Enabling information in Materials through DNA

Abstract

This thesis describes three ways of using synthetic DNA to add information to materials for technical applications. Specifically, a new concept called DNA-of-Things is proposed to store information in objects by adding encapsulated DNA to its raw materials. Furthermore, a new DNA encapsulation strategy using biodegradable dithiol silicate is presented to address the problem of secure file deletions upon disposal. Finally, the ecotoxicological impact of silica particles with encapsulated DNA used as tracer material is discussed by defining a tracing scenario and performing ecotoxicological standard tests. Chapter 1 follows the evolution of storing information from stone age to present day silicon age. It discusses the limitations of current silicon data storage technology, emphasizing the need for a new generation of data storage material. DNA with superior storage density, low energy costs and potential longevity, is presented as a suitable candidate for the challenge of storing the increasing amounts of information that is created. The synthesis and sequencing technologies for synthetic DNA represent the writing and reading for this molecular data storage approach and are discussed in detail. Furthermore, specific storage conditions and stabilization factors are presented to store DNA long-term, followed by a short introduction to strategies for encoding information in DNA. Lastly, existing non-biological applications for synthetic DNA, including trophic tracing, product barcoding and environmental tracing, are reviewed. In Chapter 2, the concept of storing information in objects through synthetic DNA, called DNA-of-Things (DoT), is established. Specifically, the workflow of DoT, including encoding information in DNA, DNA synthesis and encapsulation, mixing DNA particles with raw materials, processing and extraction, is presented in detail. The results of producing multiple generations of products based on a parent generation through DoT are discussed. In addition, DoT is also established as a method to hide information in objects by creating for example transparent glasses containing information in form of DNA without changing the properties of the glass. Chapter 3 discusses a new DNA encapsulation strategy, using dithiol functionalized silicates, to provide stability to DNA in storage conditions except for reducing environments such as anoxic composting. Adding this functionality would allow the end user a safe disposal of data stored in encapsulated DNA. The core particle synthesis is first presented along with degradation data in reducing environments. The subsequent particle functionalization to adsorb DNA on the core particles in addition to the final encapsulating layer from the same material as the core particle, are presented. Finally, the encapsulated DNA is subjected to accelerated aging conditions at 60°C to compare it with state-of-the art silica encapsulation and free DNA stability. To further understand the biodegradability of the new particle platform, a test for measuring plastic degradation in anoxic compost environment is adapted to testing DNA stability in either encapsulated or free form. The environmental impact of tracing with silica particles with encapsulated DNA is discussed in Chapter 4. Firstly, a realistic tracing scenario is established based on previous DNA tracing campaigns. Secondly, ecotoxicological tests on dissolved DNA and silica particles with different sizes are presented to establish an understanding of toxicity for each material separately. Thirdly, the tracing material is characterized and the results from acute and chronic ecotoxicity assays are reported. Finally, the results are contextualized to establish the risk portfolio of carrying out large scale tracer experiments with the tested material. In Chapter 5, the previous chapters and main findings are reviewed and concluded. To put this thesis in perspective, ongoing research and an outlook on the future of DNA data storage is presented. Finally, the remaining challenges on each project are discussed.