Influence of Divalent Cations on the Mechanical Properties of DNA Origami Six-Helix Bundles
Year: 2026
Type: preprint
Abstract: The mechanical behavior of DNA origami nanostructures (DONs) is governed by both design parameters and ionic environment, yet their coupled effects remain poorly understood. Here, atomic force microscopy (AFM)-based contour analysis is used to quantify the persistence length (Lp), contour length (Lc), and end-to-end distance (Ree) of DON six-helix bundles (6HBs) with different staple crossover densities. Non-ligated and ligated 6HBs are compared in the presence of MgCl2 and SrCl2, while oxDNA simulations employing implicit monovalent salt screening help distinguish design-dependent from ion-specific effects. While providing comparable diffuse electrostatic screening, Mg2+ and Sr2+ interact differently with DONs and produce distinct design-dependent mechanical responses. For non-ligated 6HBs, lower Lp values are obtained in Sr2+ than in Mg2+, with the magnitude of the difference depending on crossover density. Paired Ree-versus-Lc analysis further indicates greater bending heterogeneity in Sr2+. In the presence of both cations, ligation may lead to an increase or a decrease in Lp depending on crossover density. Simulations reproduce the opposite ligation responses of the two designs but not the Mg2+-associated behavior, supporting an additional contribution from specific divalent cation interactions. These results establish crossover density, backbone continuity, and cation species as coupled variables whose interplay controls DON mechanics.
Source: ChemRxiv
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7223173970