Small angle X-ray scattering (SAXS) has been widely applied as an enabling integrative technique for comprehensive analysis of the structure of biomacromolecules by multiple, complementary techniques in solution. SAXS in combination with computational modeling can be a powerful strategy bridging the secondary and 3D structural analysis of large RNAs, including the long noncoding RNAs (lncRNA). Here, we outline the major procedures and techniques in the combined use of SAXS and computational modeling for 3D structural characterization of a lncRNA, the subgenomic flaviviral RNA from Zika virus. lncRNA production and purification, RNA buffer and sample preparation for SAXS experiments, SAXS data collection and analysis, SAXS-aided RNA 3D structure prediction, and computational modeling are described.
Keywords: Computational modeling; Long noncoding RNA; RNA 3D structure; Small angle X-ray scattering; Subgenomic flavivirus RNA.
© 2023. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.