The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

Weiwei He, Yen Lin Chen, Lois Pollack, Serdal Kirmizialtin

Research output: Contribution to journalArticlepeer-review


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, elucidat ing 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 ex plore 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.

Original languageEnglish (US)
Article numbereabf6106
JournalScience Advances
Issue number17
StatePublished - Apr 21 2021

ASJC Scopus subject areas

  • General


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