title: Analysis of RNA structure using small-angle X-ray scattering.
abstract: In addition to their role in correctly attaching specific amino acids to cognate tRNAs, aminoacyl-tRNA synthetases (aaRS) have been found to possess many alternative functions and often bind to and act on other nucleic acids. In contrast to the well-defined 3D structure of tRNA, the structures of many of the other RNAs recognized by aaRSs have not been solved. Despite advances in the use of X-ray crystallography (XRC), nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (cryo-EM) for structural characterization of biomolecules, significant challenges to solving RNA structures still exist. Recently, small-angle X-ray scattering (SAXS) has been increasingly employed to characterize the 3D structures of RNAs and RNA-protein complexes. SAXS is capable of providing low-resolution tertiary structure information under physiological conditions and with less intensive sample preparation and data analysis requirements than XRC, NMR and cryo-EM. In this article, we describe best practices involved in the process of RNA and RNA-protein sample preparation, SAXS data collection, data analysis, and structural model building.
authors: Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States.
authors: William A
authors: WA
authors: Cantara
authors: Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States.
authors: Erik D
authors: ED
authors: Olson
authors: Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States. Electronic address: musier@chemistry.ohio-state.edu.
authors: Karin
authors: K
authors: Musier-Forsyth
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D000604:Amino Acyl-tRNA Synthetases / Q000235:genetics / Q000378:metabolism*; D002850:Chromatography, Gel; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D008958:Models, Molecular; D063347:Native Polyacrylamide Gel Electrophoresis; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D059370:RNA Folding; D012345:RNA, Transfer, Amino Acid-Specific / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D053838:Scattering, Small Angle; D046249:Transfer RNA Aminoacylation; D014961:X-Ray Diffraction
chemical_list: D000596:Amino Acids; D012345:RNA, Transfer, Amino Acid-Specific; D000604:Amino Acyl-tRNA Synthetases
keywords: Aminoacyl-tRNA synthetase; Native PAGE; RNA structure; SAXS; Size-exclusion chromatography; tRNA-like structures