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Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing

Billy Lau, Shubham Chandak, Sharmili Roy, Kedar Tatwawadi, Mary Wootters, Tsachy Weissman, Hanlee P. Ji
doi: https://doi.org/10.1101/2021.09.15.460571
Billy Lau
1Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, United States
2Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, United States
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Shubham Chandak
3Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, United States
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Sharmili Roy
1Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, United States
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Kedar Tatwawadi
3Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, United States
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Mary Wootters
3Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, United States
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Tsachy Weissman
3Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, United States
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Hanlee P. Ji
1Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, United States
2Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, United States
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  • For correspondence: genomics_ji@stanford.edu
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ABSTRACT

The storage of data in DNA typically involves encoding and synthesizing data into short oligonucleotides, followed by reading with a sequencing instrument. Major challenges include the molecular consumption of synthesized DNA, issues with basecalling errors, and limitations with scaling up read access operations for individual data elements. Addressing these challenges, we describe a DNA storage system called MDRAM (Magnetic DNA-based Random Access Memory) that enables repetitive and efficient readouts of targeted files with nanopore-based sequencing. Through conjugation of synthesized DNA to magnetic beads, we enabled repeated readouts of data while preserving the original DNA analyte and maintaining data readout quality. MDRAM also utilizes an efficient convolutional coding scheme that leverages soft information in raw nanopore sequencing signals to achieve information reading costs comparable to Illumina sequencing despite substantially higher error rates. Finally, we demonstrate a proof-of-concept DNA-based proto-filesystem that enables an exponentially-scalable data address space using only small numbers of targeting primers for assembly and readout.

ONE-SENTENCE SUMMARY We demonstrate a novel DNA data storage system that leverages conjugation of DNA onto magnetic beads, new computational advances in data encoding, and exponentially scalable access of individual data elements.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • CONTACT INFORMATION Hanlee P. Ji, Email: genomics_ji{at}stanford.edu, Tsachy Weissman, Email: tsachy{at}stanford.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted September 16, 2021.
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Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing
Billy Lau, Shubham Chandak, Sharmili Roy, Kedar Tatwawadi, Mary Wootters, Tsachy Weissman, Hanlee P. Ji
bioRxiv 2021.09.15.460571; doi: https://doi.org/10.1101/2021.09.15.460571
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Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing
Billy Lau, Shubham Chandak, Sharmili Roy, Kedar Tatwawadi, Mary Wootters, Tsachy Weissman, Hanlee P. Ji
bioRxiv 2021.09.15.460571; doi: https://doi.org/10.1101/2021.09.15.460571

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