Virus-mimetic structures through protein engineering and nucleic acid origami

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School of Chemical Engineering | G5 Artikkeliväitöskirja | Defence date: 2025-06-18
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Authors

Date

2025

Department

Biotuotteiden ja biotekniikan laitos
Department of Bioproducts and Biosystems

Major/Subject

Mcode

Degree programme

Language

en

Pages

126 + app. 92

Series

Aalto University publication series Doctoral Theses, 108/2025

Abstract

Viruses are fascinating and ubiquitous nanostructures that have intriguing biological properties. Their proteinaceous capsids are uniform in size and shape and serve to protect the viral genome and gate the flux of small molecules. Combined with their unique self-assembly properties, viruses have gained attention as versatile building blocks for bottom-up nanofabrication. However, the resulting virus-based assemblies are typically limited to specific morphologies. Gaining control over the assembly process to produce purpose-built nanostructures with programmable size and shape would be desirable in the development of new delivery systems and vaccines, among others. In this doctoral thesis, the use of nucleic acid origami to template functional virus-mimetic structures was explored. In publication I, the applicability of DNA origami as a binding platform to direct the assembly of virus capsid proteins was investigated. The results demonstrated precise control over the dimensions and morphology of the formed capsid protein-DNA origami assemblies, and that the approach is not limited to only one type of capsid protein. Moreover, the capsid protein coating enhanced the structural stability of DNA origami in endonuclease-rich environments. In publication II, the effect of the internal design of mR A-DNA origami on the folding and translation properties was explored. Extracellular translation studies revealed the importance of the position of the start codon within the mRNA-DNA origami for a successful translation initiation. The translation could be regulated by triggering a structural change in the structure, resulting in the accessibility of the start codon. Furthermore, the mRNA-DNA origami were complexed with virus capsid proteins, which enhanced the cellular uptake, leading to protein translation inside cells while exhibiting low toxicity. In publication III, a protein-based two-component coating, consisting of a targeting and a camouflaging agent, was applied on top of the DNA origami. Once the assembled complexes were illuminated, photolytic degradation of the camouflaging agent was triggered, resulting in the dissociation of the camouflaging agent from the DNA origami and hence the display of the targeting moiety. Finally, in publication IV, a biocatalytic nanoreactor was developed by utilizing DNA origami to spatially organize enzymes and to facilitate the assembly of virus capsid proteins. The findings also highlighted the ability of the assembled and well-defined protein shell to control enzyme-substrate interactions. In conclusion, the results demonstrate the applicability of nucleic acid origami to, in a controllable manner, template highly ordered virus-mimetic structures. Additionally, the nucleic acid origami serve as a pegboard to precisely place functional moieties or employ mRNA as a scaffold, thereby broadening the application range of virus-mimetic structures. The established methods could promote the development of functional and responsive nucleic acid origami-based multipurpose systems.

Description

Supervising professor

Kostiainen, Mauri, Prof., Aalto University, Department of Bioproducts and Biosystems, Finland

Thesis advisor

Kostiainen, Mauri, Prof., Aalto University, Department of Bioproducts and Biosystems, Finland
Linko, Veikko, Assoc. Prof., University of Tartu, Estonia

Keywords

DNA origami, mRNA-DNA origami, virus capsid protein, electrostatic self-assembly, antigen targeting, stimuli-responsiveness, biocatalysis

Other note

Parts

  • [Publication 1]: Iris Seitz, Sharon Saarinen, Esa-Pekka Kumpula, Donna McNeale, Eduardo Anaya-Plaza, Vili Lampinen, Vesa P. Hytönen, Frank Sainsbury, Jeroen J. L. M. Cornelissen, Veikko Linko, Juha T. Huiskonen, Mauri A. Kostiainen. DNA-Origami-Directed Virus Capsid Polymorphism. Nature Nanotechnology, 2023, 18, 10, 1205–1212.
    Full text in Acris/Aaltodoc: https://urn.fi/URN:NBN:fi:aalto-202311016722
    DOI: 10.1038/s41565-023-01443-x View at publisher
  • [Publication 2]: Iris Seitz, Sharon Saarinen, JuliaWierzchowiecka, Esa-Pekka Kumpula, Boxuan Shen, Jeroen J. L. M. Cornelissen, Veikko Linko, Juha T. Huiskonen, Mauri A. Kostiainen. Folding of mRNA-DNA Origami for Controlled Translation and Viral Vector Packaging. Advanced Materials, 2025, 37, 15, 2417642.
    Full text in Acris/Aaltodoc: https://urn.fi/URN:NBN:fi:aalto-202503262998
    DOI: 10.1002/adma.202417642 View at publisher
  • [Publication 3]: Iris Seitz, Heini Ijäs, Veikko Linko, Mauri A. Kostiainen. Optically Responsive Protein Coating of DNA Origami for Triggered Antigen Targeting. ACS Applied Materials and Interfaces, 2022, 14, 34, 38515—38524.
    Full text in Acris/Aaltodoc: https://urn.fi/URN:NBN:fi:aalto-202209215650
    DOI: 10.1021/acsami.2c10058 View at publisher
  • [Publication 4]: Iris Seitz, Donna McNeale, Frank Sainsbury, Veikko Linko, Mauri A. Kostiainen. Modular Virus Capsid Coatings for Biocatalytic DNA Origami Nanoreactors. Submitted, 2025

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Permanent link to this item

https://urn.fi/URN:ISBN:978-952-64-2577-1

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[diss] Kemian tekniikan korkeakoulu / CHEM