# Storing the declaration of human rights on one data DNA molecule

Gouenou Coatrieux, Chloé Berton, Elsa Dupraz, Belaid Hamoum, Thomas Derrien, Yann Audic, Dominique Lavenier, Jacques Nicolas, Julien Leblanc, Olivier Boullé, et al.

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To cite this version:

Gouenou Coatrieux, Chloé Berton, Elsa Dupraz, Belaid Hamoum, Thomas Derrien, et al. Storing the declaration of human rights on one data DNA molecule. CominLabs day 2022, Oct 2022, Rennes, France. pp.1-1. hal-03817852

HAL Id: hal-03817852

https://hal.science/hal-03817852

Submitted on 17 Oct 2022

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Distributed under a Creative Commons Attribution 4.0 International License
# STORING THE DECLARATION OF HUMAN RIGHTS ON ONE DNA MOLECULE

GenScale IRISA/INRIA, Rennes:
Dominique Lavenier,
Jacques Nicolas,
Julien Leblanc,
Olivier Boullé,
Emeline Roux

LaTIM Inserm UMR 1101 / IMT Atlantique: IGDR, CNRS-UR1 UMR 6290):
Thomas Derrien, Yann Audic

UBS, LabSTICC, Lorient, Brest:
Elsa Dupraz, Belaïd Hamoum

## ABSTRACT

Today, the **community consensus** to store information on DNA is to use **short single strand DNA (ssDNA) molecules**. This approach has some limitations: encoding constraint, DNA stability, recovering DNA, sequencing technology, etc. To overcome them, we chose to store information on **long double-strand DNA (dsDNA) molecules**.

Our demonstration consists of storing the first articles of the declaration of human rights (4,2ko text document) on a single DNA molecule.

<table><thead><tr><th>Declaration of Human Right storage features</th><th>Standard approach</th><th>dnarXiv approach</th></tr></thead><tbody><tr><td>DNA structure</td><td>Single-strand (ssDNA)</td><td>Double-strand (dsDNA)</td></tr><tr><td>DNA strand length</td><td>100-200 nucleotides (nt)</td><td>25,000 base pairs (bp)</td></tr><tr><td>DNA molecules number</td><td>210 - 420 molecules</td><td>1 molecule</td></tr><tr><td>Information density</td><td>0,81 bits/nt</td><td>1,36 bits/nt</td></tr><tr><td>Error correction method</td><td>Yes</td><td>No</td></tr><tr><td>Sequencing technology</td><td>Illumina: short read</td><td>Nanopore: long read</td></tr></tbody></table>

## ENCODING

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$$ \alpha: \begin{array}{c|c} 00 \rightarrow A & \text{if previous base } \in \{G,C\} \\ 01 \rightarrow G & \\ 10 \rightarrow T & \\ 11 \rightarrow C & \end{array} $$ $$ \beta: \begin{array}{c|c} 0 \rightarrow A & \text{if previous base } \in \{G,C\} \\ 1 \rightarrow T & \\ 0 \rightarrow G & \\ 1 \rightarrow C & \text{if previous base } \in \{A,T\} \end{array} $$

- Input: **binary sequence**

- Code respecting **biological constraints**

- Output: **dna sequence**

## SEQUENCE DESIGN

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Build 500bp dsDNA block with ssDNA oligonucleotides:

- 84,8% "Payload": encoded data.

- 7,2% "Overhangs": 9 specific 3' overhangs of 4nt.

- 8,0% "PCR primers": block amplification + add specific 3' overhangs through BsaI restriction sites.

## CONSENSUS

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## DATA

## DECODING

## ENCODING

## CONSENSUS

## SEQUENCE DESIGN

## DNA SYNTHESIS

## SEQUENCING

## DNA ASSEMBLY

## DNA SEQUENCING

- Read length: up to 1Mb

- Accuracy: 99%

- Real time sequencing

- Portable

- Similar cost to Illumina sequencing

- In progress: real-time selective sequencing and detection of chemical modification

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**Nanopore reader:** raw signal (fast5)
**BaseCALLing:** converting files in DNA sequence (fastq)

## STORAGE

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**In vitro:** DNA molecules are simply stored at room temperature in a buffer (Tris-EDTA pH8).

<table><thead><tr><th>Features</th><th>Short ssDNA</th><th>Long dsDNA</th></tr></thead><tbody><tr><td>Storage density*</td><td>+</td><td>++</td></tr><tr><td>Random access capacity°</td><td>+</td><td>+++</td></tr><tr><td>Duplication capacity**</td><td>-</td><td>+</td></tr><tr><td>Storage stability</td><td>+</td><td>++</td></tr><tr><td>Security & stenography</td><td>+</td><td>++</td></tr></tbody></table>

* Storage density: DNA molecules/mm³.

° Random access: access to a specific file without decoding the entire storage.

** Duplication: create complete copy of DNA storage.

## DNA SYNTHESIS

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- Chemical synthesis by phosphoramidite method

- High cost: 0,123€/base

- Oligonucleotide length: 350nt

- Error rate: negligible

- Synthesis speed: 100 to 200 seconds/nucleotide

- In development: enzymatic synthesis

## DNA ASSEMBLY

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Phase 1 concatenation = phosphorylation + dimerization + digestion + ligation + PCR (16 hours)

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Declaration of the Rights of Man and the Citizen of 1789