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Storage of mechanical energy in DNA nanorobotics using molecular torsion springs

Nature Physics volume 19, pages 741–751 (2023)Cite this article

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Abstract

DNA nanostructures are increasingly used for the realization of mechanically active nanodevices and DNA-based nanorobots. A fundamental challenge in this context is the design of molecular machine elements that connect the rigid structural components and are powered in an effective way. Here we investigate a pivot joint that enables rotational motion of a nanorobotic arm and show the storage and release of mechanical energy by winding up and relaxing the joint that functions as a molecular torsion spring. Using electrical manipulation of the nanorobotic arm and simultaneous observation via single molecule fluorescence microscopy, we study the mechanical properties of various joint designs. Brownian dynamics simulations suggest that breaking of stacking interactions is a major contributor to enthalpic energy storage.

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Fig. 1: The structure of the DNA nanorobotic arm.
Fig. 2: Probing the mechanics of molecular joints.
Fig. 3: Characterization of the torsion spring.
Fig. 4: Simple bifurcation model for back-skipping.
Fig. 5: Energy storage within a molecular torsion spring and directed rotation upon release.
Fig. 6: Coarse-grained simulations of the nanorobotic arm using oxDNA.

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Data availability

Localization event lists of the microscopy videos are available at https://doi.org/10.14459/2022mp1694147. Source data and all other data that support the plots within this paper and other findings of this study are available from the corresponding authors upon reasonable request.

Code availability

The source code of the data analysis routines and simulation files employed in this study is available from the corresponding authors upon reasonable request.

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Acknowledgements

We thank the group of H. Dietz for providing us with in-house produced scaffold strands. F.R. gratefully acknowledges support from the Konrad-Adenauer-Stiftung. J.L. gratefully acknowledges support from the Peter und Traudl Engelhorn Stiftung. F.C.S. acknowledges support from the Deutsche Forschungsgemeinschaft, SFB 1032 (project ID 201269156 TPA2) and SFB 863 (project ID 111166240 TPA8). This work was funded by the Federal Ministry of Education and Research and the Free State of Bavaria under the Excellence Strategy of the Federal Government and the Länder through the ONE MUNICH Project Munich Multiscale Biofabrication and the TUM Innovation Network RISE (Robotic Intelligence in the Synthesis of Life).

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  1. Physics Department E14, Technical University of Munich, Garching, Germany

    Matthias Vogt, Martin Langecker, Matthias Gouder, Enzo Kopperger, Florian Rothfischer, Friedrich C. Simmel & Jonathan List

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Contributions

M.V., E.K. and J.L. designed and produced the DNA nanostructures. E.K., M.L. and J.L. built the experimental set-up. M.V. performed single molecule measurements with support from E.K. and J.L. F.R. recorded the AFM images and prepared linearized scaffold strands supported by J.L. M.V. and M.G. programmed data analysis routines. M.V., M.L., E.K., F.C.S. and J.L. planned the research. E.K., F.C.S. and J.L. mainly developed the theoretical model. oxDNA simulations were performed by M.L. and M.G.. All the authors discussed the scientific results and contributed to the writing process.

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Correspondence to Friedrich C. Simmel or Jonathan List.

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Nature Physics thanks Pallav Kosuri and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary Information

Supplementary Notes 1–15, Figs. 1–51 and Tables 1–3.

Supplementary Video 1

Trajectory (oxDNA viewer representation) of the rotation simulation for the 3 nt spring domain variant. In the video, every 25th configuration of the trajectory is shown.

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Vogt, M., Langecker, M., Gouder, M. et al. Storage of mechanical energy in DNA nanorobotics using molecular torsion springs. Nat. Phys. 19, 741–751 (2023). https://doi.org/10.1038/s41567-023-01938-3

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