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.
