Coding schemes for secure and reliable DNA-based data storage

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MTech (Res); 2023; Electrical communication engineering

In DNA-based data storage, the desired information is encoded into the quaternary sequence of synthetic DNA molecules, called oligos. We look at secure communication via information-containing oligos in the usual three-party setting, where Alice and Bob are legitimate communicators and Eve is an eavesdropper. Our scheme for secure DNAbased communication is two-fold: First, we store secret data in synthetic DNA molecules in a properly designed oligo pool of suitably high dilution. The oligo pool comprises information-containing oligos mixed with background genomic DNA cleaved into strands of the same length as the useful oligos. Designing oligos for storing the secret data involves the design of a library of primer pairs and a code book specific to this set of primers, that satisfy constraints on homopolymer run length, GC content, primerprimer dissimilarity, and primer-sequence dissimilarity. The differential knowledge of the designed primer pairs allows Bob to retrieve most of the information-containing DNA molecules after carrying out sufficient rounds of PCR amplification on the diluted oligo pool.