Thanks to its high density and long durability, synthetic DNA has been widely considered as a promising solution to the data explosion problem. However, due to the large amount of random base insertion-deletion-substitution (IDSs) errors from sequencing, reliable data recovery remains a critical challenge, which hinders its large-scale application. Here, we propose a modulation-based DNA storage architecture. Experiments on simulation and real datasets demonstrate that it has two distinct advantages. First, modulation encoding provides a simple way to ensure the encoded DNA sequences comply with biological sequence constraints (i.e., GC balanced and no homopolymers); Second, modulation decoding is highly efficient and extremely robust for the detection of insertions and deletions, which can correct up to ~40% errors. These two advantages pave the way for future high-throughput and low-cost techniques, and will kickstart the actualization of a viable, large-scale system for DNA data storage.

Synchronization (insertions–deletions) errors are still a major challenge for reliable information retrieval in DNA storage. Unlike traditional error correction codes (ECC) that add redundancy in the stored information, multiple sequence alignment (MSA) solves this problem by searching the conserved subsequences. In this paper, we conduct a comprehensive simulation study on the error correction capability of a typical MSA algorithm, MAFFT. Our results reveal that its capability exhibits a phase transition when there are around 20% errors. Below this critical value, increasing sequencing depth can eventually allow it to approach complete recovery. Otherwise, its performance plateaus at some poor levels. Given a reasonable sequencing depth (≤ 70), MSA could achieve complete recovery in the low error regime, and effectively correct 90% of the errors in the medium error regime. In addition, MSA is robust to imperfect clustering. It could also be combined with other means such as ECC, repeated markers, or any other code constraints. Furthermore, by selecting an appropriate sequencing depth, this strategy could achieve an optimal trade-off between cost and reading speed. MSA could be a competitive alternative for future DNA storage.

Synthetic DNA has been widely considered an attractive medium for digital data storage. However, the random insertion−deletion−substitution (IDS) errors in the sequenced reads still remain a critical challenge to reliable data recovery. Motivated by the modulation technique in the communication field, we propose a new DNA storage architecture to solve this problem. The main idea is that all binary data are modulated into DNA sequences with the same AT/GC patterns, which facilitate the detection of indels in noisy reads. The modulation signal could not only satisfy the encoding constraints but also serve as prior information to detect the potential positions of errors. Experiments on simulation and real data sets demonstrate that modulation encoding provides a simple way to comply with biological constraints for sequence encoding (i.e., balanced GC content and avoiding homopolymers). Furthermore, modulation decoding is highly efficient and extremely robust, which can correct up to ∼40% of errors. In addition, it is robust to imperfect clustering reconstruction, which is very common in practice. Although our method has a relatively low logical density of 1.0 bits/nt, its high robustness may provide a wide space for developing low-cost synthetic technologies. We believe this new architecture may boost the early coming of large-scale DNA storage applications in the future.

Rapid development in synthetic technologies has boosted DNA as a potential medium for large-scale data storage. Meanwhile, how to implement data security in DNA storage system is still an unsolved problem. In this paper, we propose an image encryption method based on the modulation-based storage architecture. The key idea is to take advantage of the unpredictable modulation signals to encrypt image in highly error-prone DNA storage channel. Numerical results demonstrate that our image encryption method is feasible and effective with excellent security against various attacks (statistical, differential, noise and data loss, etc.). Compared with other methods by DNA molecules hybridization reaction, the proposed method is more reliable and feasible for large-scale applications.

No abstract