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Structural Studies of a Double-Stranded RNA from Trypanosome RNA Editing by Small-Angle X-Ray Scattering

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Book cover RNA-RNA Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1240))

Abstract

We used small-angle X-ray scattering (SAXS) to evaluate the solution structure of a double-stranded RNA with 32 base pairs. We wanted to compare the solution structure to the crystal structure to assess the impact of the crystal lattice on the overall conformation of the RNA. The RNA was designed to self-anneal and form a head-to-head fusion of two identical mRNA/oligo(U) tail domains (the U-helix) from a trypanosome RNA editing substrate formed by the annealing of a guide RNA to a pre-edited mRNA. This substrate is from the U insertion/deletion RNA editing system of trypanosomes. Each strand in the fusion RNA had 16 purines from the pre-mRNA followed by 16 uracils (Us) from the U-tail at the 3′ end of the guide RNA. The strands were designed to form a double helix with blunt ends, but each strand had the potential to form hairpins and single-stranded RNA helices. Hairpins could form by the 3′ oligouridylate tract folding back to hybridize with the 5′ oligopurine tract and forming an intervening loop. Single-stranded helices could form by the stacking of bases in the polypurine tract. Some of the 16 Us 3′ to the polypurine tract may have been unstacked and in random coils. Our SAXS studies showed that the RNA formed a mix of single-stranded structures in the absence of MgCl2. In the presence of MgCl2 at concentrations similar to those in the crystal, the solution structure was consistent with the double-stranded, blunt-ended structure, in agreement with the crystal structure. Here we describe the preparation of RNA samples, data collection with an in-house SAXS instrument designed for biological samples, and the processing and modeling of the scattering data.

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References

  1. Timasheff SN, Witz J, Luzzati V (1961) The structure of high molecular weight ribonucleic acid in solution. A small-angle x-ray scattering study. Biophys J 1:525–537

    CAS  PubMed Central  PubMed  Google Scholar 

  2. 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 An account of an unpublished small-angle X-ray scattering study.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 85:1265–1268

    CAS  PubMed  Google Scholar 

  3. Burke JE et al (2012) Structure of the yeast U2/U6 snRNA complex. RNA 18:673–683

    CAS  PubMed Central  PubMed  Google Scholar 

  4. Lipfert J et al (2007) Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J Mol Biol 365:1393–1406

    CAS  PubMed Central  PubMed  Google Scholar 

  5. Stoddard CD et al (2010) Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure 18:787–797

    CAS  PubMed Central  PubMed  Google Scholar 

  6. Kieft JS et al (1999) The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold. J Mol Biol 292:513–529

    CAS  PubMed  Google Scholar 

  7. Kazantsev AV et al (2011) Solution structure of RNase P RNA. RNA 17:1159–1171

    CAS  PubMed Central  PubMed  Google Scholar 

  8. Rambo RP, Tainer JA (2010) Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering. Curr Opin Struct Biol 20:128–137

    CAS  PubMed Central  PubMed  Google Scholar 

  9. Petoukhov MV et al (2012) New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr 45:342–350

    CAS  PubMed Central  PubMed  Google Scholar 

  10. Garst AD et al (2008) Crystal structure of the lysine riboswitch regulatory mRNA element. J Biol Chem 283:22347–22351

    CAS  PubMed Central  PubMed  Google Scholar 

  11. Grant TD et al (2011) Small angle X-ray scattering as a complementary tool for high-throughput structural studies. Biopolymers 95:517–530

    CAS  PubMed Central  PubMed  Google Scholar 

  12. Zuo X et al (2010) Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus. Proc Natl Acad Sci U S A 107:1385–1390

    CAS  PubMed Central  PubMed  Google Scholar 

  13. Grishaev A et al (2008) Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data. J Biomol NMR 42:99–109

    CAS  PubMed Central  PubMed  Google Scholar 

  14. Zou X et al (2008) Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data. J Am Chem Soc 130:3292–3293

    Google Scholar 

  15. Wang J et al (2009) A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements. J Mol Biol 393:717–734

    CAS  PubMed Central  PubMed  Google Scholar 

  16. Wang YX et al (2010) Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering. Methods 52:180–191

    CAS  PubMed  Google Scholar 

  17. Fang X et al (2000) Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. Biochemistry 39:11107–11113

    CAS  PubMed  Google Scholar 

  18. Russell R et al (2002) Rapid compaction during RNA folding. Proc Natl Acad Sci U S A 99:4266–4271

    CAS  PubMed Central  PubMed  Google Scholar 

  19. Russell R et al (2002) Exploring the folding landscape of a structured RNA. Proc Natl Acad Sci U S A 99:155–160

    CAS  PubMed Central  PubMed  Google Scholar 

  20. Das R et al (2003) The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. J Mol Biol 332:311–319

    CAS  PubMed  Google Scholar 

  21. Lipfert J et al (2010) Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. RNA 16:708–719

    CAS  PubMed Central  PubMed  Google Scholar 

  22. Das R et al (2003) Counterion distribution around DNA probed by solution X-ray scattering. Phys Rev Lett 90:188103

    CAS  PubMed  Google Scholar 

  23. Pollack L (2011) SAXS studies of ion-nucleic acid interactions. Annu Rev Biophys 40:225–242

    CAS  PubMed  Google Scholar 

  24. Kilburn D et al (2010) Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J Am Chem Soc 132:8690–8696

    CAS  PubMed Central  PubMed  Google Scholar 

  25. Blose JM et al (2011) Effects of a protecting osmolyte on the ion atmosphere surrounding DNA duplexes. Biochemistry 50:8540–8547

    CAS  PubMed Central  PubMed  Google Scholar 

  26. Li L et al (2011) Double-stranded RNA resists condensation. Phys Rev Lett 106:108101

    PubMed Central  PubMed  Google Scholar 

  27. Jensen LB et al (2010) Molecular characterization of the interactions between siRNA and PAMAM G7 dendrimers by SAXS, ITC, and molecular dynamics simulations. Biomacromolecules 11:3571–3577

    CAS  PubMed  Google Scholar 

  28. Doniach S, Lipfert J (2009) Use of small angle X-ray scattering (SAXS) to characterize conformational states of functional RNAs. Methods Enzymol 469:237–251

    CAS  PubMed  Google Scholar 

  29. Rambo RP, Tainer JA (2010) Improving small-angle X-ray scattering data for structural analyses of the RNA world. RNA 16:638–646

    CAS  PubMed Central  PubMed  Google Scholar 

  30. Pabit SA, Finkelstein KD, Pollack L (2009) Using anomalous small angle X-ray scattering to probe the ion atmosphere around nucleic acids. Methods Enzymol 469:391–410

    CAS  PubMed  Google Scholar 

  31. Pabit SA et al (2009) Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA. Nucleic Acids Res 37:3887–3896

    CAS  PubMed Central  PubMed  Google Scholar 

  32. Kirmizialtin S et al (2012) RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations. Biophys J 102:819–828

    CAS  PubMed Central  PubMed  Google Scholar 

  33. Jonikas MA et al (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA 15:189–199

    CAS  PubMed Central  PubMed  Google Scholar 

  34. Yang S et al (2010) RNA structure determination using SAXS data. J Phys Chem B 114:10039–10048

    CAS  PubMed Central  PubMed  Google Scholar 

  35. Bernado P et al (2007) Structural characterization of flexible proteins using small-angle X-ray scattering. J Am Chem Soc 129:5656–5664

    CAS  PubMed  Google Scholar 

  36. Bernado P, Svergun DI (2012) Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering. Mol Biosyst 8:151–167

    CAS  PubMed  Google Scholar 

  37. Pollack L (2011) Time resolved SAXS and RNA folding. Biopolymers 95:543–549

    CAS  PubMed  Google Scholar 

  38. Svergun DI, Koch MHJ, Timmins PA, May RP (2013) Small angle X-ray and neutron scattering from solutions of biological macromolecules. Oxford University Press, 358 p

    Google Scholar 

  39. Koch MH, Vachette P, Svergun DI (2003) Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q Rev Biophys 36:147–227

    CAS  PubMed  Google Scholar 

  40. Putnam CD 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 40:191–285

    CAS  PubMed  Google Scholar 

  41. Forstner M (2000) SAXS, SANS and X-ray crystallography as complementary methods in the study of biological form and function. J Appl Crystallogr 33:519–523

    CAS  Google Scholar 

  42. Svergun DI (2010) Small-angle X-ray and neutron scattering as a tool for structural systems biology. Biol Chem 391:737–743

    CAS  PubMed  Google Scholar 

  43. Vachette P, Koch MH, Svergun DI (2003) Looking behind the beamstop: X-ray solution scattering studies of structure and conformational changes of biological macromolecules. Methods Enzymol 374:584–615

    CAS  PubMed  Google Scholar 

  44. Svergun DI (2007) Small-angle scattering studies of macromolecular solutions. J Appl Crystallogr 40:s10–s17

    CAS  Google Scholar 

  45. Lipfert J, Doniach S (2007) Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu Rev Biophys Biomol Struct 36:307–327

    CAS  PubMed  Google Scholar 

  46. Stuhrmann HB (2008) Small-angle scattering and its interplay with crystallography, contrast variation in SAXS and SANS. Acta Crystallogr A 64:181–191

    CAS  PubMed  Google Scholar 

  47. Bonneté F et al (2004) Protein crystallization: contribution of small angle X-ray scattering (SAXS). J Phys IV (Proc) 118:3–13

    Google Scholar 

  48. Hura GL et al (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods 6:606–612

    CAS  PubMed Central  PubMed  Google Scholar 

  49. Jacques DA, Trewhella J (2010) Small-angle scattering for structural biology – expanding the frontier while avoiding the pitfalls. Protein Sci 19:642–657

    CAS  PubMed Central  PubMed  Google Scholar 

  50. Mertens HD, Svergun DI (2010) Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J Struct Biol 172:128–141

    CAS  PubMed  Google Scholar 

  51. Westenhoff S et al (2010) Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches. Acta Crystallogr A 66:207–219

    CAS  PubMed Central  PubMed  Google Scholar 

  52. Jacques DA et al (2012) Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution. Acta Crystallogr D Biol Crystallogr 68:620–626

    CAS  PubMed  Google Scholar 

  53. Jacques DA, Guss JM, Trewhella J (2012) Reliable structural interpretation of small-angle scattering data from bio-molecules in solution–the importance of quality control and a standard reporting framework. BMC Struct Biol 12:9

    PubMed Central  PubMed  Google Scholar 

  54. Markham NR, Zuker M (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res 33:W577–W581

    CAS  PubMed Central  PubMed  Google Scholar 

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

    CAS  PubMed Central  PubMed  Google Scholar 

  56. Broennimann C et al (2006) The PILATUS 1 M detector. J Synchrotron Radiat 13:120–130

    CAS  PubMed  Google Scholar 

  57. Toft KN et al (2008) High-throughput small angle X-ray scattering from proteins in solution using a microfluidic front-end. Anal Chem 80:3648–3654

    CAS  PubMed  Google Scholar 

  58. Seifert S et al (2000) Design and performance of a ASAXS instrument at the Advanced Photon Source. J Appl Crystallogr 33:782–784

    CAS  Google Scholar 

  59. Förster F et al (2008) Integration of small angle X-ray scattering data into structural modeling of proteins and their assemblies. J Mol Biol 382:1089–1106

    PubMed Central  PubMed  Google Scholar 

  60. Kellermann G et al (1997) The small-angle X-ray scattering beamline of the Brazilian Synchrotron Light Laboratory. J Appl Crystallogr 30:880–883

    CAS  Google Scholar 

  61. Dong SQ et al (2008) Investigation of the topological shape of bovine serum albumin in solution by small-angle x-ray scattering at Beijing synchrotron radiation facility. Chin Phys B 17:4574–4579

    CAS  Google Scholar 

  62. Englich U et al (2011) Microcrystallography, high-pressure cryocooling and BioSAXS at MacCHESS. J Synchrotron Radiat 18:70–73

    CAS  PubMed Central  PubMed  Google Scholar 

  63. Krywka C et al (2007) The small-angle and wide-angle X-ray scattering set-up at beamline BL9 of DELTA. J Synchrotron Radiat 14:244–251

    CAS  PubMed  Google Scholar 

  64. Zanini F, Lausi A, Savoia A (1999) The beamlines of ELETTRA and their application to structural biology. Genetica 106:171–180

    CAS  PubMed  Google Scholar 

  65. Round AR et al (2008) Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33. J Appl Crystallogr 41:913–917

    CAS  PubMed Central  PubMed  Google Scholar 

  66. Roessle MW et al (2007) Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg. J Appl Crystallogr 40:S190–S194

    CAS  Google Scholar 

  67. Abernathy DL et al (1998) Small-angle X-ray scattering using coherent undulator radiation at the ESRF. J Synchrotron Radiat 5:37–47

    CAS  PubMed  Google Scholar 

  68. Amenitsch H et al (1997) Performance and first results of the ELETTRA high-flux beamline for small-angle X-ray scattering. J Appl Crystallogr 30:872–876

    CAS  Google Scholar 

  69. Borsboom M et al (1998) The Dutch-Belgian beamline at the ESRF. J Synchrotron Radiat 5:518–520

    CAS  PubMed  Google Scholar 

  70. Narayanan T, Diat O, Bosecke P (2001) SAXS and USAXS on the high brilliance beamline at the ESRF. Nucl Instr Meth Phys Res A Accel Spectr Detectors Assoc Equip 467:1005–1009

    Google Scholar 

  71. Pernot P et al (2010) New beamline dedicated to solution scattering from biological macromolecules at the ESRF. J Phys Conf 247:012009

    Google Scholar 

  72. Knaapila M et al (2009) A new small-angle X-ray scattering set-up on the crystallography beamline I711 at MAX-lab. J Synchrotron Radiat 16:498–504

    CAS  PubMed  Google Scholar 

  73. Yang L (2005) The X21 SAXS instrument at NSLS for studying macromolecular systems. Macromol Res 13:538–541

    CAS  Google Scholar 

  74. Allaire M, Yang L (2011) Biomolecular solution X-ray scattering at the National Synchrotron Light Source. J Synchrotron Radiat 18:41–44

    CAS  PubMed Central  PubMed  Google Scholar 

  75. Igarashi N et al (2011) Upgrade of the small angle X-ray scattering beamlines at the Photon Factory. J Phys Conf 272:012026

    Google Scholar 

  76. 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 42:892–900

    CAS  Google Scholar 

  77. Yamamoto M et al (1998) Trichromatic concept at SPring-8 RIKEN beamline I. J Synchrotron Radiat 5:222–225

    CAS  PubMed  Google Scholar 

  78. Fujisawa T et al (2000) Small-angle X-ray scattering station at the SPring-8 RIKEN beamline. J Appl Crystallogr 33:797–800

    CAS  Google Scholar 

  79. Inoue K et al (2001) Present status of high flux beamline (BL40XU) at SPring-8. Nucl Instr Meth Phys Res A Accel Spectr Detectors Assoc Equip 467:674–677

    Google Scholar 

  80. Smolsky IL et al (2007) Biological small-angle x-ray scattering facility at the Stanford Synchrotron Radiation Laboratory. J Appl Crystallogr 40:S453–S458

    CAS  Google Scholar 

  81. Petoukhov MV, Svergun D (2006) ATSAS 2.1, a program package for small-angle scattering data analysis. J Appl Crystallogr 39:277–286

    Google Scholar 

  82. Poitevin F et al (2011) AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models. Nucleic Acids Res 39:W184–W189

    CAS  PubMed Central  PubMed  Google Scholar 

  83. Grishaev A et al (2010) Improved fitting of solution X-ray scattering data to macromolecular structures and structural ensembles by explicit water modeling. J Am Chem Soc 132:15484–15486

    CAS  PubMed Central  PubMed  Google Scholar 

  84. Pelikan M, Hura GL, Hammel M (2009) Structure and flexibility within proteins as identified through small angle X-ray scattering. Gen Physiol Biophys 28:174–189

    CAS  PubMed Central  PubMed  Google Scholar 

  85. Nielsen SS et al (2009) BioXTAS RAW, a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysis. J Appl Crystallogr 42:959–964

    CAS  Google Scholar 

  86. Schneidman-Duhovny D, Hammel M, Sali A (2010) FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res 38:W540–W544

    CAS  PubMed Central  PubMed  Google Scholar 

  87. Schneidman-Duhovny D, Hammel M, Sali A (2011) Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol 173:461–471

    CAS  PubMed Central  PubMed  Google Scholar 

  88. Ortega A, Amoros D, Garcia de la Torre J (2011) Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models. Biophys J 101:892–898

    CAS  PubMed Central  PubMed  Google Scholar 

  89. Liu H et al (2012) Computation of small-angle scattering profiles with three-dimensional Zernike polynomials. Acta Crystallogr A 68:278–285

    CAS  PubMed  Google Scholar 

  90. Kojima M et al (2008) SaxsMDView: a three-dimensional graphics program for displaying force vectors. J Synchrotron Radiat 15:535–537

    CAS  PubMed  Google Scholar 

  91. Fischer H 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 43:101–109

    CAS  Google Scholar 

  92. Gajda et al (2013) modeling the structure of RNA molecules with small-angle X-ray scattering data. PLoS ONE 48:e78007

    Google Scholar 

  93. Birmanns S, Rusu M, Wriggers W (2011) Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes. J Struct Biol 173:428–435

    CAS  PubMed Central  PubMed  Google Scholar 

  94. Wriggers W (2010) Using Situs for the integration of multi-resolution structures. Biophys Rev 2:21–27

    PubMed Central  PubMed  Google Scholar 

  95. Blanton TN, Barnes CL, Lelental M (2000) Preparation of silver behenate coatings to provide low- to mid-angle diffraction calibration. J Appl Crystallogr 33:172–173

    CAS  Google Scholar 

  96. Konarev P et al (2003) PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J Appl Crystallogr 36:1277–1282

    CAS  Google Scholar 

  97. Glatter O, Kratky O (eds) (1982) Small angle X-ray scattering. Academic Press, London

    Google Scholar 

  98. Svergun DI, Koch MHJ (2003) Small-angle scattering studies of biological macromolecules in solution. Rep Prog Phys 66:1735–1782

    CAS  Google Scholar 

  99. Mylonas E, Svergun DI (2007) Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering. J Appl Crystallogr 40:S245–S249

    CAS  Google Scholar 

  100. Petoukhov MV et al (2007) ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis. J Appl Crystallogr 40:s223–s228

    CAS  Google Scholar 

  101. Fischer S et al (2010) Simulating and evaluating small-angle X-ray scattering of micro-voids in polypropylene during mechanical deformation. J Appl Crystallogr 43:603–610

    CAS  Google Scholar 

  102. Kozin M, Svergun D (2001) Automated matching of high-and low-resolution structural models. J Appl Crystallogr 34:33–41

    CAS  Google Scholar 

  103. Volkova VV, Svergun D (2003) Uniqueness of ab initio shape determination in small-angle scattering. J Appl Crystallogr 36:860–864

    Google Scholar 

  104. Voss NR, Gerstein M (2005) Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly. J Mol Biol 346:477–492

    CAS  PubMed  Google Scholar 

  105. Durand D et al (2010) NADPH oxidase activator p67(phox) behaves in solution as a multidomain protein with semi-flexible linkers. J Struct Biol 169:45–53

    CAS  PubMed  Google Scholar 

  106. Rambo RP, Tainer JA (2011) Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers 95:559–571

    CAS  PubMed Central  PubMed  Google Scholar 

  107. Ciccariello S (1988) On the Porod law. J Appl Cryst 21:117–128

    Google Scholar 

  108. Porod G (1951) Die Rontgenkleinwinkelstreuung Von Dichtgepackten Kolloiden Systemen.1. Kolloid Zeitsch Zeitsch Polymer 124:83–114

    CAS  Google Scholar 

  109. Debeye P, Anderson R, Brumberger H (1957) Scattering by an inhomogeneous solid. II. The correlation function and its applicaiton. J Appl Phys 28:679–683

    Google Scholar 

  110. Doudna JA (1997) Preparation of homogeneous ribozyme RNA for crystallization. Methods Mol Biol 74:365–370

    CAS  PubMed  Google Scholar 

  111. Lipfert J, Herschlag D, Doniach S (2009) Riboswitch conformations revealed by small-angle X-ray scattering. Methods Mol Biol 540:141–159

    CAS  PubMed  Google Scholar 

  112. Rodrigues AR, Craievich AF, Goncalves Da Silva CE (1998) Commissioning and operation of the first brazilian synchrotron light source. J Synchrotron Radiat 5:1157–1161

    CAS  PubMed  Google Scholar 

  113. Fischetti R et al (2004) The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the advanced photon source. J Synchrotron Radiat 11:399–405

    CAS  PubMed  Google Scholar 

  114. Koch MHJ (2010) SAXS Instrumentation for Synchrotron Radiation then and now. J Phys Conf 247:012001

    Google Scholar 

  115. Brunner-Popela J, Glatter O (1997) Small-angle scattering of interacting particles. I. Basic principles of a global evaluation technique. J Appl Crystallogr 30:431–442

    CAS  Google Scholar 

  116. Ducruix A et al (1996) Protein interactions as seen by solution X-ray scattering prior to crystallogenesis. J Cryst Growth 168:28–39

    CAS  Google Scholar 

  117. Kirby NM et al (2013) A low-background-intensity focusing small-angle X-ray scattering undulator beamline. J Appl Cryst 46:1670–1680

    CAS  Google Scholar 

  118. Rambo RP, Tainer JA (2013) Accurate assessment of mass, models and resolution by small-angle scattering. Nature 496:477–481

    Google Scholar 

  119. Shannon CE, Weaver W (1949) The Mathematical Theory of Communication. Urbana, IL: University of Illinois Press

    Google Scholar 

  120. Brookes E, Perez J, Cardinali B, Profumo A, Vachette P, Rocco M (2013) Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler (US-SOMO) enhanced SAS module. J App Cryst 46:1823–1833

    Google Scholar 

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Acknowledgements

This research was supported by grants to BHMM from the Presbyterian Health Foundation (PHF #1545-Mooers), Oklahoma Center for the Advancement of Science and Technology (HR08-138), and the NIH-NIAID (R01-AI088011). This work was also supported in part by an Institutional Development Award (IDeA) from the NIH-GMS under grant P20-GM103640.

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  1. Rigaku Americas Inc., 9009 New Trails Drive, The Woodlands, TX, 77381, USA

    Angela Criswell

  2. Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 975 NE 10th St., Stanton L. Young, Biomedical Research Center Rm. 466, Oklahoma City, OK, 73104-5419, USA

    Blaine H. M. Mooers

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  1. Angela Criswell
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Correspondence to Blaine H. M. Mooers .

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  1. Department of Biochemistry, University of Missouri, Columbia, Missouri, USA

    Frank J. Schmidt

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Criswell, A., Mooers, B.H.M. (2015). Structural Studies of a Double-Stranded RNA from Trypanosome RNA Editing by Small-Angle X-Ray Scattering. In: Schmidt, F. (eds) RNA-RNA Interactions. Methods in Molecular Biology, vol 1240. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1896-6_13

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  • DOI: https://doi.org/10.1007/978-1-4939-1896-6_13

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