Oligo-Snoop: A Non-Invasive Side Channel Attack Against DNA Synthesis Machines

Synthetic biology is developing into a promising science and engineering field. One of the enabling technologies for this field is the DNA synthesizer. It allows researchers to custom-build sequences of oligonucleotides (short DNA strands) using the nucleobases: Adenine (A), Guanine (G), Cytosine (C), and Thymine (T). Incorporating these sequences into organisms can result in improved disease resistance and lifespan for plants, animals, and humans. Hence, many laboratories spend large amounts of capital researching and developing unique sequences of oligonucleotides. However, these DNA synthesizers are fully automated systems with cyber-domain processes and physical domain components. Hence, they may be prone to security breaches like any other computing system. In our work, we present a novel acoustic side-channel attack methodology which can be used on DNA synthesizers to breach their confidentiality and steal valuable oligonucleotide sequences. Our proposed attack methodology achieves an average accuracy of 88.07% in predicting each base and is able to reconstruct short sequences with 100% accuracy by making less than 21 guesses out of 4 possibilities. We evaluate our attack against the effects of the microphone’s distance from the DNA synthesizer and show that our attack methodology can achieve over 80% accuracy when the microphone is placed as far as 0.7 meters from the DNA synthesizer despite the presence of common room noise. In addition, we reconstruct DNA sequences to show how effectively an attacker with biomedical-domain knowledge would be able to derive the intended functionality of the sequence using the proposed attack methodology. To the best of our knowledge, this is the first methodology that highlights the possibility of such an attack on systems used to synthesize DNA molecules.