DP-DNA: A Digital Pattern-Aware DNA Encoding Scheme to Improve Encoding Density of DNA Storage

With the rapid increase of available digital data, Deoxyribonucleic Acid (DNA) storage is identified as such a promising candidate due to its long persistency and high areal density, especially for archival storage systems. However, due to biochemical constraints, currently the encoding densities of various DNA storage systems are much less than this upper bound. In this paper, we propose a new Digital Pattern-aware DNA encoding scheme, called DP-DNA, which satisfies the DNA biochemical constraints and efficiently stores digital data in DNA storage with high encoding density. To satisfy the biochemical constraints, our proposed scheme is based on several rotation codes. DP-DNA first analyzes the patterns of each short binary sequence, which will be encoded to a DNA strand, and then selects an appropriate code for encoding the target binary sequence to achieve a high encoding density. An additional encoding field is added to the DNA encoding format, which can distinguish the encoding scheme used for each DNA strand, and thus we can decode DNA data back to its original digital data. Moreover, a new 2bit-code with the highest encoding density (i.e., 2bits/nt) is proposed to add to the pool of code candidates to further increase the encoding density. In addition, a variable-length scheme is applied to increase the feasibility of using 2bit-code scheme. Finally, the experimental results indicate that the proposed DP-DNA achieves 5.9% - 103.5% higher encoding density than the existing encoding schemes with various datasets.