Mobile and Self-Sustained Data Storage in an Extremophile Genomic DNA

DNA storage: The future direction for medical cold data storage

DNA storage, characterized by its durability, data density, and cost-effectiveness, is a promising solution for managing the increasing data volumes in healthcare. This review explores state-of-the-art DNA storage technologies, and provides insights into designing a DNA storage system tailored for medical cold data. We anticipate that a practical approach for medical cold data storage will involve establishing regional, in vitro DNA storage centers that can serve multiple hospitals. The immediacy of DNA storage for medical data hinges on the development of novel, high-density, specialized coding methods. Established commercial techniques, such as DNA chemical synthesis and next-generation sequencing (NGS), along with mixed drying with alkaline salts and refined Polymerase Chain Reaction (PCR), potentially represent the optimal options for data writing, reading, storage, and accessing, respectively. Data security could be promised by the integration of traditional digital encryption and DNA steganography. Although breakthrough developments like artificial nucleotides and DNA nanostructures show potential, they remain in the laboratory research phase. In conclusion, DNA storage is a viable preservation strategy for medical cold data in the near future.

Engineered Living Memory Microspheroid-Based Archival File System for Random Accessible In Vivo DNA Storage

Given its exceptional durability and high information density, deoxyribonucleic acid (DNA) has the potential to meet the escalating global demand for data storage if it can be stored efficiently and accessed randomly in exabyte-to-yottabyte-scale databases. Here, this work introduces the Engineered Living Memory Microspheroid (ELMM) as a novel material for DNA data storage, retrieval, and management. This work engineers a plasmid library and devises a random access strategy pairing plasmid function with DNA data in a key-value format. Each DNA segment is integrated with its corresponding plasmid, introduced into bacteria, and encapsulated within matrix material via droplet microfluidics within 5 min. ELMMs can be stored at room temperature following lyophilization and, upon rehydration, each type of ELMM exhibits specific functions expressed by the plasmids, allowing for physical differentiation based on these characteristics. This work demonstrates fluorescent expression as the plasmid function and employs fluorescence-based sorting access image files in a prototype database. By utilizing N optical channels, to retrieve 2N file types, each with a minimum of 10 copies. ELMM offers a digital-to-biological information solution, ensuring the preservation, access, replication, and management of files within large-scale DNA databases.

Pragmatic soft-decision data readout of encoded large DNA

The encoded large DNA can be cloned and stored in vivo, capable of write-once and stable replication for multiple retrievals, offering potential in economic data archiving. Nanopore sequencing is advantageous in data access of large DNA due to its rapidity and long-read sequencing capability. However, the data readout is commonly limited by insertion and deletion (indel) errors and sequence assembly complexity. Here, a pragmatic soft-decision data readout is presented, achieving assembly-free sequence reconstruction, indel error correction, and ultra-low coverage data readout. Specifically, the watermark is cleverly embedded within large DNA fragments, allowing for the direct localization of raw reads via watermark alignment to avoid complex read assembly. A soft-decision forward-backward algorithm is proposed, which can identify indel errors and provide probability information to the error correction code, enabling error-free data recovery. Additionally, a minimum state transition is maintained, and a read segmentation is incorporated to achieve fast information reading. The readout assays for two circular plasmids (~51 kb) with different coding rates were demonstrated and achieved error-free recovery directly from noisy reads (error rate ~1%) at coverage of 1-4×. Simulations conducted on large-scale datasets across various error rates further confirm the scalability of the method and its robust performance under extreme conditions. This readout method enables nearly single-molecule recovery of large DNA, particularly suitable for rapid readout of DNA storage.

Enzymes as green and sustainable tools for DNA data storage

DNA is considered as an ideal supramolecular material for information storage with high storage density and long-term stability. Enzymes, as green and sustainable tools, offer several unique advantages for DNA-based information storage. These advantages include low cost and reduced generation of hazardous wastes during DNA synthesis, as well as the improvements in data reading speed and data recovery accuracy. Moreover, enzymes could achieve scalable data steganography. In this review, we introduced the exciting application strategies of enzymatic tools in each step of DNA information storage (writing, storing, retrieval and reading). We further address the challenges and opportunities associated with enzymatic tools for DNA information storage, aiming at developing new techniques to overcome these obstacles.

The zettabyte era is in our DNA

This Perspective surveys the critical computational challenges associated with in vitro DNA-based data storage. As digital data expand exponentially, traditional storage media are becoming less viable, making DNA a promising solution due to its density and durability. However, numerous obstacles remain, including error correction, data retrieval from large volumes of noisy reads, and scalability. The Perspective also highlights challenges for DNA-based data centers, such as fault tolerance, random access, and data removal, which must be addressed to make DNA-based storage practical.

Composite Hedges Nanopores codec system for rapid and portable DNA data readout with high INDEL-Correction

Reading digital information from highly dense but lightweight DNA medium nowadays relies on time-consuming next-generation sequencing. Nanopore sequencing holds the promise to overcome the efficiency problem, but high indel error rates lead to the requirement of large amount of high quality data for accurate readout. Here we introduce Composite Hedges Nanopores, capable of handling indel rates up to 15.9% and substitution rates up to 7.8%. The overall information density can be doubled from 0.59 to 1.17 by utilizing a degenerated eight-letter alphabet. We demonstrate that sequencing times of 20 and 120 minutes are sufficient for processing representative text and image files, respectively. Moreover, to achieve complete data recovery, it is estimated that text and image data require 4× and 8× physical redundancy of composite strands, respectively. Our codec system excels on both molecular design and equalized dictionary usage, laying a solid foundation approaching to real-time DNA data retrieval and encoding.

Flow Cytometry Sorting for Random Access in DNA Data Storage: Encapsulation for Enhanced Stability and Sequence Integrity of DNA

As digital data undergo explosive growth, deoxyribonucleic acid (DNA) has emerged as a promising storage medium due to its high density, longevity, and ease of replication, offering vast potential in data storage solutions. This study focuses on the protection and retrieval of data during the DNA storage process, developing a technique that employs flow cytometry sorting (FCS) to segregate multicolored fluorescent DNA microparticles encoded with data and facilitating efficient random access. Moreover, the encapsulated fluorescent DNA microparticles, formed through layer-by-layer self-assembly, preserve structural and sequence integrity even under harsh conditions while also supporting a high-density DNA payload. Experimental results have shown that the encoded data can still be successfully recovered from encapsulated DNA microparticles following de-encapsulation. We also successfully demonstrated the automated encapsulation process of fluorescent DNA microparticles using a microfluidic chip. This research provides an innovative approach to the long-term stability and random readability of DNA data storage.

High-throughput DNA synthesis for data storage

With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized.

"Cell Disk" DNA Storage System Capable of Random Reading and Rewriting

DNA has emerged as an appealing material for information storage due to its great storage density and durability. Random reading and rewriting are essential tasks for practical large-scale data storage. However, they are currently difficult to implement simultaneously in a single DNA-based storage system, strongly limiting their practicability. Here, a "Cell Disk" storage system is presented, achieving high-density in vivo DNA data storage that enables both random reading and rewriting. In this system, each yeast cell is used as a chamber to store information, similar to a "disk block" but with the ability to self-replicate. Specifically, each genome of yeast cell has a customized CRISPR/Cas9-based "lock-and-key" module inserted, which allows selective retrieval, erasure, or rewriting of the targeted cell "block" from a pool of cells ("disk"). Additionally, a codec algorithm with lossless compression ability is developed to improve the information density of each cell "block". As a proof of concept, target-specific reading and rewriting of the compressed data from a mimic cell "disk" comprising up to 105 "blocks" are demonstrated and achieve high specificity and reliability. The "Cell Disk" system described here concurrently supports random reading and rewriting, and it should have great scalability for practical data storage use.

Highly Accurate Sequence- and Position-Independent Error Profiling of DNA Synthesis and Sequencing

A comprehensive error analysis of DNA-stored data during processing, such as DNA synthesis and sequencing, is crucial for reliable DNA data storage. Both synthesis and sequencing errors depend on the sequence and the transition of bases of nucleotides; ignoring either one of the error sources leads to technical challenges in minimizing the error rate. Here, we present a methodology and toolkit that utilizes an oligonucleotide library generated from a 10-base-shifted sequence array, which is individually labeled with unique molecular identifiers, to delineate and profile DNA synthesis and sequencing errors simultaneously. This methodology enables position- and sequence-independent error profiling of both DNA synthesis and sequencing. Using this toolkit, we report base transitional errors in both synthesis and sequencing in general DNA data storage as well as degenerate-base-augmented DNA data storage. The methodology and data presented will contribute to the development of DNA sequence designs with minimal error.