Cited by 164DNA and Biological ComputingAlgorithms and Data CompressionAdvanced Data Storage Technologies

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Reading and writing digital data in DNA

Meiser, Linda C., Antkowiak, Philipp L., Koch, Julian, Chen, Weida D., Kohll, A. Xavier, Stark, Wendelin J., Heckel, Reinhard, Grass, Robert N.·2020·Nature Protocols

DOI 10.1038/s41596-019-0244-5

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Abstract

Because of its longevity and enormous information density, DNA is considered a promising data storage medium. In this work, we provide instructions for archiving digital information in the form of DNA and for subsequently retrieving it from the DNA. In principle, information can be represented in DNA by simply mapping the digital information to DNA and synthesizing it. However, imperfections in synthesis, sequencing, storage and handling of the DNA induce errors within the molecules, making error-free information storage challenging. The procedure discussed here enables error-free storage by protecting the information using error-correcting codes. Specifically, in this protocol, we provide the technical details and precise instructions for translating digital information to DNA sequences, physically handling the biomolecules, storing them and subsequently re-obtaining the information by sequencing the DNA. Along with the protocol, we provide computer code that automatically encodes digital information to DNA sequences and decodes the information back from DNA to a digital file. The required software is provided on a Github repository. The protocol relies on commercial DNA synthesis and DNA sequencing via Illumina dye sequencing, and requires 1-2 h of preparation time, 1/2 d for sequencing preparation and 2-4 h for data analysis. This protocol focuses on storage scales of ~100 kB to 15 MB, offering an ideal starting point for small experiments. It can be augmented to enable higher data volumes and random access to the data and also allows for future sequencing and synthesis technologies, by changing the parameters of the encoder/decoder to account for the corresponding error rates.

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Authors: Meiser, L. C., Antkowiak, P. L., Koch, J., Chen, W. D., Kohll, A. X., Stark, W. J., Heckel, R., & Grass, R. N.
Affiliations: ETH Zurich (CH)
Rice University (US)
Corresponding author: Heckel, Reinhard
Grass, Robert N.
ORCID: Antkowiak, Philipp L.
Koch, Julian
Stark, Wendelin J.
Heckel, Reinhard
Grass, Robert N.
Venue: Nature Protocols
Publisher: Springer Science and Business Media LLC
Published: 2019-11-29
Volume: 15
Issue: 1
Pages: 86-101
ISSN: 1750-2799 (ISSN-L)
1754-2189
DOI: 10.1038/s41596-019-0244-5
OpenAlex: W2989744057
Cited by: 164
References: 42
Citations by year: 2026: 19 · 2025: 35 · 2024: 29 · 2023: 28 · 2022: 19 · 2021: 25 · 2020: 9
FWCI: 4.38
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature Protocols (publishedVersion)
PubMed (publishedVersion)
mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion)
Topics: Physical Sciences › Mathematics › Theoretical Computer Science › DNA and Biological Computing
Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
Physical Sciences › Computer Science › Computer Networks and Communications › Advanced Data Storage Technologies
Keywords: DNA data storage, error-correcting codes, DNA synthesis, DNA sequencing
MeSH terms: Base Sequence, DNA, Models, Molecular, Nucleic Acid Conformation, Sequence Analysis, DNA

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