Skip to main content
SpringerLink
Log in

Analyses of RNA Structure and Dynamics

  • Living reference work entry
  • First Online:
Modern Magnetic Resonance

  • 177 Accesses

Abstract

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.

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

Access this chapter

Log in via an institution

Institutional subscriptions

References

  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. 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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  7. Bondensgaard K, Mollova ET, Pardi A. The global conformation of the hammerhead ribozyme determined using residual dipolar couplings. Biochemist. 2002;41:11532–42.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  10. Varani G, Chen Y, Leeper TC. NMR studies of protein-nucleic acid interactions. Methods Mol Biol. 2004;278:289–312.

    Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  13. Fitzkee NC, Bax A. Facile measurement of 1H-15N residual dipolar couplings in larger perdeuterated proteins. J Biomol NMR. 2010;48:65–70.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  25. Ishima R. CPMG Relaxation Dispersion. In: Livesay DR, editor. Protein dynamics methods and protocols. Humana Press; 2014. p. 29–49.

    Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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. Zhao B, Hansen AL, Zhang Q. Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R 1ρ NMR spectroscopy. J Am Chem Soc. 2014;136:20–3.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  33. Al-Hashimi HM, Walter NG. RNA dynamics: it is about time. Curr Opin Struct Biol. 2008;18:321–9.

    Article  Google Scholar 

  34. Dethoff EA, Chugh J, Mustoe AM, Al-Hashimi HM. Functional complexity and regulation through RNA dynamics. Nature. 2012;482:322–30.

    Article  Google Scholar 

  35. Al-Hashimi HM. NMR studies of nucleic acid dynamics. J Magn Reson. 2013;237:191–204.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  37. Lee J, Dethoff EA, Al-Hashimi HM. Invisible RNA state dynamically couples distant motifs. Proc Natl Acad Sci. 2014;111:9485–90.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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. 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.

    Article  Google Scholar 

  42. Cash DD, Feigon J. Structure and folding of the Tetrahymena telomerase RNA pseudoknot. Nucleic Acids Res. 2016;45:482–95.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1, Tsudanuma, Narashino-shi, Chiba, 275-0016, Japan

    Gota Kawai

Authors
  1. Gota Kawai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gota Kawai .

Editor information

Editors and Affiliations

  1. Royal Society of Chemistry, London, United Kingdom

    Graham A. Webb

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this entry

Cite this entry

Kawai, G. (2017). Analyses of RNA Structure and Dynamics. In: Webb, G. (eds) Modern Magnetic Resonance. Springer, Cham. https://doi.org/10.1007/978-3-319-28275-6_61-1

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-28275-6_61-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-28275-6

  • Online ISBN: 978-3-319-28275-6

  • eBook Packages: Springer Reference Chemistry and Mat. ScienceReference Module Physical and Materials ScienceReference Module Chemistry, Materials and Physics

Publish with us

Policies and ethics

Search

Navigation