Genomically encoded analog memory with precise in vivo DNA writing in living cell populations
Open accessAbstract
Cellular memory is crucial to many natural biological processes and sophisticated synthetic biology applications. Existing cellular memories rely on epigenetic switches or recombinases, which are limited in scalability and recording capacity. In this work, we use the DNA of living cell populations as genomic “tape recorders” for the analog and distributed recording of long-term event histories. We describe a platform for generating single-stranded DNA (ssDNA) in vivo in response to arbitrary transcriptional signals. When coexpressed with a recombinase, these intracellularly expressed ssDNAs target specific genomic DNA addresses, resulting in precise mutations that accumulate in cell populations as a function of the magnitude and duration of the inputs. This platform could enable long-term cellular recorders for environmental and biomedical applications, biological state machines, and enhanced genome engineering strategies.
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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 [151]
Amplified material was pure and ready for re-encapsulation into silica particles, which could be re-introduced directly back into the data pool and thereby represents a complete write-store-access-read cycle that in principle may be applied to larger-scale datasets, with periodic renewal of single-stranded DNA barcodes and bacterial replication of DNA data following reading.
“Amplified material was pure and ready for re-encapsulation into silica particles, which could be re-introduced directly back into the data pool and thereby represents a complete write-store-access-read cycle that in principle may be applied larger-scale datasets, with periodic renewal of single-stranded DNA barcodes and bacterial replication of DNA data following reading25–27.”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [26]
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- Authors
- Farzadfard, F., & Lu, T. K.
- Affiliations
- Massachusetts Institute of Technology (US)
- Corresponding author
- Lu, Timothy K.
- Venue
- Science
- Published
- 2014-11-14
- Volume
- 346
- Issue
- 6211
- Pages
- 1256272-1256272
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC4266475
- OpenAlex
- W2065515388
- Cited by
- 298
- References
- 61
- Citations by year
- 2026: 17 · 2025: 23 · 2024: 24 · 2023: 20 · 2022: 30 · 2021: 26 · 2020: 24 · 2019: 26 · 2018: 27 · 2017: 26 · 2016: 29 · 2015: 23 · 2014: 3
- FWCI
- 11.08
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- PMC
- Funders
- National Institutes of Health (1dp2od008435-01)
- National Institute of General Medical Sciences (P50GM098792)
- 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 › Advanced biosensing and bioanalysis techniques
- Keywords
- cellular memory, analog memory, single-stranded DNA, recombinases, genome editing
- MeSH terms
- Base Sequence, Cells, DNA, Single-Stranded, Escherichia coli, Genetic Code, Memory, Molecular Sequence Data, Tape Recording, Transcription, Genetic, Writing, Information Storage and Retrieval, Genomics, Bioengineering, Synthetic Biology
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