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.

A Quaternary Code Correcting a Burst of at Most Two Deletion or Insertion Errors in DNA Storage

Due to the properties of DNA data storage, the errors that occur in DNA strands make error correction an important and challenging task. In this paper, a new code design of quaternary code suitable for DNA storage is proposed to correct at most two consecutive deletion or insertion errors. The decoding algorithms of the proposed codes are also presented when one and two deletion or insertion errors occur, and it is proved that the proposed code can correct at most two consecutive errors. Moreover, the lower and upper bounds on the cardinality of the proposed quaternary codes are also evaluated, then the redundancy of the proposed code is provided as roughly 2log48n.

On Models and Capacity Bounds for DNA-based Storage Channels

In recent years, DNA-based systems have become a promising medium for long-term data storage. There are two layers of errors in DNA-based storage systems. The first is the dropouts of the DNA strands, which has been characterized in the shuffling-sampling channel. The second is insertions, deletions, and substitutions of nucleotides in individual DNA molecules. In this paper, we describe a DNA noisy synchronization error channel to characterize the errors in individual DNA molecules. We derive non-trivial lower and upper capacity bounds of the DNA noisy synchronization error channel based on information theory. By cascading these two channels, we provide theoretical capacity limits of the DNA storage system. These results reaffirm that DNA is a reliable storage medium with high storage density potential.

On Models and Capacity Bounds for DNA-based Storage Channels

In recent years, DNA-based systems have become a promising medium for long-term data storage. There are two layers of errors in DNA-based storage systems. The first is the dropouts of the DNA strands, which has been characterized in the shuffling-sampling channel. The second is insertions, deletions, and substitutions of nucleotides in individual DNA molecules. In this paper, we describe a DNA noisy synchronization error channel to characterize the errors in individual DNA molecules. We derive non-trivial lower and upper capacity bounds of the DNA noisy synchronization error channel based on information theory. By cascading these two channels, we provide theoretical capacity limits of the DNA storage system. These results reaffirm that DNA is a reliable storage medium with high storage density potential.

UV-Vis Spectrophotometric Analysis of DNA Retrieval for DNA Storage Applications

Informational Deoxyribonucleic Acid (iDNA) has gained the attention of many researchers and pioneer companies for the development of novel storage systems for the long-term and high-density storing of information. This research focuses on the physical storage of iDNA strands to address some of the current challenges by evaluating the accuracy of the process of iDNA retrieval from the surface after the dehydration process. For this aim, a UV-Vis spectrophotometric technique was used to measure the concentration of the DNA samples. Although spectroscopy has been widely employed for the evaluation of DNA concentration and contamination in a solution, it has not been used to investigate dry-state DNA, which is one of the preferred storage formats for the long-term retention of information. These results demonstrate that the UV-Vis spectrophotometric technique can be used to accurately measure dry-state DNA before the retrieval and its residues after the DNA retrieval process. This paper further examines the storage/retrieval process by investigating the relationship between the storage time and the amount of retrieved DNA or the DNA residue left on various surfaces. Based on the experimental results demonstrated and discussed in this paper, UV-Vis spectrophotometry can be used for monitoring dry-state DNA with a high accuracy larger than 98%. Moreover, these results reveal that the hydrophilicity and hydrophobicity of the surface do not significantly affect DNA retrieval over a one-month time period.

Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing

The storage of data in DNA typically involves encoding and synthesizing data into short oligonucleotides, followed by reading with a sequencing instrument. Major challenges include the molecular consumption of synthesized DNA, issues with basecalling errors, and limitations with scaling up read access operations for individual data elements. Addressing these challenges, we describe a DNA storage system called MDRAM (Magnetic DNA-based Random Access Memory) that enables repetitive and efficient readouts of targeted files with nanopore-based sequencing. Through conjugation of synthesized DNA to magnetic beads, we enabled repeated readouts of data while preserving the original DNA analyte and maintaining data readout quality. MDRAM also utilizes an efficient convolutional coding scheme that leverages soft information in raw nanopore sequencing signals to achieve information reading costs comparable to Illumina sequencing despite substantially higher error rates. Finally, we demonstrate a proof-of-concept DNA-based proto-filesystem that enables an exponentially-scalable data address space using only small numbers of targeting primers for assembly and readout.

A self-contained and self-explanatory DNA storage system

Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention. Consequently, the current DNA storage systems are often not self-contained, implying that they have to resort to external tools for the restoration of the stored DNA data. This may result in high risks in data loss since the required tools might not be available due to the high uncertainty in far future. To address this issue, we propose in this paper a self-contained DNA storage system that can bring self-explanatory to its stored data without relying on any external tool. To this end, we design a specific DNA file format whereby a separate storage scheme is developed to reduce the data redundancy while an effective indexing is designed for random read operations to the stored data file. We verified through experimental data that the proposed self-contained and self-explanatory method can not only get rid of the reliance on external tools for data restoration but also minimise the data redundancy brought about when the amount of data to be stored reaches a certain scale.

Effect of Hydrated Deep Eutectic Solvents on the Thermal Stability of DNA

DNA’s structure stability in hydrated deep eutectic solvents (DESs) is getting growing attention for emerging bio-applications. The employment of DESs as novel co-solvents in water media could favor eco-friendly and biodegradable materials for DNA storage and handling. Understanding the molecular interactions between nucleic acids and aqueous DES is crucial for developing new-generation solvents for biomolecules. In this work, we exploit the molecular sensitivity and selectivity of synchrotron radiation UV resonance raman (SR-UVRR) spectroscopy to explore the interplay between a choline chloride:urea (ChCl:U) DES and double-stranded DNA. Our study analyzes the impact of ChCl:U on the DNA’s thermal unfolding pathway by focusing on the guanine nucleobases whose Raman signal could be strongly enhanced through careful tuning of the excitation wavelength.