Baird Nathan J, Ferré-D'Amaré Adrian R
Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
Methods Mol Biol. 2014;1103:211-25. doi: 10.1007/978-1-62703-730-3_16.
Small-angle X-ray scattering (SAXS) is a powerful tool for examining the global conformation of riboswitches in solution, and how this is modulated by binding of divalent cations and small molecule ligands. SAXS experiments, which typically require only minutes per sample, directly yield two quantities describing the size and shape of the RNA: the radius of gyration (Rg) and the maximum linear dimension (Dmax). Examination of these quantities can reveal if a riboswitch undergoes cation-induced compaction. Comparison of the Rg and Dmax values between samples containing different concentrations of ligand reveals the overall structural response of the riboswitch to ligand. The Kratky plot (a graphical representation that emphasizes the higher-resolution SAXS data) and the P(r) plot or pair-probability distribution (an indirect Fourier transform, or power spectrum of the data) can provide additional evidence of riboswitch conformational changes. Simulation methods have been developed for generating three-dimensional reconstructions consistent with the one-dimensional SAXS data. These low-resolution molecular envelopes can aid in deciphering the relative helical arrangement within the RNA.
小角X射线散射（SAXS）是一种用于研究溶液中核糖开关全局构象以及二价阳离子和小分子配体结合如何对其进行调节的强大工具。SAXS实验通常每个样品只需几分钟，可直接得出描述RNA大小和形状的两个量：回转半径（Rg）和最大线性尺寸（Dmax）。对这些量的检测可以揭示核糖开关是否经历阳离子诱导的压缩。比较含有不同浓度配体的样品之间的Rg和Dmax值，可以揭示核糖开关对配体的整体结构响应。Kratky图（一种强调高分辨率SAXS数据的图形表示）和P(r)图或对概率分布（数据的间接傅里叶变换或功率谱）可以提供核糖开关构象变化的额外证据。已经开发出模拟方法来生成与一维SAXS数据一致的三维重建。这些低分辨率的分子包络有助于解读RNA内相对螺旋排列。
