Ion-mediated control of structural integrity and reconfigurability of DNA nanostructures

Aleksandra Maria Bednarz*, Steffan Møller Sønderskov, Mingdong Dong, Victoria Birkedal

*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Abstract

Nucleic acids-based biomolecular self-assembly enables creating versatile functional architectures. Electrostatic screening
of the nucleic acids negative charges is essential for their folding and stability; thus, ions play a critical role in nucleic acids
self-assembly in both biology and nanotechnology. However, the ion-DNA interplay and resulting ion-specific structural
integrity and responsiveness of DNA constructs is underexploited. Here, we harness a wide range of mono- and divalent ions
to control structural features of DNA origami constructs. Using Atomic Force Microscopy and Förster Resonance Energy
Transfer (FRET) spectroscopy down to the single-molecule level, we report on the global and local structural performance
and responsiveness of DNA origami constructs following self-assembly, upon post-assembly ionic exchange, and post-assembly ion-mediated reconfiguration. We determined conditions for highly efficient DNA origami folding in the presence
of several mono- (Li+, Na+, K+, Cs+) and divalent (Ca2+, Sr2+, Ba2+) ions, expanding the range where DNA origami structures can
be exploited for custom-specific applications. We then manipulated fully folded constructs by exposing them to unfavorable
ionic conditions that led to the emergence of substantial disintegrities but not to unfolding. Moreover, we found that poorly
assembled nanostructures at low ion concentrations undergo substantial self-repair upon ion addition in the absence of free
staple strands. This reconfigurability occurs in an ion type- and concentration-specific manner. Our findings provide a
fundamental understanding of the ion-mediated structural responsiveness of DNA origami at the nanoscale enabling
applications in a wide range of ionic conditions.
Original languageEnglish
JournalNanoscale
Volume15
Issue3
Pages (from-to)1317-1326
Number of pages10
ISSN2040-3364
DOIs
Publication statusPublished - Jan 2023

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