DNA Assembly for Nanopore Data Storage Readout

The digital revolution has led to the explosive growth of electronic data, and a large amount of data needs to be stored. With the development of life science, synthetic DNA sequences have been listed as storage media with research prospects and application value. The technology of high-throughput synthesis of DNA and sequencing of DNA sequences has also developed rapidly in recent years. Commercial nanopore sequencing is more portable, inexpensive, and automated than Illumina’s sequencing by synthesis (SBS), but nanopore sequencing itself also has some problems, such as higher error rate and lower sequencing throughput than SBS.

This paper reports a method that combines random access, DNA assembly, and nanopore sequencing to decode the information stored in DNA. Multiple digital files were mapped into 150 nucleotide DNA sequences and synthesized. Gibson assembly and Overlap-Extension PCR (OE-PCR) successfully decoded 1.67MB of digital information stored in DNA. Nanopore sequencing can estimate the decoding coverage of digital files stored in DNA in real time. Four different DNA coding files were amplified, assembled, and sequenced using the ONT MinION platform. An assembly of 6, 10, or 24 fragments were built for each file. By storing 1.67 megabytes of digital information in 111,499 oligonucleotides, the ability of sequencing and decoding has been improved by two orders of magnitude, and a faster and more flexible DNA storage scheme has been developed.

Fig.1 Overview of the DNA data storage workflow

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Randolph Lopez, Yuan-Jyue Chen, et al. DNA assembly for nanopore data storage readout. Nat Commun. 2019; 10: 2933.