Correction to: Recent progress in DNA data storage based on high-throughput DNA synthesis (Biomedical Engineering Letters, (2024), 14, 5, (993-1009), 10.1007/s13534-024-00386-z)

Seokwoo Jo, Haewon Shin, Sung Yune Joe, David Baek, Chaewon Park, Honggu Chun

Research output: Contribution to journalComment/debatepeer-review

Abstract

In this article, few errors are identified in the text and figure captions. The details are given below. In Introduction section, the text ‘Ref’ should be removed at the end of sentence and the correct sentence should read as ‘Conventional storage methods relying on optical (e.g., CD, DVD, Blu-ray), magnetic (e.g., hard disk drives), and semiconductor (e.g., solid-state drives) media for binary data representation, have reached their data density limits [2].’ Under the Sect. 2.3 Preservation, the text ‘Ref’ should be removed at the end of sentence and the corrected text should read as 'The DNA capsule is designed to provide protection through a physical barrier (Fig. 5a) [76].’ The captions of Figs. 2 and 3, the words ‘(Figure revision)’ should be removed from the end. The correct figure captions are given below. Fig. 2 Comparison between solid state memory (e.g., flash memory) and DNA memory. Solid state memory records data within physically fixed addresses. By contrast, DNA memory encodes address information in the sequence of DNA strands. In the sequencing and decoding steps, DNA strands also necessitate sequencing adapter and error correction sequences. Fig. 3 Phosphoramidite chemistry-based oligonucleotide synthesis consists of five steps: deprotection, coupling, capping, oxidation, and cleavage. Red: A dimethoxytrityl (DMT) group (protection group). Green: A diisopropylamino group. Blue: A 2-cyanoethyl group. In the original publication, the figures were published in low resolution. The high-resolution images are given below. (Figure presented.) (Figure presented.) (Figure presented.) (Figure presented.) (Figure presented.) (Figure presented.) (Figure presented.) (Figure presented.) (Figure presented.) (Figure presented.) (Figure presented.) DNA data storage process consists of encoding, DNA synthesis, preservation, retrieval, DNA sequencing, and decoding Comparison between solid state memory (e.g., flash memory) and DNA memory. Solid state memory records data within physically fixed addresses. By contrast, DNA memory encodes address information in the sequence of DNA strands. In the sequencing and decoding steps, DNA strands also necessitate sequencing adapter and error correction sequences Phosphoramidite chemistry-based oligonucleotide synthesis consists of five steps: deprotection, coupling, capping, oxidation, and cleavage. Red: A dimethoxytrityl (DMT) group (protection group). Green: A diisopropylamino group. Blue: A 2-cyanoethyl group Array-based oligonucleotide synthesis. a Photochemical method involves deprotecting the 5’-protected oligonucleotide through patterned illumination. b Electrochemical method employs an electrode array controlled by a CMOS active matrix to deprotect the 5’-protected oligonucleotide. c Inkjet printer method introduces the printing reagents containing the 5’-protected nucleoside for the elongation of the 5’-deprotected oligonucleotide DNA preservation methods for DNA data storage. a DNA capsule (SecuriGene Labs). This storage, which safeguards the stored DNA, offers protection against ultraviolet light, shock, and humidity. b Synthetic fossils. DNA is encapsulated within silica micro particles. c DNA micro-disks. DNA is immobilized onto QR code polymers, introducing addressable capacity. Reprinted with permission from [70] DNA retrieval methods for targeted sequence reading. a PCR-based method employing the high selectivity of primers and exponential amplification for target sequences. b Physical isolation method using fluorescence-activated sorting, which tags the fluorescence probe to the encapsulated DNA plasmid with the surface of silica particle Next-generation sequencing technologies. a Illumina employs identical DNA clusters through bridge amplification to boost the fluorescent signal during sequencing by synthesis. b Oxford Nanopore Technology allows DNA to pass through a nanopore, and the shape of each base generates a distinct ionic current. c Pacific Bioscience, Single Molecule Real-Time (SMRT) sequencing detects the fluorescence signal of a single molecule utilizing a Zero-Mode Waveguide. d Thermo Fisher Scientific’s Ion Torrent technology detects electrical signal through pH alterations when polymerase elongates the incoming nucleotides. Reproduced with permission from [95] In contrast to binary data, each base of nucleotides has the distinct signal distributions and spacing. a Nanopore sequencing signal distribution. b Illumina sequencing’s three different fluorescent signal measurement for A, G, T, and C detection The photochemical deprotection and coupling steps for oligonucleotide synthesis. (1) The 5’-end of oligonucleotide is blocked by a protecting group. (2) Patterned UV light deprotects the protecting group. (3) The deprotected oligonucleotide exposes the hydroxyl group. (4) Desired 5’-protected nucleoside (e.g., G) is introduced into the flow cell, initiating a coupling reaction with the hydroxyl group. (5) Repeat steps (2)–(4) with the other bases of nucleotides (e.g., T, C, and A) Error factors in array-based oligonucleotide synthesis methods. a Photochemical: the edge gradient of light exposure results in stochastic deprotection. b Electrochemical: acid diffusion contributes to crosstalk. c Inkjet printer: misalignment of each droplet leads to deletion error Patents addressing limitations in array-based oligonucleotide synthesis methods. a To confine the reaction area to the uniform illumination region, a self-aligned micropattern is implemented using a DMD through image reversal to block the edge of the feature in the photochemical method. b CustomArray utilizes electrochemical synthesis on a CMOS chip with a virtual flask to quench diffused protons.

Original languageEnglish
Pages (from-to)1147-1152
Number of pages6
JournalBiomedical Engineering Letters
Volume14
Issue number5
DOIs
Publication statusPublished - 2024 Sept

Bibliographical note

Publisher Copyright:
© Korean Society of Medical and Biological Engineering 2024.

ASJC Scopus subject areas

  • Biomedical Engineering

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