DNA Origami as a Tool in Biosensing and Nanofabrication

Petteri Piskunen

Research output: ThesisDoctoral ThesisCollection of Articles


Self-assembling DNA (deoxyribonucleic acid) origami nanostructures provide an approachable pathway for making a wide array of programmable, precise and highly addressable platforms at the nanometer-scale. These custom nanoshapes can be employed as versatile tools for applications in e.g. medicine, sensing, and solid-state nanofabrication, but the integration of these DNA-based structures to the various demanding application-specific environments is not always straightforward. Therefore methods for improving the stability of DNA origami or using them as templates for materials with more desirable physical properties are often required. Thus, in publication I of this thesis, the structural dependence of the environmental stability of DNA origami was investigated by comparing two DNA origami designs with identical superstructures but different internal structures. It was shown how the structures behave very differently in buffers with low electrostatic screening and under endonuclease digestion. In publication II, DNA origami were used as new components for amplifying the sensitivity of an electrochemical DNA biosensor by up to two orders of magnitude via manipulation of the effective size of an analyte. Then, in publications III and IV, lithographic pathways for transforming DNA origami shapes into fully solid-state nano-objects are shown. Of these, III presents an optimized workflow for DNA-assisted lithography (DALI), while publication IV develops the method much further into the more versatile biotemplated lithography of inorganic nanostructures (BLIN) technique, that makes the process compatible with a greatly expanded range of materials. Finally, publications V and VI use the techniques presented in III and IV for fabricating nanopatterned substrates for SERS measurements and then characterize their properties using practical measurements and simulations. In V, solely particle-patterned substrates as natively fabricated with BLIN are discussed, while in VI, also more complex architectures based on coupled particle-aperture features are introduced. Overall, the works shown in this thesis provide important insights into the behavior of DNA origami in various environments and demonstrate how their structural properties can be leveraged in promising tools for optical and electrochemical biosensing. Additionally, by enabling the use of DNA origami in solid-state nanofabrication, the methods developed herein could also facilitate the efficient manufacturing of otherwise demanding multifunctional and intricate nanopatterned surfaces for a variety of uses.
Translated title of the contributionDNA-Origamit Biosensorien ja Nanovalmistuksen Työkaluina
Original languageEnglish
QualificationDoctor's degree
Awarding Institution
  • Aalto University
  • Kostiainen, Mauri, Supervising Professor
  • Linko, Veikko, Thesis Advisor
  • Shen, Boxuan, Thesis Advisor
Print ISBNs978-952-64-1290-0
Electronic ISBNs978-952-64-1291-7
Publication statusPublished - 2023
MoE publication typeG5 Doctoral dissertation (article)


  • DNA nanostructures
  • nanolithography
  • plasmonics
  • sensing


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