On Designing DNA Databases for the Storage and Retrieval of Digital Signals

In this paper we propose a procedure for the storage and retrieval of digital signals utilizing DNA. Digital signals are encoded in DNA sequences that satisfy among other constraints the Noise Tolerance Constraint (NTC) that we have previously introduced. NTC takes into account the presence of noise in digital signals by exploiting the annealing between non-perfect complementary sequences. We discuss various issues arising from the development of DNA-based database solutions (i) in vitro (in test tubes, or other materials) for short-term storage and (ii) in vivo (inside organisms) for long-term storage. We discuss the benefits and drawbacks of each scheme and its effects on the codeword design problem and performance. We also propose a new way of constructing the database elements such that a short-term database can be converted into a long term one and vice versa without the need for a re-synthesis. The latter improves efficiency and reduces the cost of a