Robust Storage of Chinese Language in a Pool of Small Single-Stranded DNA Rings and Its Facile Reading-Out

Abstract

Archival storage in DNA is one of the most challenging themes in rapidly growing information technology. In addition, its practical applications are more difficult due to complicated data analysis, instability of long and linear DNA strands (>1000 nt), and other factors. In the present study, we have developed a simple and eminent DNA-based storage system in which small DNA rings are employed as memory units. Compared with previous approaches, this methodology has advantages of robustness, low cost, convenience and so on. In high density, Chinese language was directly stored in a pool of 76-nt-long single-stranded DNA rings (designated as “Info-Store”), in which each ring memorized the index number and five Chinese characters (or marks). During “Read-Out”, all the ssDNA rings in the pool were simultaneously amplified by hyper-branched rolling cycle amplification (HRCA), and their sequences were accurately determined by a portable MinION sequencer aided by a personal computer. Then, the original Chinese text was precisely and smoothly decoded by simple data analysis.

Unexpected Mechanism and Inhibition Effect for Nonspecific Amplification Involving Dynamic Binding of Primers with Background DNA

“…The reads with repetitive sequences of these primers are selected. If a read is long enough (repeating more than 15 times), the sequence can be determined simply by the most frequent occurrence principle, as described in our previous report . If one read is not long enough, two or several reads are selected so that the total repetitions are more than 15, and the obtained sequence has an accuracy higher than 99%.…”

“…The difficulty comes from the fact that these products are mixtures of various sequences, whose accurate and relatively comprehensive sequence analysis is laborious in the presence of large amounts of bgDNA. For Sanger sequencing, it is complicated and does not yield complete sequences of the products. , For next-generation sequencing (NGS) and nanopore sequencing (Oxford Nanopore), these byproducts are usually too short. , Several efforts have been made to sequence short double-stranded DNA (dsDNA) using nanopore sequencing. − In our previous work, for example, the mixture of long repetitive products obtained by RCA from various short single-stranded DNA (ssDNA) circles was successfully sequenced . The key contribution of this research is that precise sequences can be analyzed from single reads without interfering with other reads when the repetitive times are enough (e.g., >15).…”

“…30−32 In our previous work, for example, the mixture of long repetitive products obtained by RCA from various short single-stranded DNA (ssDNA) circles was successfully sequenced. 33 The key contribution of this research is that precise sequences can be analyzed from single reads without interfering with other reads when the repetitive times are enough (e.g., >15). Here, inspired by this, we developed a novel approach to convert nonspecific PCR products into long tandem repeats, which can be easily sequenced using nanopore sequencing.…”

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

“…Additionally, another of the most interesting applications of genome sequencing is personalized medicine, like sequencing single gametes [44,45]. Nucleic acids can also be used to store any kind of information in a compact and efficient way which can be retrieved by sequencing and decoding [46].…”

DNA sequencing: an overview of solid-state and biological nanopore-based methods

“…Artificial intelligence, machine learning, and similar fields have been developed (Chachar et al 2021;Jovčevska 2020). The importance of nucleic acid data is listed as several examples below: sequencing of nucleic acid technologies is the vaccine design to treat COVID-19 disease (Wang et al 2021); the Human Genome Project (HGP) paved the way for whole-genome sequencing (Wang et al 2021); nucleic acids could be utilized as well to put in store any sort of data in a dense and efficacious manner that could be recovered and decoded by sequencing (Wang et al 2021); functional genomics used in diverse arenas such as medicine and agronomy; and could be inspection of disease resistance or abiotic and biotic stresses in animals and plants with impressive consequences in health programs (Jha et al 2021). This is so vital in disease diagnostics and clinical treatments (Caspar et al 2021).…”