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Fabrication and use of silicon hollow-needle arrays to achieve tissue nanotransfection in mouse tissue in vivo

Nature Protocols volume 16, pages 5707–5738 (2021)Cite this article

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Abstract

Tissue nanotransfection (TNT) is an electromotive gene transfer technology that was developed to achieve tissue reprogramming in vivo. This protocol describes how to fabricate the required hardware, commonly referred to as a TNT chip, and use it for in vivo TNT. Silicon hollow-needle arrays for TNT applications are fabricated in a standardized and reproducible way. In <1 s, these silicon hollow-needle arrays can be used to deliver plasmids to a predetermined specific depth in murine skin in response to pulsed nanoporation. Tissue nanotransfection eliminates the need to use viral vectors, minimizing the risk of genomic integration or cell transformation. The TNT chip fabrication process typically takes 5–6 d, and in vivo TNT takes 30 min. This protocol does not require specific expertise beyond a clean room equipped for basic nanofabrication processes.

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Fig. 1: A schematic view of the TNT process, chip designs and scanning electron microscope (SEM) images of the fabricated chips.
Fig. 2: Quality control: clogging problem in the fabricated hollow needles.
Fig. 3: Typical lithography patterns for needle arrays in the fabrication process.
Fig. 4: Schematics of the fabrication process of the primary hollow needles with flat tip (type I).
Fig. 5: Etching and dicing processes.
Fig. 6: Controlling hole size with oxide deposition.
Fig. 7: Schematics of the fabrication process for the hollow needles with sharp tip and centered bore (Type II).
Fig. 8: Isotropic etching of Si to fabricate the sharp needle (Type II).
Fig. 9: Schematics of the fabrication process for the hollow-needle array with sharp tip and off-center bore (Type III).
Fig. 10: Preparation of the reservoir-mounted chip (Steps 2–8).
Fig. 11: Cutaneous TNT and in vivo reprogramming.
Fig. 12: Depth of cutaneous gene delivery as a function of applied voltage.

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Data availability

The individual images used to compile the figures shown and additional examples of the types of results obtained are available from Yi Xuan upon reasonable request. The design lithography patterns we used for needle fabrication are available at https://doi.org/10.6084/m9.figshare.16528311. Source data are provided with this paper.

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Acknowledgements

This work made use of the Pritzker Nanofabrication Facility, which receives partial support from the SHyNE Resource, a node of the National Science Foundation’s National Nanotechnology Coordinated Infrastructure (NSF ECCS-2025633). We thank Parker Evans for his help in measuring the force applied during the TNT process. This work was supported in part by NIH grant DK128845; Department of Defense grants W81XWH-21-1-0097, W81XWH-21-1-0033 and W81XWH-20-1-251 to C.K.S.; Department of Defense grant W81XWH-21-1-0047 to S.K.; and NIH grant GM143572 to Y.X.

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Author notes

  1. These authors contributed equally: Yi Xuan, Subhadip Ghatak.

Authors and Affiliations

  1. Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA

    Yi Xuan, Subhadip Ghatak, Andrew Clark, Savita Khanna, Sashwati Roy & Chandan K. Sen

  2. Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA

    Yi Xuan, Zhigang Li & Chandan K. Sen

  3. Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA

    Dongmin Pak

  4. Integrated Nanosystems Development Institute, IUPUI, Indianapolis, IN, USA

    Mangilal Agarwal

  5. Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN, USA

    Sashwati Roy

  6. Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA

    Peter Duda

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Contributions

C.K.S. conceived the idea and provided design guidelines to Y.X. Y.X. finalized the designs and fabricated TNT chips with support from Z.L. and P.D. A.C., S.G., S.K. and S.R. designed and performed the TNT procedure on mice and other biological experiments. Z.L. carried out the SEM imaging and focused ion beam operation with support from D.P. M.A. integrated the TNT chip and the plasmid reservoir. All authors contributed to writing and editing the manuscript. C.K.S. supervised, resourced and led this project.

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Correspondence to Yi Xuan or Chandan K. Sen.

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Peer review information Nature Protocols thanks Tarun Bhattacharyya, Kui Cheng, Yuanyu Huang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Key reference using this protocol

Gallego-Perez, D. et al. Nat. Nanotechnol. 12, 974–979 (2017): https://doi.org/10.1038/nnano.2017.134

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Source Data Fig. 11

Gene expression fold change raw data for Fig. 11c.

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Xuan, Y., Ghatak, S., Clark, A. et al. Fabrication and use of silicon hollow-needle arrays to achieve tissue nanotransfection in mouse tissue in vivo. Nat Protoc 16, 5707–5738 (2021). https://doi.org/10.1038/s41596-021-00631-0

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