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A core-shell strategy was developed to protect synthetic DNA in organosilica particles encompassing dithiol linkages allowing for a DNA loading of 1.1 wt %. DNA stability tests involving bleach as an oxidant showed that following the procedure DNA was sandwiched between core particles of ca. 450 nm size and a protective outer layer, separating the DNA from the environment. Rapid aging tests at 60 °C and 50% relative humidity revealed that the DNA protected within this material was significantly more stable than nonprotected DNA, with an expected ambient temperature half-life of over 60 years. Still, and due to the presence of the dithiol linkages in the backbone of the organosilica material, the particles degraded in the presence of reducing agents (TCEP and glutathione) and disintegrated within several days in a simulated compost environment, which was employed to test the biodegradability of the material. This is in contrast to DNA encapsulated following state of the art procedures in pure SiO

The resilience of ancient DNA (aDNA) in bone gives rise to the preservation of synthetic DNA with bioinorganic materials such as calcium phosphate (CaP). Accelerated aging experiments at elevated temperature and humidity displayed a positive effect of co-precipitated, crystalline dicalcium phosphate on the stability of synthetic DNA in contrast to amorphous CaP. Quantitative PXRD in combination with SEM and EDX measurements revealed distinct CaP phase transformations of calcium phosphate dihydrate (brushite) to anhydrous dicalcium phosphate (monetite) influencing DNA stability., Chemical Communications, 58 (19), ISSN:1359-7345, ISSN:1364-548X

Synthetic DNA has been proposed as a storage medium for digital information due to its high theoretical storage density and anticipated long storage horizons. However, under all ambient storage conditions, DNA undergoes a slow chemical decay process resulting in nicked (broken) DNA strands, and the information stored in these strands is no longer readable. In this work we design an enzymatic repair procedure, which is applicable to the DNA pool prior to readout and can partially reverse the damage. Through a chemical understanding of the decay process, an overhang at the 3' end of the damaged site is identified as obstructive to repair via the base excision-repair (BER) mechanism. The obstruction can be removed via the enzyme apurinic/apyrimidinic endonuclease I (APE1), thereby enabling repair of hydrolytically damaged DNA via Bst polymerase and Taq ligase. Simulations of damage and repair reveal the benefit of the enzymatic repair step for DNA data storage, especially when data is stored in DNA at high storage densities (=low physical redundancy) and for long time durations.

Using DNA as a durable, high-density storage medium with eternal format relevance can address a future data storage deficiency. The proposed storage format incorporates dehydrated particle spots on glass, at a theoretical capacity of more than 20 TB per spot, which can be efficiently retrieved without significant loss of DNA. The authors measure the rapid decay of dried DNA at room temperature and present the synthesis of encapsulated DNA in silica nanoparticles as a possible solution. In this form, the protected DNA can be readily applied to digital microfluidics (DMF) used to handle retrieval operations amenable to full automation. A storage architecture is demonstrated, which can increase the storage capacity of today's archival storage systems by more than three orders of magnitude: A DNA library containing 7373 unique sequences is encapsulated and stored under accelerated aging conditions (4 days at 70 °C, 50% RH) corresponding to 116 years at room temperature and the stored information is successfully recovered., Small, 18 (15), ISSN:1613-6810, ISSN:1613-6829

Synthetic DNA is a growing alternative to electronic-based technologies in fields such as data storage, product tagging, or signal processing. Its value lies in its characteristic attributes, namely Watson-Crick base pairing, array synthesis, sequencing, toehold displacement and polymerase chain reaction (PCR) capabilities. In this review, we provide an overview of the most prevalent applications of synthetic DNA that could shape the future of information technology. We emphasize the reasons why the biomolecule can be a valuable alternative for conventional electronic-based media, and give insights on where the DNA-analog technology stands with respect to its electronic counterparts., Nature Communications, 13, ISSN:2041-1723

Synthetic DNA has recently risen as a viable alternative for long‐term digital data storage. To ensure that information is safely recovered after storage, it is essential to appropriately preserve the physical DNA molecules encoding the data. While preservation of biological DNA has been studied previously, synthetic DNA differs in that it is typically much shorter in length, it has different sequence profiles with fewer, if any, repeats (or homopolymers), and it has different contaminants. In this paper, nine different methods used to preserve data files encoded in synthetic DNA are evaluated by accelerated aging of nearly 29 000 DNA sequences. In addition to a molecular count comparison, the DNA is also sequenced and analyzed after aging. These findings show that errors and erasures are stochastic and show no practical distribution difference between preservation methods. Finally, the physical density of these methods is compared and a stability versus density trade‐offs discussion provided.

Synthetic DNA has recently risen as a viable alternative for long-term digital data storage. To ensure that information is safely recovered after storage, it is essential to appropriately preserve the physical DNA molecules encoding the data. While preservation of biological DNA has been studied previously, synthetic DNA differs in that it is typically much shorter in length, it has different sequence profiles with fewer, if any, repeats (or homopolymers), and it has different contaminants. In this paper we evaluate nine different methods used to preserve data files encoded in synthetic DNA by accelerated aging of nearly 29,000 DNA sequences. In addition to a molecular count comparison, we also sequence and analyze the DNA after aging. Our findings show that errors and erasures are stochastic and show no practical distribution difference between preservation methods. Finally, we compare the physical density of these methods and provide a stability versus density trade-offs discussion.

Rapid aging tests (70 °C, 50% RH) of solid state DNA dried in the presence of various salt formulations, showed the strong stabilizing effect of calcium phosphate, calcium chloride and magnesium chloride, even at high DNA loadings (>20 wt%). A DNA-based digital information storage system utilizing the stabilizing effect of MgCl2 was tested by storing a DNA file, encoding 115 kB of digital data, and the successful readout of the file by sequencing after accelerated aging., Chemical Communications, 56 (25), ISSN:1359-7345, ISSN:1364-548X

Synthetic DNA has emerged as a novel substrate to encode computer data with the potential to be orders of magnitude denser than contemporary cutting edge techniques. However, even with the help of automated synthesis and sequencing devices, many intermediate steps still require expert laboratory technicians to execute. We have developed an automated end-to-end DNA data storage device to explore the challenges of automation within the constraints of this unique application. Our device encodes data into a DNA sequence, which is then written to a DNA oligonucleotide using a custom DNA synthesizer, pooled for liquid storage, and read using a nanopore sequencer and a novel, minimal preparation protocol. We demonstrate an automated 5-byte write, store, and read cycle with a modular design enabling expansion as new technology becomes available.

DNA promises to be a high density data storage medium, but physical storage poses a challenge. To store large amounts of data, pools must be physically isolated so they can share the same addressing scheme. We propose the storage of dehydrated DNA spots on glass as an approach for scalable DNA data storage. The dried spots can then be retrieved by a water droplet using a digital microfluidic device. Here we show that this storage schema works with varying spot organization, spotted masses of DNA, and droplet retrieval dwell times. In all cases, the majority of the DNA was retrieved and successfully sequenced. We demonstrate that the spots can be densely arranged on a microfluidic device without significant contamination of the retrieval. We also demonstrate that 1 TB of data could be stored in a single spot of DNA and successfully retrieved using this method., DNA as a high density storage medium is receiving increasing attention, but long term physical storage is an unsolved problem. Here the authors show that up to 1 TB of data stored as dehydrated DNA spots on a glass cartridge can be retrieved in a spot of water using digital microfluidics with minimal data loss and contamination.

200 MB of digital data is stored in DNA, randomly accessed and recovered using an error-free approach. Synthetic DNA is durable and can encode digital data with high density, making it an attractive medium for data storage. However, recovering stored data on a large-scale currently requires all the DNA in a pool to be sequenced, even if only a subset of the information needs to be extracted. Here, we encode and store 35 distinct files (over 200 MB of data), in more than 13 million DNA oligonucleotides, and show that we can recover each file individually and with no errors, using a random access approach. We design and validate a large library of primers that enable individual recovery of all files stored within the DNA. We also develop an algorithm that greatly reduces the sequencing read coverage required for error-free decoding by maximizing information from all sequence reads. These advances demonstrate a viable, large-scale system for DNA data storage and retrieval.

Current storage technologies can no longer keep pace with exponentially growing amounts of data. 1 Synthetic DNA offers an attractive alternative due to its potential information density of ~ 1018 B/mm3, 107 times denser than magnetic tape, and potential durability of thousands of years.2 Recent advances in DNA data storage have highlighted technical challenges, in particular, coding and random access, but have stored only modest amounts of data in synthetic DNA. 3,4,5 This paper demonstrates an end-to-end approach toward the viability of DNA data storage with large-scale random access. We encoded and stored 35 distinct files, totaling 200MB of data, in more than 13 million DNA oligonucleotides (about 2 billion nucleotides in total) and fully recovered the data with no bit errors, representing an advance of almost an order of magnitude compared to prior work. 6 Our data curation focused on technologically advanced data types and historical relevance, including the Universal Declaration of Human Rights in over 100 languages,7 a high-definition music video of the band OK Go,8 and a CropTrust database of the seeds stored in the Svalbard Global Seed Vault.9 We developed a random access methodology based on selective amplification, for which we designed and validated a large library of primers, and successfully retrieved arbitrarily chosen items from a subset of our pool containing 10.3 million DNA sequences. Moreover, we developed a novel coding scheme that dramatically reduces the physical redundancy (sequencing read coverage) required for error-free decoding to a median of 5x, while maintaining levels of logical redundancy comparable to the best prior codes. We further stress-tested our coding approach by successfully decoding a file using the more error-prone nanopore-based sequencing. We provide a detailed analysis of errors in the process of writing, storing, and reading data from synthetic DNA at a large scale, which helps characterize DNA as a storage medium and justify our coding approach. Thus, we have demonstrated a significant improvement in data volume, random access, and encoding/decoding schemes that contribute to a whole-system vision for DNA data storage.

In this paper the practical density of long‐term DNA storage is increased. Specifically, the DNA weight loading of silica sphere DNA storage is increased to 3.4 wt%, a ten‐fold increase compared to the previous state‐of‐the‐art. By applying a Layer‐by‐Layer (LbL) design with alternating layers of DNA and a polycationic molecule, namely polyethyleneimine (PEI), another dimension to DNA surface binding onto magnetic nanoparticles is added. A protective silica layer is grown on top of the multilayered nanoparticles to shield the DNA from external sources of damage. Accelerated aging experiments of the nanoparticles and the subsequent quantification of DNA stability via qPCR show a significantly lower degradation rate compared to unprotected DNA. The novel material is compared to previous DNA storage technologies, outperforming those in DNA storage density as well as stability. Finally, the storage of an 83 kB digital file in DNA through a successful readout of a 4991 oligonucleotide pool is demonstrated from particle encapsulation, through accelerated aging, to sequencing.