Methods in Enzymology

Publication date: 2009-01
Volume: 469 Pages: 237 - 251
ISSN: 0076-6879, 1079-2376 PMID: 20946792
DOI: 10.1016/S0076-6879(09)69011-X
Publisher: Academic Press

Author:

Doniach, Sebastian
Lipfert, Jan

Keywords:

Science & Technology, Life Sciences & Biomedicine, Biochemical Research Methods, Biochemistry & Molecular Biology, DIRECT SHAPE DETERMINATION, NUCLEIC-ACIDS, RESOLUTION, PROTEINS, RIBOZYME, MODELS, RIBOSWITCH, PREDICTION, SITUS, IONS, Nucleic Acid Conformation, RNA, Scattering, Small Angle, X-Rays, 0601 Biochemistry and Cell Biology

Abstract:

Small-angle X-ray scattering (SAXS) is emerging as an important technique to characterize the structure of RNA molecules. While lower in resolution than X-ray crystallography or NMR spectroscopy, SAXS has the great advantage to have virtually no molecular weight limitations and does not require crystallization. In addition, SAXS can be readily applied under a large range of solution conditions, allowing to monitor RNA folding, ligand binding, and to characterize partially folded intermediates. Here, we review how the development of SAXS as a structural technique is driven by advances in computer algorithms that allow to reconstruct low-resolution electron density maps ab initio from scattering profiles. In addition, we delineate how these low-resolution models can be used in free energy electrostatics calculations. Finally, we discuss how one can exploit the hierarchical nature of RNA folding by combining the low resolution, global information provided by SAXS with local information on RNA structure, from either experiments or state-of-the-art RNA structure prediction algorithms, to further increase the resolution and quality of models obtained from SAXS.