Open AccessThe structural plasticity of nucleic acid duplexes revealed by WAXS and MD
Author(s) -
Weiwei He,
Yen-Lin Chen,
Lois Pollack,
Serdal Kırmızıaltın
Publication year - 2021
Publication title -
science advances
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.928
H-Index - 146
ISSN - 2375-2548
DOI - 10.1126/sciadv.abf6106
Subject(s) - rna , duplex (building) , dna , rna silencing , nucleic acid , crystallography , molecular dynamics , nucleic acid structure , biophysics , computational biology , valence (chemistry) , chemistry , biology , genetics , gene , rna interference , computational chemistry , organic chemistry
Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA's diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.