Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile
Name
applsci-11-02357-v2.pdf
Size
3.15 MB
Format
Adobe PDF
Checksum (MD5)
ddc191dc15237f7ff13a9e853ef8f937
Author(s)
Li, Ruixin
Chen, Haorong
Lee, Hyeongwoon
Choi, Jong Hyun
Date Issued
March 6, 2021
Publisher
Multidisciplinary Digital Publishing Institute
Citation
Applied Sciences 11 (5): 2357 (2021)
Version
Final published version
Abstract
DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn, which is slightly different from that of native B-form DNA (~10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Terms of Use
Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.3390/app11052357
