Precision Placement of DNA Origami onto Patterned Silicon Wafer Surfaces

Leo Huang

EECS Department
University of California, Berkeley
Technical Report No. UCB/EECS-2025-76
May 15, 2025

http://www2.eecs.berkeley.edu/Pubs/TechRpts/2025/EECS-2025-76.pdf

Structural DNA nanotechnology offers a promising route for constructing nanometer-scale components with high spatial precision, while top-down photolithographic techniques remain essential for producing patterned substrates at scale. Previous work – most notably by Gopinath et al. – has demonstrated precise placement of DNA origami using electron beam lithography, but this approach’s low throughput poses challenges for broader application. Here, we extend this approach by exploring the use of fractal-assembled DNA origami tiles for site-specific deposition onto photolithographically patterned silicon surfaces. This work initiates a systematic exploration of how tile geometry, surface chemistry, and binding conditions influence the integration of DNA nanostructures with scalable fabrication platforms, specifically their impact on placement yield and quality. Our work compares electrostatically and thermodynamically driven binding strategies as a step towards a more generalizable framework for hybrid bottom-up/top-down nanofabrication methods. We envision this method to complement existing approaches and expand the role of DNA origami in applications such as biosensing and programmable nanosystems.

Advisor: Grigory Tikhomirov

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BibTeX citation:

@mastersthesis{Huang:EECS-2025-76,
    Author = {Huang, Leo},
    Editor = {Park, Yunjeong and Tikhomirov, Grigory},
    Title = {Precision Placement of DNA Origami onto Patterned Silicon Wafer Surfaces},
    School = {EECS Department, University of California, Berkeley},
    Year = {2025},
    Month = {May},
    URL = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2025/EECS-2025-76.html},
    Number = {UCB/EECS-2025-76},
    Abstract = {Structural DNA nanotechnology offers a promising route for constructing nanometer-scale components with high spatial precision, while top-down photolithographic techniques remain essential for producing patterned substrates at scale. Previous work – most notably by Gopinath et al. – has demonstrated precise placement of DNA origami using electron beam lithography, but this approach’s low throughput poses challenges for broader application. Here, we extend this approach by exploring the use of fractal-assembled DNA origami tiles for site-specific deposition onto photolithographically patterned silicon surfaces. This work initiates a systematic exploration of how tile geometry, surface chemistry, and binding conditions influence the integration of DNA nanostructures with scalable fabrication platforms, specifically their impact on placement yield and quality. Our work compares electrostatically and thermodynamically driven binding strategies as a step towards a more generalizable framework for hybrid bottom-up/top-down nanofabrication methods. We envision this method to complement existing approaches and expand the role of DNA origami in applications such as biosensing and programmable nanosystems.}
}

EndNote citation:

%0 Thesis
%A Huang, Leo
%E Park, Yunjeong
%E Tikhomirov, Grigory
%T Precision Placement of DNA Origami onto Patterned Silicon Wafer Surfaces
%I EECS Department, University of California, Berkeley
%D 2025
%8 May 15
%@ UCB/EECS-2025-76
%U http://www2.eecs.berkeley.edu/Pubs/TechRpts/2025/EECS-2025-76.html
%F Huang:EECS-2025-76