DNA origami protection and molecular interfacing through engineered sequence-defined peptoids

Edited by Joanna Aizenberg, Harvard University, Cambridge, MA, and approved February 7, 2020 (received for review November 10, 2019)
March 12, 2020
117 (12) 6339-6348

Significance

DNA nanotechnology provides a structural toolkit for the fabrication of programmable DNA nano-constructs; however, their use in biomedical applications is challenging due the limited structural integrity in complex biological fluids. Here, we report a class of tailorable molecular coatings, peptoids, which can efficiently stabilize three-dimensional wireframed DNA constructs under a variety of biomedically relevant conditions, including magnesium-ion depletion and presence of degrading nuclease. Furthermore, we show that peptoid-coated DNA constructs offer a controllable anticancer drug release and an ability to display functional biomolecules on the DNA surfaces. Our study demonstrates an approach for building multifunctional and environmentally robust DNA-based molecular structures for nanomedicine and biosensing.

Abstract

DNA nanotechnology has established approaches for designing programmable and precisely controlled nanoscale architectures through specific Watson−Crick base-pairing, molecular plasticity, and intermolecular connectivity. In particular, superior control over DNA origami structures could be beneficial for biomedical applications, including biosensing, in vivo imaging, and drug and gene delivery. However, protecting DNA origami structures in complex biological fluids while preserving their structural characteristics remains a major challenge for enabling these applications. Here, we developed a class of structurally well-defined peptoids to protect DNA origamis in ionic and bioactive conditions and systematically explored the effects of peptoid architecture and sequence dependency on DNA origami stability. The applicability of this approach for drug delivery, bioimaging, and cell targeting was also demonstrated. A series of peptoids (PE1–9) with two types of architectures, termed as “brush” and “block,” were built from positively charged monomers and neutral oligo-ethyleneoxy monomers, where certain designs were found to greatly enhance the stability of DNA origami. Through experimental and molecular dynamics studies, we demonstrated the role of sequence-dependent electrostatic interactions of peptoids with the DNA backbone. We showed that octahedral DNA origamis coated with peptoid (PE2) can be used as carriers for anticancer drug and protein, where the peptoid modulated the rate of drug release and prolonged protein stability against proteolytic hydrolysis. Finally, we synthesized two alkyne-modified peptoids (PE8 and PE9), conjugated with fluorophore and antibody, to make stable DNA origamis with imaging and cell-targeting capabilities. Our results demonstrate an approach toward functional and physiologically stable DNA origami for biomedical applications.

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Acknowledgments

This work was supported by the Center for Functional Nanomaterials, the Molecular Foundry, the Laboratory Directed Research and Development grant, and the Office of Science, Office of Basic Energy Sciences, of the US Department of Energy (DOE) under Contracts DE-SC0012704 and DE-AC02-05CH11231. The DNA origami work was supported by the US DOE, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, under Grant DE-SC0008772. The LiX beamline is part of the Life Science Biomedical Technology Research resource, cofunded by National Institute of General Medical Sciences Grant P41 GM111244 and by DOE Office of Biological and Environmental Research Grant KP1605010, with additional support from NIH Grant S10 OD012331. The operation of National Synchrotron Light Source II is supported by US DOE, Office of Basic Energy Sciences Contract DE-SC0012704. MD simulations were supported by computational resources provided by the Australian Government through National Computational Infrastructure Project e90 under the National Computational Merit Allocation Scheme. We thank Dr. David Rabuka (Catalent) for generously providing fGly-modified antibody and the Stanford University Mass Spectrometry facility and Theresa McLaughlin for performing characterization of the intact proteins. Y.L. and M.M.S. acknowledge support from the European Research Council Seventh Framework Programme Consolidator Grant “Naturale CG” (616417).

Supporting Information

Appendix (PDF)

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Information & Authors

Information

Published in

Go to Proceedings of the National Academy of Sciences
Go to Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences
Vol. 117 | No. 12
March 24, 2020
PubMed: 32165539

Classifications

Submission history

Published online: March 12, 2020
Published in issue: March 24, 2020

Keywords

  1. DNA nanotechnology
  2. peptoid
  3. molecular coating

Acknowledgments

This work was supported by the Center for Functional Nanomaterials, the Molecular Foundry, the Laboratory Directed Research and Development grant, and the Office of Science, Office of Basic Energy Sciences, of the US Department of Energy (DOE) under Contracts DE-SC0012704 and DE-AC02-05CH11231. The DNA origami work was supported by the US DOE, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, under Grant DE-SC0008772. The LiX beamline is part of the Life Science Biomedical Technology Research resource, cofunded by National Institute of General Medical Sciences Grant P41 GM111244 and by DOE Office of Biological and Environmental Research Grant KP1605010, with additional support from NIH Grant S10 OD012331. The operation of National Synchrotron Light Source II is supported by US DOE, Office of Basic Energy Sciences Contract DE-SC0012704. MD simulations were supported by computational resources provided by the Australian Government through National Computational Infrastructure Project e90 under the National Computational Merit Allocation Scheme. We thank Dr. David Rabuka (Catalent) for generously providing fGly-modified antibody and the Stanford University Mass Spectrometry facility and Theresa McLaughlin for performing characterization of the intact proteins. Y.L. and M.M.S. acknowledge support from the European Research Council Seventh Framework Programme Consolidator Grant “Naturale CG” (616417).

Notes

This article is a PNAS Direct Submission.

Authors

Affiliations

Shih-Ting Wang
Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973;
Melissa A. Gray
Department of Chemistry, Stanford University, Stanford, CA 94305;
The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
Yiyang Lin
Department of Materials, Imperial College London, SW7 2AZ, London, UK;
Department of Bioengineering, Imperial College London, SW7 2AZ, London, UK;
Institute of Biomedical Engineering, Imperial College London, SW7 2AZ, London, UK;
James Byrnes
Photon Science Division, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973;
Energy Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973;
Andy I. Nguyen
The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
School of Engineering, Royal Melbourne Institute of Technology, Melbourne, VIC 3001, Australia;
Molly M. Stevens
Department of Materials, Imperial College London, SW7 2AZ, London, UK;
Department of Bioengineering, Imperial College London, SW7 2AZ, London, UK;
Institute of Biomedical Engineering, Imperial College London, SW7 2AZ, London, UK;
Department of Chemistry, Stanford University, Stanford, CA 94305;
Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305;
The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973;
Department of Chemical Engineering, Columbia University, New York, NY 10027;
Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027

Notes

1
To whom correspondence may be addressed. Email: [email protected].
Author contributions: S.-T.W., C.R.B., R.N.Z., and O.G. designed research; S.-T.W., M.A.G., S.X., Y.L., J.B., A.I.N., N.T., and R.N.Z. performed research; S.X., Y.L., J.B., A.I.N., and M.M.S. contributed new reagents/analytic tools; S.-T.W., M.A.G., N.T., and O.G. analyzed data; and S.-T.W. and O.G. wrote the paper.

Competing Interests

The authors declare no competing interest.

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    DNA origami protection and molecular interfacing through engineered sequence-defined peptoids
    Proceedings of the National Academy of Sciences
    • Vol. 117
    • No. 12
    • pp. 6279-6953

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