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 to store encrypted data in DNA form, taking into account biological constraints (G-C content and homopolymers) and prohibited nucleotide motifs used for data indexing. The originality of our approach is twofold. First, it is based on a new dynamic encoding (DE) which takes advantage of variable-length DNA codewords to encode binary data while avoiding 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 such cases, our method inserts a non-coding base into the sequence to prevent the encoding of the motif. Unlike existing schemes, our approach scales extremely easily for high values of homopolymers and of prohibited motifs. 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 significantly higher performances, particularly in terms of information rate, than existing schemes while maintaining G-C content within the desired range with extremely high probability. Moreover, experiments conducted with a recent DNA storage chain simulator show that our method requires a similar amount of sequence copies as other encoding strategies for error-free DNA sequence recovery.