VL-DNA: Enhance DNA Storage Capacity with Variable Payload (Strand) Lengths (2403.14204v1)

Abstract: DNA storage is a promising archival data storage solution to today's big data problem. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. For efficient target data retrieving, existing Polymerase Chain Reaction PCR based DNA storage systems apply primers as specific identifier to tag different set of DNA strands. However, the PCR based DNA storage system suffers from primer-payload collisions, causing a significant reduction of storage capacity. This paper proposes using variable strand length, which takes advantage of the inherent payload-cutting process, to split collisions and recover primers. The executing time of our scheme is linear to the number of primer-payload collisions. The scheme serves as a post-processing method to any DNA encoding scheme. The evaluation of three state-of-the-art encoding schemes shows that the scheme can recover thousands of usable primers and improve tube capacity ranging from 18.27% to 19x.