A Dynamic Sliding Window Encoding for Secured DNA Data Storage Compliant With Biological and Indexing Constraints

In this paper, we propose a novel dynamic sliding window encoding for storing encrypted data in a DNA form taking into account biological constraints (G-C content and homopolymers) and prohibited nucleotide motifs used for data indexing. Its originality is twofold. First, it stands on a new dynamic encoding (DE) which takes advantage of variable length DNA codewords to encode binary data and to avoid homopolymers longer than N bases. Second, DE is combined with a sliding window strategy to detect whether a prohibited motif is about to appear. In this case, our proposal will add a non-coding base to the sequence to prevent the encoding of this motif. Unlike existing schemes, its scaling for high values of N and of prohibited motifs is extremely simple. It is furthermore independent of the cryptosystem. We provide the theoretical information rate of our proposal for a given number of prohibited motifs and a maximum homopolymer length. In general, it offers much higher performances, particularly in terms of information rate, than existing schemes while controlling G-C content with an extremely high probability. Moreover, experiments conducted with a recent DNA storage chain simulator show that our proposal does not require more copies than other encoding strategies for the correct reading of DNA sequences.