Nucleic Acid Nanostructures - Design, Reconfigurability, and Applications

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School of Science | Doctoral thesis (article-based) | Defence date: 2023-03-24
Degree programme
102 + app. 110
Aalto University publication series DOCTORAL THESES, 20/2023
Self-assembly with near-atomic precision forms the basis for synthesizing biological structures found in living cells. These self-assembled structures retain the accuracy across sizes ranging from nanometers to macroscopic scale by exploiting the information encoded in the biomolecules. The fabrication of complex 3D synthetic molecular structures with such precision and controllability is cumbersome. Nucleic acid nanotechnology eases this process by enabling bottom-up construction of well-defined nanoscale objects through the predictability and programmability of interactions within DNA and RNA. The design, reconfigurability and a potential application of such nucleic acid nanostructures are presented in this thesis, which is based on three publications. Publication I presents a highly general and automated approach for the design and assembly of 3D RNA wireframe polyhedral nanostructures. Grounded on the principles of spanning tree-based strand routing, the method renders the target 3D wireframe structure as a single-stranded RNA. The output RNA sequence can be readily transcribed from the corresponding DNA template and assembled into the intended shape. As case examples, the design of three RNA polyhedral models: a tetrahedron, a triangular bipyramid, and a triangular prism were experimentally realized. The developed design pipeline is not restricted to polyhedral models and can be used to render arbitrary straight-line 3D meshes as RNA strands. Publication II and Publication III focus on the DNA origami approach to fabricate dynamic nanostructures. Publication II presents a reconfigurable chiral plasmonic molecule (CPM) that can be modulated remotely using visible light. The native CPMs are non-responsive to light but can change their spatial configuration by forming DNA triplex locks upon a decrease in the solution pH. To this end, a merocyanine-based photoacid was utilized as a photoresponsive medium that decreases the pH upon exposure to visible light. The chiral response from the CPMs was thus modulated by the intensity of the incident light, which alters the pH. By tuning the intensity, distinct steady out-of-equilibrium states were achieved, both in the pH and in the chiral response. In Publication III, the precise positioning capability and reconfigurability of the DNA origami technique were exploited. A DNA-origami-based device was fabricated to investigate DNA bending induced by TATA-binding protein. This bending was translated into an angular change in the DNA origami structures directly observable using a transmission electron microscope. Further, the role of transcription factors II A and II B in DNA bending was investigated. Our approach can be readily expanded to other DNA-distorting proteins with careful design considerations.Overall, this thesis contributes to various facets of nucleic acid nanotechnology from design to reconfigurability to applications. In essence, the findings presented in the individual sections illustrate that nucleic acid nanotechnology still has a large unexplored design space, novel switching mechanisms, and under-explored applications.
Supervising professor
Kuzyk, Anton, Assoc. Prof., Aalto University, Department of Neuroscience and Biomedical Engineering, Finland
Thesis advisor
Kuzyk, Anton, Assoc. Prof., Aalto University, Department of Neuroscience and Biomedical Engineering, Finland
DNA origami, RNA polyhedra, photoacid, chiral plasmonics, DNA bending proteins
Other note
  • [Publication 1]: Antti Elonen, Ashwin Karthick Natarajan, Ibuki Kawamata, Lukas Oesinghaus, Abdulmelik Mohammed, Jani Seitsonen, Yuki Suzuki, Friedrich C Simmel, Anton Kuzyk, and Pekka Orponen. Algorithmic design of 3D wireframe RNA polyhedra. ACS Nano, 16, 10, 16608–16616, September 2022.
    Full text in Acris/Aaltodoc:
    DOI: 10.1021/acsnano.2c06035 View at publisher
  • [Publication 2]: Joonas Ryssy, Ashwin Karthick Natarajan, Jinhua Wang, Arttu J Lehtonen, Minh-Kha Nguyen, Rafal Klajn, and Anton Kuzyk. Light-Responsive Dynamic DNA-Origami-Based Plasmonic Assemblies. Angewandte Chemie International Edition, 60, 11, 5859-5863, January 2021.
    Full text in Acris/Aaltodoc:
    DOI: 10.1002/anie.202014963 View at publisher
  • [Publication 3]: Ashwin Karthick Natarajan, Joonas Ryssy, and Anton Kuzyk. A DNA origami-based device for investigating DNA bending proteins by transmission electron microscopy. Accepted for publication in Nanoscale, January 2023.
    Full text in Acris/Aaltodoc:
    DOI: 10.1039/d2nr05366g View at publisher