Information decay and enzymatic information recovery for DNA data storage

• Published in: Communications biology Vol. 5; no. 1; pp. 1117 - 9
• Main Authors: Meiser, Linda C., Gimpel, Andreas L., Deshpande, Tejas, Libort, Gabriela, Chen, Weida D., Heckel, Reinhard, Nguyen, Bichlien H., Strauss, Karin, Stark, Wendelin J., Grass, Robert N.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 20.10.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 45/23; 45/77; 631/114/1314; 631/337/1427/2123; 631/61/514/1948; Biology; Biomedical and Life Sciences; Data integrity; Data storage; Deoxyribonuclease I; Deoxyribonucleic acid; DNA; DNA - genetics; DNA Repair; DNA-(Apurinic or Apyrimidinic Site) Lyase - genetics; DNA-(Apurinic or Apyrimidinic Site) Lyase - metabolism; Endonuclease; Enzymes; Error correction & detection; Information Storage and Retrieval; Life Sciences; Ligases; Mutation; Storage conditions
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-022-04062-9

Synthetic DNA has been proposed as a storage medium for digital information due to its high theoretical storage density and anticipated long storage horizons. However, under all ambient storage conditions, DNA undergoes a slow chemical decay process resulting in nicked (broken) DNA strands, and the information stored in these strands is no longer readable. In this work we design an enzymatic repair procedure, which is applicable to the DNA pool prior to readout and can partially reverse the damage. Through a chemical understanding of the decay process, an overhang at the 3’ end of the damaged site is identified as obstructive to repair via the base excision-repair (BER) mechanism. The obstruction can be removed via the enzyme apurinic/apyrimidinic endonuclease I (APE1), thereby enabling repair of hydrolytically damaged DNA via Bst polymerase and Taq ligase. Simulations of damage and repair reveal the benefit of the enzymatic repair step for DNA data storage, especially when data is stored in DNA at high storage densities (=low physical redundancy) and for long time durations. An enzymatic repair system is described which repairs nicked DNA in DNA libraries, and simulations of damage and repair suggests this enzymatic repair step is beneficial for DNA data storage.