Permanent genetic memory with >1-byte capacity
Open accessAbstract
Genetic memory enables the recording of information in the DNA of living cells. Memory can record a transient environmental signal or cell state that is then recalled at a later time. Permanent memory is implemented using irreversible recombinases that invert the orientation of a unit of DNA, corresponding to the [0,1] state of a bit. To expand the memory capacity, we have applied bioinformatics to identify 34 phage integrases (and their cognate attB and attP recognition sites), from which we build 11 memory switches that are perfectly orthogonal to each other and the FimE and HbiF bacterial invertases. Using these switches, a memory array is constructed in Escherichia coli that can record 1.375 bytes of information. It is demonstrated that the recombinases can be layered and used to permanently record the transient state of a transcriptional logic gate.
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Preservation of DNA digital archives can be implemented using not only in vitro substrates but also in vivo approaches.
“It is also important to mention that the preservation of DNA digital archives can be implemented using not only in vitro substrates but also in vivo approaches.150−153”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [152]
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- Authors
- Yang, L., Nielsen, A. A. K., Fernandez-Rodriguez, J., McClune, C. J., Laub, M. T., Lu, T. K., & Voigt, C. A.
- Affiliations
- Massachusetts Institute of Technology (US)
- Corresponding author
- Voigt, Christopher A
- Venue
- Nature Methods
- Published
- 2014-10-26
- Volume
- 11
- Issue
- 12
- Pages
- 1261-1266
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC4245323
- OpenAlex
- W1586524232
- Cited by
- 243
- References
- 49
- Citations by year
- 2026: 16 · 2025: 20 · 2024: 22 · 2023: 19 · 2022: 24 · 2021: 16 · 2020: 20 · 2019: 22 · 2018: 21 · 2017: 23 · 2016: 27 · 2015: 13
- FWCI
- 8.56
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- PMC
- Funders
- National Institute of General Medical Sciences (P50GM098792, R01GM095765, GM095765, T32GM007287)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Keywords
- ancestral memory, phage integrase, memory arrays, Escherichia coli
- MeSH terms
- Bacteriophages, DNA-Binding Proteins, DNA, Bacterial, Escherichia coli, Memory, Recombination, Genetic, Gene Expression Regulation, Bacterial, Computational Biology, Integrases, Escherichia coli Proteins, Recombinases
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