Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
Methods Mol Biol. 2023;2568:147-163. doi: 10.1007/978-1-0716-2687-0_10.
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.
小角 X 射线散射（SAXS）已被广泛应用于通过多种互补技术在溶液中对生物大分子结构进行综合分析的一种辅助性综合技术。SAXS 与计算建模相结合可以成为一种强大的策略，用于连接大型 RNA（包括长非编码 RNA（lncRNA））的二级和 3D 结构分析。在这里，我们概述了用于 Zika 病毒亚基因组黄病毒 RNA 的 lncRNA 的 3D 结构特征的 SAXS 和计算建模联合使用的主要步骤和技术。lncRNA 的生产和纯化、用于 SAXS 实验的 RNA 缓冲液和样品制备、SAXS 数据收集和分析、SAXS 辅助的 RNA 3D 结构预测和计算建模都有描述。
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