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Cyrus Clarke
RA: MIT Media Lab, Tangible Media Group
As DNA data storage evolves as a dense and durable medium for digital information, most systems still rely on expensive sequencing for data retrieval, limiting accessibility and interaction. This project proposes an alternative interface: a molecular system that detects RNA-encoded digital messages and expresses them as scent. By translating digital memory into a tangible, sensory experience, it offers a new paradigm for interacting with molecular data.
The system comprises a genetic circuit delivered via plasmid into E. coli, consisting of (1) a synthetic RNA message encoding “Smello World,” (2) a toehold switch that detects this message, and (3) a downstream scent-producing gene (ATF1). When the specific RNA message is present, the toehold switch unfolds to permit ATF1 translation, producing isoamyl acetate (banana scent) detectable by humans.
This initial proof-of-concept combines DNA synthesis, Gibson Assembly, and microbial expression to demonstrate an expressive mode of biological data sensing. Future iterations will explore a cell-free version, enabling portable, biosafe biosensors for applications in data authentication, biosecurity, and human-computer interaction.
DNA data storage has emerged as a powerful archival medium, capable of encoding vast amounts of digital information in compact, stable molecular form (Ceze et al., 2019). However, existing systems typically require expensive sequencing technologies to retrieve stored data, limiting their accessibility and interactivity (Doricchi et al., 2022).
Recent advances in synthetic biology and cell-free systems suggest new possibilities for molecular computation and biosensing, where molecular information can be detected and interpreted without sequencing (Pardee et al., 2016). Making such systems programmable and logic based is also possible using programmable circuits like toehold switches (Huang et al., 2018). While these technologies have primarily focused on diagnostics, little work has explored their use for more expressive, consumer-facing applications.
This project addresses that gap by creating a programmable system that detects RNA-encoded digital messages and translates them into expressive outputs, offering a novel, embodied mode of interaction with molecular information.
