Anion-specific structure and stability of guanidinium-bound DNA origami

While the folding of DNA into rationally designed DNA origami nanostructures has been studied extensively with the aim of increasing structural diversity and introducing functionality, the fundamental physical and chemical properties of these nanostructures remain largely elusive. Here, we investigate the correlation between atomistic, molecular, nanoscopic, and thermodynamic properties of DNA origami triangles. Using guanidinium (Gdm) as a DNA-stabilizing but potentially also denaturing cation, we explore the dependence of DNA origami stability on the identity of the accompanying anions. The statistical analyses of atomic force microscopy (AFM) images and circular dichroism (CD) spectra reveals that sulfate and chloride exert stabilizing and destabilizing effects, respectively, already below the global melting temperature of the DNA origami triangles. We identify structural transitions during thermal denaturation and show that heat capacity changes delta C-p determine the temperature sensitivity of structural damage. The different hydration shells of the anions and their potential to form Gdm(+) ion pairs in concentrated salt solutions modulate delta C-p by altered wetting properties of hydrophobic DNA surface regions as shown by molecular dynamics simulations. The underlying structural changes on the molecular scale become amplified by the large number of structurally coupled DNA segments and thereby find nanoscopic correlations in AFM images. (C) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.

Automated summary

This study investigates the correlation between atomistic, molecular, nanoscopic, and thermodynamic properties of DNA origami triangles. The results show that sulfate and chloride ions have stabilizing and destabilizing effects on DNA origami stability, respectively. The study also reveals that heat capacity changes delta C-p determine the temperature sensitivity of structural damage in DNA origami.