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bioRxiv · 10.1101/2023.06.20.545769

A method for storing information in DNA with improved dropout tolerance

Mortuza, G. M.·Tobiason, M. D.·Suyehira, K.·Hughes, W. L.·Andersen, T.·Zadegan, R.
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Abstract

Storing information in synthetic DNA oligomers is attractive for archival purposes due to the favorable physical density, stability, and energy efficiency of this storage medium. However, issues with this medium sometimes cause dropout (i.e., loss of oligomers) which may prevent the recovery of stored information. Here, an improved information storage method derived from the existing "DNA Fountain" method is reported. In this work we have developed and experimentally tested a robust algorithm to write digital data in pools of DNA strands by applying a rateless erasure code (i.e., fountain code), a Reed Solomon code, and an oligomer mapping code. Our new method includes changes to the fountain code, the oligomer mapping code, and the encoding and decoding processes. We have tested and benchmarked our algorithm vs similar algorithms and found that our method increases robustness to dropout, decreases encoding time, and decreases decoding time. The new method was validated in-vitro by successfully storing and recovering 105,360 bits of information. The advantages of the new method make it more appropriate for applications where information recovery is critical, where substantial sequence loss is expected, and/or where computational resources are limited. Furthermore, the inclusion of the novel oligomer mapping code enabled us to mitigate errors by restricting sequences of repeated bases and enhance security by eliminating start/stop codons, thus minimizing the risk of interaction with living cells.

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Mortuza, G. M., Tobiason, M. D., Suyehira, K., Hughes, W. L., Andersen, T., Zadegan, R.. 2023-06-24. A method for storing information in DNA with improved dropout tolerance. https://doi.org/10.1101/2023.06.20.545769

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