Structural Analysis of RNA by Small-Angle X-ray Scattering

  • Anne Théobald-Dietrich
  • Raphaël de Wijn
  • Kévin Rollet
  • Alexandra Bluhm
  • Joëlle Rudinger-Thirion
  • Caroline Paulus
  • Bernard Lorber
  • Aurélien Thureau
  • Magali Frugier
  • Claude SauterEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2113)


Over the past two decades small-angle X-ray scattering (SAXS) has become a popular method to characterize solutions of biomolecules including ribonucleic acid (RNA). In an integrative structural approach, SAXS is complementary to crystallography, NMR, and electron microscopy and provides information about RNA architecture and dynamics. This chapter highlights the practical advantages of combining size-exclusion chromatography and SAXS at synchrotron facilities. It is illustrated by practical case studies of samples ranging from single hairpins and tRNA to a large IRES. The emphasis is also put on sample preparation which is a critical step of SAXS analysis and on optimized protocols for in vitro RNA synthesis ensuring the production of mg amount of pure and homogeneous molecules.

Key words

SEC-SAXS RNA tRNA IRES Structure Integrative structural biology 



The authors thank the team of the SWING beamline (SOLEIL synchrotron, Saint-Aubin, France), in particular Pierre Roblin and Javier Pérez, for beam time provision and assistance during data collection and processing, as well as José Teixeira (LLB, CEA Saclay, France) for his critical reading of the manuscript and fruitful discussion. The work described in this chapter was supported by the French Centre National de la Recherche Scientifique, the University of Strasbourg, the LabEx consortium “NetRNA” (ANR-10-LABX-0036_NETRNA).


  1. 1.
    Putnam CD, Hammel M, Hura GL et al (2007) X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 40:191Google Scholar
  2. 2.
    Guinier A (1939) La diffraction des rayons X aux très petits angles: application à l’étude de phénomènes ultramicroscopiques. Ann Phys 11:161–237Google Scholar
  3. 3.
    Glatter O, Kratky O (1982) Small angle X-ray scattering. Academic Press Inc Ltd., LondonGoogle Scholar
  4. 4.
    Witz J (2003) 1964: The first model for the shape of a transfer RNA molecule. An account of an unpublished small-angle X-ray scattering study. Biochimie 85:1265–1268PubMedGoogle Scholar
  5. 5.
    Lake JA, Beeman WW (1967) Yeast transfer RNA: a small-angle X-ray study. Science 156:1371–1373PubMedGoogle Scholar
  6. 6.
    Ninio J, Luzzati V, Yaniv M (1972) Comparative small-angle X-ray scattering studies on unacylated, acylated and cross-linked Escherichia coli transfer RNAIVal. J Mol Biol 71:217–229PubMedGoogle Scholar
  7. 7.
    Svergun DI, Nierhaus KH (2000) A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome. J Biol Chem 275:14432–14439Google Scholar
  8. 8.
    Chen Y, Pollack L (2016) SAXS studies of RNA: structures, dynamics, and interactions with partners. Wiley Interdiscip Rev RNA 7:512–526PubMedPubMedCentralGoogle Scholar
  9. 9.
    Fang X-W, Yang X-J, Littrell K et al (2001) The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits. RNA 7:233–241PubMedPubMedCentralGoogle Scholar
  10. 10.
    Russell R, Millett IS, Tate MW et al (2002) Rapid compaction during RNA folding. Proc Natl Acad Sci 99:4266–4271PubMedGoogle Scholar
  11. 11.
    Lipfert J, Ouellet J, Norman DG et al (2008) The complete vs ribozyme in solution studied by small-angle X-ray scattering. Structure 16:1357–1367PubMedPubMedCentralGoogle Scholar
  12. 12.
    Hammond JA, Rambo RP, Filbin ME et al (2009) Comparison and functional implications of the 3D architectures of viral tRNA-like structures. RNA 15:294–307PubMedPubMedCentralGoogle Scholar
  13. 13.
    Schmitt E, Panvert M, Lazennec-Schurdevin C et al (2012) Structure of the ternary initiation complex aIF2–GDPNP–methionylated initiator tRNA. Nat Struct Mol Biol 19:450–454PubMedGoogle Scholar
  14. 14.
    Jones CP, Cantara WA, Olson ED et al (2014) Small-angle X-ray scattering-derived structure of the HIV-1 5′ UTR reveals 3D tRNA mimicry. Proc Natl Acad Sci 111:3395–3400PubMedGoogle Scholar
  15. 15.
    Colussi TM, Costantino DA, Hammond JA et al (2014) The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA. Nature 511:366–369PubMedPubMedCentralGoogle Scholar
  16. 16.
    Tuukkanen AT, Spilotros A, Svergun DI (2017) Progress in small-angle scattering from biological solutions at high-brilliance synchrotrons. IUCrJ 4:518–528PubMedPubMedCentralGoogle Scholar
  17. 17.
    Mathew E, Mirza A, Menhart N (2004) Liquid-chromatography-coupled SAXS for accurate sizing of aggregating proteins. J Synchrotron Radiat 11:314–318PubMedGoogle Scholar
  18. 18.
    Watanabe Y, Inoko Y (2009) Size-exclusion chromatography combined with small-angle X-ray scattering optics. J Chromatogr A 1216:7461–7465PubMedGoogle Scholar
  19. 19.
    David G, Pérez J (2009) Combined sampler robot and high-performance liquid chromatography: a fully automated system for biological small-angle X-ray scattering experiments at the Synchrotron SOLEIL SWING beamline. J Appl Crystallogr 42:892–900Google Scholar
  20. 20.
    Rambo RP, Tainer JA (2010) Improving small-angle X-ray scattering data for structural analyses of the RNA world. RNA 16:638–646PubMedPubMedCentralGoogle Scholar
  21. 21.
    Jühling T, Duchardt-Ferner E, Bonin S et al (2018) Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax. Nucleic Acids Res 46:9170–9180PubMedPubMedCentralGoogle Scholar
  22. 22.
    Baronti L, Karlsson H, Marušič M et al (2018) A guide to large-scale RNA sample preparation. Anal Bioanal Chem 410:3239–3252PubMedPubMedCentralGoogle Scholar
  23. 23.
    Beckert B, Masquida B (2011) Synthesis of RNA by in vitro transcription. In: Nielsen H (ed) RNA. Humana Press, Totowa, pp 29–41Google Scholar
  24. 24.
    Franke D, Petoukhov MV, Konarev PV et al (2017) ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions. J Appl Crystallogr 50:1212–1225PubMedPubMedCentralGoogle Scholar
  25. 25.
    Lipfert J, Doniach S (2007) Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu Rev Biophys Biomol Struct 36:307–327PubMedGoogle Scholar
  26. 26.
    Jacques DA, Trewhella J (2010) Small-angle scattering for structural biology—expanding the frontier while avoiding the pitfalls. Protein Sci 19:642–657PubMedPubMedCentralGoogle Scholar
  27. 27.
    Mertens HDT, Svergun DI (2010) Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J Struct Biol 172:128–141PubMedGoogle Scholar
  28. 28.
    Cantara WA, Olson ED, Musier-Forsyth K (2017) Analysis of RNA structure using small-angle X-ray scattering. Methods 113:46–55PubMedGoogle Scholar
  29. 29.
    Pollack L (2011) Time resolved SAXS and RNA folding. Biopolymers 95:543–549PubMedGoogle Scholar
  30. 30.
    Förster S, Apostol L, Bras W (2010) Scatter: software for the analysis of nano- and mesoscale small-angle scattering. J Appl Crystallogr 43:639–646Google Scholar
  31. 31.
    Hopkins JB, Gillilan RE, Skou S (2017) BioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis. J Appl Crystallogr 50:1545–1553PubMedPubMedCentralGoogle Scholar
  32. 32.
    Fischer H, Neto MDO, Napolitano HB et al (2010) Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale. J Appl Crystallogr 43:101–109Google Scholar
  33. 33.
    Rambo RP, Tainer JA (2013) Accurate assessment of mass, models and resolution by small-angle scattering. Nature 496:477–481PubMedPubMedCentralGoogle Scholar
  34. 34.
    Franke D, Svergun DI (2009) DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J Appl Crystallogr 42:342–346PubMedPubMedCentralGoogle Scholar
  35. 35.
    Svergun DI, Petoukhov MV, Koch MH (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80:2946–2953PubMedPubMedCentralGoogle Scholar
  36. 36.
    Svergun D, Barberato C, Koch MHJ (1995) CRYSOL—a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28:768–773Google Scholar
  37. 37.
    Panjkovich A, Svergun DI (2016) SASpy: a PyMOL plugin for manipulation and refinement of hybrid models against small angle X-ray scattering data. Bioinformatics 32(13):2062–2064PubMedPubMedCentralGoogle Scholar
  38. 38.
    Trewhella J, Duff AP, Durand D et al (2017) 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr Sect Struct Biol 73:710–728Google Scholar
  39. 39.
    Francklyn C, Schimmel P (1989) Aminoacylation of RNA minihelices with alanine. Nature 337:478PubMedGoogle Scholar
  40. 40.
    Oakley JL, Strothkamp RE, Sarris AH et al (1979) T7 RNA polymerase: promoter structure and polymerase binding. Biochemistry 18:528–537PubMedGoogle Scholar
  41. 41.
    Rong M, He B, McAllister WT et al (1998) Promoter specificity determinants of T7 RNA polymerase. Proc Natl Acad Sci 95:515–519PubMedGoogle Scholar
  42. 42.
    Fechter P, Rudinger J, Giegé R, ThÕobald-Dietrich A (1998) Ribozyme processed tRNA transcripts with unfriendly internal promoter for T7 RNA polymerase: production and activity. FEBS Lett 436:99–103PubMedGoogle Scholar
  43. 43.
    Price SR, Ito N, Oubridge C et al (1995) Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallographic studies. J Mol Biol 249:398–408PubMedGoogle Scholar
  44. 44.
    Koubek J, Lin KF, Chen YR et al (2013) Strong anion-exchange fast performance liquid chromatography as a versatile tool for preparation and purification of RNA produced by in vitro transcription. RNA 19:1449–1459PubMedPubMedCentralGoogle Scholar
  45. 45.
    Lorber B, Fischer F, Bailly M et al (2012) Protein analysis by dynamic light scattering: methods and techniques for students. Biochem Mol Biol Educ 40:372–382PubMedGoogle Scholar
  46. 46.
    Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr 25:495–503Google Scholar
  47. 47.
    Rambo RP, Tainer JA (2011) Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers 95:559–571PubMedPubMedCentralGoogle Scholar
  48. 48.
    Reyes FE, Schwartz CR, Tainer JA et al (2014) Methods for using new conceptual tools and parameters to assess RNA structure by small-angle X-ray scattering. Methods Enzymol 549:235–263PubMedGoogle Scholar
  49. 49.
    Durand D, Vivès C, Cannella D et al (2010) NADPH oxidase activator p67phox behaves in solution as a multidomain protein with semi-flexible linkers. J Struct Biol 169:45–53PubMedGoogle Scholar
  50. 50.
    Suhre K, Sanejouand Y-H (2004) ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 32:W610–W614PubMedPubMedCentralGoogle Scholar
  51. 51.
    Jossinet F, Ludwig TE, Westhof E (2010) Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics 26:2057–2059PubMedPubMedCentralGoogle Scholar
  52. 52.
    Biesiada M, Pachulska-Wieczorek K, Adamiak RW et al (2016) RNAComposer and RNA 3D structure prediction for nanotechnology. Methods 103:120–127PubMedGoogle Scholar
  53. 53.
    Yang S, Parisien M, Major F et al (2010) RNA structure determination using SAXS data. J Phys Chem B 114:10039–10048PubMedPubMedCentralGoogle Scholar
  54. 54.
    Gajda MJ, Martinez Zapien D, Uchikawa E et al (2013) Modeling the structure of RNA molecules with small-angle X-ray scattering data. PLoS One 8:e78007PubMedPubMedCentralGoogle Scholar
  55. 55.
    Bhandari YR, Fan L, Fang X et al (2017) Topological structure determination of RNA using small-angle X-ray scattering. J Mol Biol 429:3635–3649PubMedPubMedCentralGoogle Scholar
  56. 56.
    Shi H, Moore PB (2000) The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited. RNA 6:1091–1105PubMedPubMedCentralGoogle Scholar
  57. 57.
    Pinker F, Schelcher C, Fernandez-Millan P et al (2017) Biophysical analysis of Arabidopsis protein-only RNase P alone and in complex with tRNA provides a refined model of tRNA binding. J Biol Chem 292:13904–13913PubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Anne Théobald-Dietrich
    • 1
  • Raphaël de Wijn
    • 2
  • Kévin Rollet
    • 2
  • Alexandra Bluhm
    • 1
  • Joëlle Rudinger-Thirion
    • 2
  • Caroline Paulus
    • 2
  • Bernard Lorber
    • 2
  • Aurélien Thureau
    • 3
  • Magali Frugier
    • 2
  • Claude Sauter
    • 2
    Email author
  1. 1.Architecture et Réactivité de l’ARN, UPR 9002, IBMCCNRS, Université de StrasbourgStrasbourgFrance
  2. 2.Architecture et Réactivité de l’ARN - CNRS UPR 9002Institut de Biologie Moléculaire et Cellulaire, Université de StrasbourgStrasbourgFrance
  3. 3.Synchrotron SOLEILSaint-AubinFrance

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