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PreprintCC BYChemRxiv

Influence of Divalent Cations on the Mechanical Properties of DNA Origami Six-Helix Bundles

  • Emilia Juricke1
  • Mohammed Fatafta1
  • Guido Grundmeier1
  • Antonio Suma2
  • Adrian Keller1
  1. 1Technical and Macromolecular Chemistry, Paderborn University, Warburger Strasse 100, Paderborn, Germany, 33098
  2. 2Dipartimento Interateneo di Fisica, Università degli Studi di Bari and INFN, via Amendola 173, Bari, Italy, I-70121
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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.

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Cite

BibTeXRIS
BibTeX
@misc{juricke2026influence,
  title = {{Influence of Divalent Cations on the Mechanical Properties of DNA Origami Six-Helix Bundles}},
  author = {Emilia Juricke and Mohammed Fatafta and Guido Grundmeier and Antonio Suma and Adrian Keller},
  howpublished = {ChemRxiv},
  year = {2026},
  month = oct,
  doi = {10.26434/chemrxiv.15010878/v1},
  url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010878/v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Influence of Divalent Cations on the Mechanical Properties of DNA Origami Six-Helix Bundles
AU  - Emilia Juricke
AU  - Mohammed Fatafta
AU  - Guido Grundmeier
AU  - Antonio Suma
AU  - Adrian Keller
PY  - 2026
DA  - 2026/10/22
PB  - ChemRxiv
DO  - 10.26434/chemrxiv.15010878/v1
UR  - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010878/v1
AB  - 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.
ER  -