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Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies

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  • Jae Young Lee

    (Seoul National University)

  • Yanggyun Kim

    (Seoul National University)

  • Do-Nyun Kim

    (Seoul National University
    Seoul National University
    Seoul National University
    Seoul National University)

Abstract

Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding ligands has offered promising avenues for biological and therapeutic applications. However, it remains elusive how to effectively model and predict their effects on the deformation and mechanical properties of DNA structures. Here, we present a computational framework for simulating chemo-mechanical change of structured DNA assemblies. We particularly quantify the effects of ethidium bromide (EtBr) intercalation on the geometry and mechanical properties of DNA base-pairs through molecular dynamics simulations and integrated them into finite-element-based structural analysis to predict the shape and properties of DNA objects. The proposed model captures various structural changes induced by EtBr-binding such as shape variation, flexibility modulation, and supercoiling instability. It enables a rational design of structured DNA assemblies with tunable shapes and mechanical properties by binding molecules.

Suggested Citation

  • Jae Young Lee & Yanggyun Kim & Do-Nyun Kim, 2024. "Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50871-3
    DOI: 10.1038/s41467-024-50871-3
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    References listed on IDEAS

    as
    1. Young-Joo Kim & Junho Park & Jae Young Lee & Do-Nyun Kim, 2021. "Programming ultrasensitive threshold response through chemomechanical instability," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    2. Nadrian C. Seeman, 2003. "DNA in a material world," Nature, Nature, vol. 421(6921), pages 427-431, January.
    3. Hyungmin Jun & Xiao Wang & William P. Bricker & Mark Bathe, 2019. "Automated sequence design of 2D wireframe DNA origami with honeycomb edges," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
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