High-scale random access on DNA storage systems

Abstract

Due to the rapid cost decline of synthesizing and sequencing deoxyribonucleic acid (DNA), high information density, and its durability of up to centuries, utilizing DNA as an information storage medium has received the attention of many scientists. State-of-the-art DNA storage systems exploit the high capacity of DNA and enable random access (predominantly random reads) by primers, which serve as unique identifiers for directly accessing data. However, primers come with a significant limitation regarding the maximum available number per DNA library. The number of different primers within a library is typically very small (e.g. ≈10). We propose a method to overcome this deficiency and present a general-purpose technique for addressing and directly accessing thousands to potentially millions of different data objects within the same DNA pool. Our approach utilizes a fountain code, sophisticated probe design, and microarray technologies. A key component is locality-sensitive hashing, making checks for dissimilarity among such a large number of probes and data objects feasible.

DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage

“…We constrained the encoder output not to include homopolymers longer than three bp to be consistent for all codes to the fixed homopolymer length of the Grass code. We also used the common constraints of a GC content between 40 and 60% 6 , 7 , 21 , 22 in 10 bp intervals for all codes that support it. As an additional constraint for DNA-Aeon, it had to have the lowest total number of encoded bases of all codes evaluated.…”

“…Several other works in the literature provide solutions for challenges in the field of DNA data storage, e.g., image processing for DNA storage 13 , adaptation of the JPEG image coding algorithm for DNA data storage 14 , error correction codes using LDPC 15 or Polar codes 16 , random access solutions 6,17,18 , and constrained codes 19 .…”

Design considerations for advancing data storage with synthetic DNA for long-term archiving

“…To retrieve the data, different approaches based on DNA extraction or selective PCR amplification of the required synthetic DNA sample using a specific primer are often used during the retrieval process [ 24 ]. Other random access approaches based on microarray [ 37 ], immobilization of DNA molecules [ 38 ], digital microfluidic droplets [ 39 ], and DNA barcoded silica beads [ 40 ] have been explored to improve and enable random access.…”

DNAsmart: Multiple attribute ranking tool for DNA data storage systems

“…These aspects specifically target the capacity of the storage channel [12] , [13] and the design of error correction codes (ECC) [14] , [15] for the specific errors [16] that arise inside a DNA data storage system. Additionally, in the field of ECC development, efforts have been made to provide solutions for other areas of DNA data storage, for example, constrained coding for DNA data storage [17] , random access in DNA storage systems [18] and image storage solutions for DNA [19] , [20] . Although ECCs have different approaches to correct information loss, one, if not the most important characteristic of an ECC is the ability to successfully recover the input data from the channel output.…”