Issue 41, 2023

Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants

Abstract

The structural stability of DNA origami nanostructures in various chemical environments is an important factor in numerous applications, ranging from biomedicine and biophysics to analytical chemistry and materials synthesis. In this work, the stability of six different 2D and 3D DNA origami nanostructures is assessed in the presence of three different chaotropic salts, i.e., guanidinium sulfate (Gdm2SO4), guanidinium chloride (GdmCl), and tetrapropylammonium chloride (TPACl), which are widely employed denaturants. Using atomic force microscopy (AFM) to quantify nanostructural integrity, Gdm2SO4 is found to be the weakest and TPACl the strongest DNA origami denaturant, respectively. Despite different mechanisms of actions of the selected salts, DNA origami stability in each environment is observed to depend on DNA origami superstructure. This is especially pronounced for 3D DNA origami nanostructures, where mechanically more flexible designs show higher stability in both GdmCl and TPACl than more rigid ones. This is particularly remarkable as this general dependence has previously been observed under Mg2+-free conditions and may provide the possibility to optimize DNA origami design toward maximum stability in diverse chemical environments. Finally, it is demonstrated that melting temperature measurements may overestimate the stability of certain DNA origami nanostructures in certain chemical environments, so that such investigations should always be complemented by microscopic assessments of nanostructure integrity.

Graphical abstract: Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants

Supplementary files

Article information

Article type
Paper
Submitted
03 May 2023
Accepted
14 Sep 2023
First published
19 Sep 2023

Nanoscale, 2023,15, 16590-16600

Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants

M. Hanke, D. Dornbusch, E. Tomm, G. Grundmeier, K. Fahmy and A. Keller, Nanoscale, 2023, 15, 16590 DOI: 10.1039/D3NR02045B

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