Kreutz C. A novel paramagnetic relaxation enhancement tag for nucleic acids: a tool to study structure and dynamics of RNA. ACS Chem Biol. 2013;8:2697–706.CrossRefGoogle Scholar
  21. 21.
    Helmling C, Bessi I, Wacker A, Schnorr KA, Jonker HRA, Richter C, Wagner D, Kreibich M, Schwalbe H. Noncovalent spin labeling of riboswitch RNAs to obtain long-range structural NMR restraints. ACS Chem Biol. 2014;9:1330–9.CrossRefGoogle Scholar
  22. 22.
    Bonneau E, Legault P. NMR localization of divalent cations at the active site of the Neurospora VS ribozyme provides insights into RNA-metal-ion interactions. Biochemistry. 2014;53:579–90.CrossRefGoogle Scholar
  23. 23.
    Bonneau E, Legault P. Nuclear magnetic resonance structure of the III-IV-V three-way junction from the Varkud satellite ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement. Biochemistry. 2014;53:6264–75.CrossRefGoogle Scholar
  24. 24.
    Büttner L, Seikowski J, Wawrzyniak K, Ochmann A, Höbartner C. Synthesis of spin-labeled riboswitch RNAs using convertible nucleosides and DNA-catalyzed RNA ligation. Bioorg Med Chem. 2013;21:6171–80.CrossRefGoogle Scholar
  25. 25.
    Ishima R. CPMG Relaxation Dispersion. In: Livesay DR, editor. Protein dynamics methods and protocols. Humana Press; 2014. p. 29–49.Google Scholar
  26. 26.
    Johnson Jr JE, Hoogstraten CG. Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling. J Am Chem Soc. 2008;130:16757–69.CrossRefGoogle Scholar
  27. 27.
    Kloiber K, Spitzer R, Tollinger M, Konrat R, Kreutz C. Probing RNA dynamics via longitudinal exchange and CPMG relaxation dispersion NMR spectroscopy using a sensitive 13C-methyl label. Nucleic Acids Res. 2011;39:4340–51.CrossRefGoogle Scholar
  28. 28.
    Moschen T, Wunderlich CH, Spitzer R, Levic J, Micura R, Tollinger M, Kreutz C. Ligand-detected relaxation dispersion NMR spectroscopy: dynamics of preQ1-RNA binding. Angew Chem Int Ed. 2015;54:560–3.Google Scholar
  29. 29.
    Zhao B, Hansen AL, Zhang Q. Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R NMR spectroscopy. J Am Chem Soc. 2014;136:20–3.CrossRefGoogle Scholar
  30. 30.
    Xue Y, Kellogg D, Kimsey IJ, Sathyamoorthy B, Stein ZW, McBrairty M, Al-Hashimi HM. Characterizing RNA excited states using NMR relaxation dispersion. Methods Enzymol. 2015;558:39–73.CrossRefGoogle Scholar
  31. 31.
    Juen MA, Wunderlich CH, Nußbaumer F, Tollinger M, Kontaxis G, Konrat R, Hansen DF, Kreutz C. Excited states of nucleic acids probed by proton relaxation dispersion NMR spectroscopy. Angew Chem Int Ed. 2016;55:12008–12.CrossRefGoogle Scholar
  32. 32.
    Longhini AP, LeBlanc RM, Becette O, Salguero C, Wunderlich CH, Johnson BA, D′Souza VM, Kreutz C, Dayie TK. Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations. Nucleic Acids Res. 2016;44:e52.CrossRefGoogle Scholar
  33. 33.
    Al-Hashimi HM, Walter NG. RNA dynamics: it is about time. Curr Opin Struct Biol. 2008;18:321–9.CrossRefGoogle Scholar
  34. 34.
    Dethoff EA, Chugh J, Mustoe AM, Al-Hashimi HM. Functional complexity and regulation through RNA dynamics. Nature. 2012;482:322–30.CrossRefGoogle Scholar
  35. 35.
    Al-Hashimi HM. NMR studies of nucleic acid dynamics. J Magn Reson. 2013;237:191–204.CrossRefGoogle Scholar
  36. 36.
    Kimsey IJ, Petzold K, Sathyamoorthy B, Stein ZW, Al-Hashimi HM. Visualizing transient Watson–Crick-like mispairs in DNA and RNA duplexes. Nature. 2015;519:315–20.CrossRefGoogle Scholar
  37. 37.
    Lee J, Dethoff EA, Al-Hashimi HM. Invisible RNA state dynamically couples distant motifs. Proc Natl Acad Sci. 2014;111:9485–90.CrossRefGoogle Scholar
  38. 38.
    Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM. Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nat Commun. 2016;7:11768.CrossRefGoogle Scholar
  39. 39.
    Andrałojć W, Ravera E, Salmon L, Parigi G, Al-Hashimi HM, Luchinat C. Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations. Phys Chem Chem Phys. 2016;18:5743–52.CrossRefGoogle Scholar
  40. 40.
    Bourbigot S, Dock-Bregeon A-C, Eberling P, Coutant J, Kieffer B, Lebars I. Solution structure of the 5′-terminal hairpin of the 7SK small nuclear. RNA. 2016;22:1844–58.Google Scholar
  41. 41.
    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. 2005;138:583–92.CrossRefGoogle Scholar
  42. 42.
    Cash DD, Feigon J. Structure and folding of the Tetrahymena telomerase RNA pseudoknot. Nucleic Acids Res. 2016;45:482–95.CrossRefGoogle Scholar
  43. 43.
    Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera: a visualization system for exploratory research and analysis. J Comput Chem. 2004;25:1605–12.CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Faculty of Advanced EngineeringChiba Institute of TechnologyNarashino-shiJapan

Personalised recommendations