Understanding Nucleic Acid Structural Changes by Comparing Wide-Angle X-ray Scattering (WAXS) Experiments to Molecular Dynamics Simulations

TL;DR

This paper demonstrates how wide-angle X-ray scattering (WAXS) can be used to analyze nucleic acid structures and their changes, validating molecular dynamics simulations and revealing ion-induced structural modifications.

Contribution

It introduces WAXS as a tool for nucleic acid structural analysis and shows its effectiveness in testing MD simulations and detecting ion-driven structural changes.

Findings

WAXS can qualitatively characterize nucleic acid structures.

MD simulations accurately capture CoHex-induced RNA structural changes.

WAXS reveals structural effects of multivalent ions on nucleic acids.

Abstract

Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight in understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.