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Random access and semantic search in DNA data storage enabled by Cas9 and machine-guided design

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Publicado en:Nature Communications vol. 16, no. 1 (2025), p. 6388
Autor Principal: Imburgia, Carina
Outros autores: Organick, Lee, Zhang, Karen, Cardozo, Nicolas, McBride, Jeff, Bee, Callista, Wilde, Delaney, Roote, Gwendolin, Jorgensen, Sophia, Ward, David, Anderson, Charlie, Strauss, Karin, Ceze, Luis, Nivala, Jeff
Publicado:
Nature Publishing Group
Materias:
Databases
Similarity
Metadata
CRISPR
Random access
Information retrieval
Digital data
Artificial neural networks
Data storage
Clusters
Nucleotide sequence
Machine learning
Data retrieval
Storage systems
Information storage
Gene sequencing
Searching
Deoxyribonucleic acid > DNA
Multiplexing
Design
Images
Information processing
Latency
Embedding
Neural networks
Semantics
Environmental
Acceso en liña:Citation/Abstract
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Resumo:DNA is a promising medium for digital data storage due to its exceptional data density and longevity. Practical DNA-based storage systems require selective data retrieval to minimize decoding time and costs. In this work, we introduce CRISPR-Cas9 as a user-friendly tool for multiplexed, low-latency molecular data extraction. We first present a one-pot, multiplexed random access method in which specific data files are selectively cleaved using a CRISPR-Cas9 addressing system and then sequenced via nanopore technology. This approach was validated on a pool of 1.6 million DNA sequences, comprising 25 unique data files. We then developed a molecular similarity-search approach combining machine learning with Cas9-based retrieval. Using a deep neural network, we mapped a database of 1.74 million images into a reduced-dimensional embedding, encoding each embedding as a Cas9 target sequence. These target sequences act as molecular addresses, capturing clusters of semantically related images. By leveraging Cas9’s off-target cleavage activity, query sequences cleave both exact and closely related targets, enabling high-fidelity retrieval of molecular addresses corresponding to in silico image clusters similar to the query. These approaches move towards addressing key challenges in molecular data retrieval by offering simplified, rapid isothermal protocols and new DNA data access capabilities.CRISPR-Cas9 has potential as an efficient tool for information retrieval in DNA data storage. Here the authors present a Cas9-based random access and similarity search approach and test on DNA databases, progressing toward simpler, isothermal protocols.
ISSN:2041-1723
DOI:10.1038/s41467-025-61264-5
Fonte:Health & Medical Collection