Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing
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Abstract
DNA is a promising next-generation data storage medium, but challenges remain with synthesis costs and recording latency. Here, we describe a prototype of a DNA data storage system that uses an extended molecular alphabet combining natural and chemically modified nucleotides. Our results show that MspA nanopores can discriminate different combinations and ordered sequences of natural and chemically modified nucleotides in custom-designed oligomers. We further demonstrate single-molecule sequencing of the extended alphabet using a neural network architecture that classifies raw current signals generated by Oxford Nanopore sequencers with an average accuracy exceeding 60% (39× larger than random guessing). Molecular dynamics simulations show that the majority of modified nucleotides lead to only minor perturbations of the DNA double helix. Overall, the extended molecular alphabet may potentially offer a nearly 2-fold increase in storage density and potentially the same order of reduction in the recording latency, thereby enabling new implementations of molecular recorders.
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Nanopore has the advantage over Illumina of single-molecule sequencing of an extended alphabet, including chemically modified nucleotides, which could significantly improve data storage in DNA by increasing storage density and possibly writing speed.
“One of the biggest advantages of Nanopore over Illumina for data output purposes is its single-molecule sequencing of the extended alphabet, or its ability to sequence not only natural nucleotides, but also chemically modified nucleotides. The applicability of such an extended alphabet could significantly improve data storage in DNA by increasing storage density and, possibly, writing speed [79].”
From DNA Data Storage. (2023) · cites this paper as [79]
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Experimental — accuracy not yet measuredPhysical and logical redundancy lower the storage density of DNA.
“While physical and logical redundancy lower the storage density of DNA, recent works have proposed to raise it by expanding the DNA alphabet using composite natural letters7,51,52 or chemically modified nucleotides.53”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [53]
Contrary to SBS, nanopore sequencing is able to identify modified and unnatural nucleotides such that readout of data encoded using an expanded molecular alphabet is possible.
“Contrary to SBS, it is therefore also able to identify modified and unnatural nucleotides such that the readout of data encoded using an expanded molecular alphabet is possible.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [53]
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Emerging Approaches to DNA Data Storage: Challenges and Prospects
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“The applicability of such an extended alphabet could significantly improve data storage in DNA by increasing storage density and, possibly, writing speed [79].”
BackgroundRebimbas, R., Glória, I., Chegão, J., Al-Rawi, M., Mousakhani Ganjeh, A., & Saraiva, J. A. (2026) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2026.03.003
- Authors
- Tabatabaei, S. K., Pham, B., Pan, C., Liu, J., Chandak, S., Shorkey, S. A., Hernandez, A. G., Aksimentiev, A., Chen, M., Schroeder, C. M., & Milenkovic, O.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- University of Massachusetts Amherst (US)
- Stanford University (US)
- Department of Electrical and Computer Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Corresponding author
- Aksimentiev, Aleksei
- Chen, Min
- Schroeder, Charles M.
- ORCID
- Venue
- Nano Letters
- Publisher
- American Chemical Society (ACS)
- Published
- 2022-02-25
- Volume
- 22
- Issue
- 5
- Pages
- 1905-1914
- ISSN
- 1530-6984 (ISSN-L)
- 1530-6992
- PMC
- PMC8915253
- OpenAlex
- W4221106659
- Cited by
- 63
- References
- 50
- Citations by year
- 2026: 11 · 2025: 21 · 2024: 15 · 2023: 9 · 2022: 7
- FWCI
- 3.77
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nano Letters (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- Division of Computing and Communication Foundations (1618366, 1807526, 2008125)
- National Human Genome Research Institute (R21-HG011741)
- National Institute of General Medical Sciences (R01 GM115442)
- Topics
- Physical Sciences › Engineering › Biomedical Engineering › Nanopore and Nanochannel Transport Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Keywords
- DNA data storage, chemically modified nucleotides, single-molecule sequencing, Oxford Nanopore, DNA double helix stability, molecular dynamics simulation, storage density
- MeSH terms
- Data Systems, DNA, Nucleotides, Information Storage and Retrieval, Neural Networks, Computer, Sequence Analysis, DNA, Nanopores
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