Abstract
Oligonucleotide multiplicity is an inherent property of current DNA synthesis technology. Composite letter DNA storage exploits this property to improve logical density and reduce costs. However, letter indistinguishability and high molecular diversity pose challenges for reliable recovery. Here, we formulate a composite letter constellation model, named DNA diamond, consisting of 15 decomposable points. Inspired by set partitioning in telecommunications, we propose a two-stage letter detection framework that partitions these letters into four distinguishable subsets based on their discrete entropy. Furthermore, we incorporate encoded double-end indices to eliminate crosstalk between synthesis sites and simultaneously apply length filtering to suppress error propagation during readout. We validate the eight-letter and 15-letter composite letter DNA storage under DNA diamond model, each with 10,000 composite strands. The eight-letter system achieves a payload density of 2.5 bits per letter and enables error-free recovery at 14× coverage, surpassing the storage density of prior six-letter systems while requiring lower coverage. The full 15-letter constellation enables 3.125 bits per letter for payload with error-free recovery at 33× coverage, corresponding to a density of 2.23 bits per letter for payload plus indices. The proposed decomposable DNA diamond model advances a practical and scalable framework for high-density composite DNA data storage.
Data availability
The encoded composite letter sequences are available via Zenodo at https://doi.org/10.5281/zenodo.1735030747. The sequencing data (FASTQ format) from the array-based synthesis pools have been deposited in the Sequence Read Archive under accession number PRJNA1345374, and are also available via Zenodo at https://doi.org/10.5281/zenodo.1735030747. The sequencing data from the column-based synthesis experiments have been deposited in the Sequence Read Archive under accession number PRJNA1258704, and are also available via Zenodo at https://doi.org/10.5281/zenodo.1533715748. Source data are provided with this paper.
Code availability
The source code for composite letter detection and data readout is publicly available and has been deposited in GitHub at https://github.com/TJU-QiGe/Two-stage-composite-letter-detection-method-using-set-partitioning, under MIT license. The specific version of the code associated with this publication is archived in Zenodo and is accessible via https://doi.org/10.5281/zenodo.1790599349. This implementation makes use of several third-party software packages under their respective licenses, including RS codes by Morelos-Zaragoza, R. (https://www.eccpage.com), seqtk by Li, H. (https://github.com/lh3/seqtk), and edlib by Šošić, M. (https://github.com/Martinsos/edlib).
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Acknowledgements
This work was supported by grants from the National Key R&D Program of China (2023YFA0913800 and 2021YFF1200200 to W.C.; 2024YFF1500500 to Y.Y.). The authors thank Dashun Huang (Hippobio Co., Ltd., Huzhou, China) for assistance with the column-based synthesis of composite DNA strands, and Dynegene Technologies (Shanghai, China) for their support in the array-based synthesis of large-scale composite pools. The authors also thank Lulu Li (LC-Bio Technology Co., Ltd., Hangzhou, China) for support in library preparation and sequencing, and Rui Qin for performing the amplification and accelerated aging experiments.
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W.C. and Y.Y. conceived the project and reviewed the results. Q.G., C.H., and W.C. designed the composite DNA storage system and wrote the encoding and decoding programs. Q.G. developed the two-stage composite letter detection program and performed the simulations and experimental validation. Q.G., M.R., and T.Q. analyzed sequencing data. Q.G. and W.C. validated the results and wrote the manuscript. All authors supervised the results, revised the manuscript, and approved the final manuscript.
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Q.G., C.H., and W.C. have been granted a Chinese patent related to the encoding and decoding approach for composite letter DNA data storage (patent number CN119649874B). The remaining authors declare no competing interests.
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Ge, Q., Ren, M., Qi, T. et al. DNA diamond formulates a decomposable composite letter constellation model for DNA data storage. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68861-y
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DOI: https://doi.org/10.1038/s41467-026-68861-y
