VL-DNA: Enhance DNA Storage Capacity with Variable Payload/Strand Lengths

Deoxyribonucleic Acid (DNA) storage is promising to be an ultimate data storage solution with ultra-high storage density and long durability. A DNA storage system encodes and stores digital data with synthetic DNA sequences, and decodes DNA sequences back to digital data via DNA sequencing. Using primers and polymerase chain reaction (PCR) based random access has also been introduced to DNA storage for efficient data retrieval. However, a DNA storage system equipped with PCR-based random access suffers from primer-payload collisions. Primers with this type of collisions cannot be reliably used and must be discarded. Since the numer of usable primers determines the DNA tube capacity, it is critical to reduce the impact of primer-payload collisions and increase the tube capacity. In this paper, we propose to use variable length payloads to recover primers from collisions and enhance DNA storage capacity. With the proposed heuristic algorithms and four payload lengths, the scheme can recover thousands of collided primers with three state-of-the-art encoding schemes. For an existing collision resistant encoding scheme, Rotation code, it can further improve 18.27% of tube capacity, from 217.59 GB to 257.35 GB. For the other two encoding schemes, the improvements of tube capacity are 4.3X and 18,3X. respectively.