Advances, Applications, and Perspectives in Small‐Angle X‐ray Scattering of RNA

Abstract

RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA‐regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X‐ray crystallography, and cryo‐electron microscopy can provide high‐resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small‐angle X‐ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large‐sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.

Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment

“…These NMR structures are advantageous because they are determined in aqueous solution and capture the dynamics of the RNA. Modern NMR is laborious as it requires resonances to be assigned despite signal overlap and may need to be combined with complementary methods such as small-angle X-ray scattering . As a last step, NMR structure refinement methods may also incorporate molecular dynamics methods to find low-energy structures that satisfy the experimental restraints .…”

“…Modern NMR is laborious as it requires resonances to be assigned despite signal overlap 71 and may need to be combined with complementary methods such as small-angle X-ray scattering. 72 As a last step, NMR structure refinement methods may also incorporate molecular dynamics methods to find lowenergy structures that satisfy the experimental restraints. 73 The overall structures examined herein are expected to be reliable.…”