Storing Thousands of Terabytes in a Single Gram of DNA

Researchers from Peking University have unveiled a groundbreaking approach to DNA data storage, which leverages enzymatic methylation to store data densely and efficiently.

This new method, named “epi-bits,” allows for high-capacity data storage that is both scalable and cost-effective, demonstrating the practicality of using DNA as a versatile storage medium.

Advantages and Innovations in DNA Storage

Recently, researchers from Peking University, led by Cheng Zhang, Dean of the Department of Computer Science, and Long Qian from the Center for Quantitative Biology, published a groundbreaking study in Nature titled “Parallel Molecular Data Storage by Printing Epigenetic Bits on DNA.”

The study introduces a pioneering method for DNA-based data storage. By using enzymatic methylation, researchers developed a way to encode data as epigenetic modifications, called “epi-bits,” which can be precisely added to universal DNA templates. This innovation offers a scalable and programmable approach to molecular data storage.

As the world faces increasing challenges in managing the ever-growing flow of digital information, DNA presents an attractive solution. With its remarkable storage density — just one gram of DNA can hold 215,000 terabytes, equivalent to 10 million hours of high-definition video (Imburgia & Nivala, 2024) — and its long-term stability, DNA is an ideal medium for data storage. However, traditional methods rely on de novo synthesis, where nucleotides are sequentially added, making the process slow and expensive. The method developed by Zhang and his team overcomes these limitations by enabling parallel, programmable DNA assembly, making data writing faster and more efficient.

Additionally, the epi-bit method can be used by individuals to personalize their DNA storage, as shown by the implementation of the method by 60 volunteers from diverse academic backgrounds. This clearly demonstrates the potential Zhang et al.’s epi-bit method has as an accessible, versatile, fast, and low-cost method for DNA storage. 

Methodology of Epigenetic DNA Storage

• Information is encoded through selective methylation on cytosine bases in DNA.
• Pre-synthesized DNA fragments, called DNA bricks, are assembled on a reusable DNA strand. Each DNA brick binds to a unique location on the strand.
• The precise binding of the brick guides an enzyme to methylate a specific position on the template, which effectively “prints” the data onto the template.  
• Following the same binary system as computer hardware, each DNA brick carries a methylated or unmethylated site to encode a 1 or 0, respectively. 
• Epi-bits are read using a nanopore sequencing device.

Key Findings and Practical Applications

Using the epi-bit method, the researchers were able to write 275,000 information bits onto five templates on an automated platform, with no synthesizing of DNA required, including two high-definition photos of a white tiger and a giant panda. 

On iDNAdrive, a platform created by Zhang et al. that allows users to encode data themselves, volunteers encoded approximately 5,000 bits of data using epi-bit writing kits. The error rate when reading the data was as low as 1.42%.

Reference: “Parallel molecular data storage by printing epigenetic bits on DNA” by Cheng Zhang, Ranfeng Wu, Fajia Sun, Yisheng Lin, Yuan Liang, Jiongjiong Teng, Na Liu, Qi Ouyang, Long Qian and Hao Yan, 23 October 2024, Nature.
DOI: 10.1038/s41586-024-08040-5

Never miss a breakthrough: Join the SciTechDaily newsletter.
Follow us on Google and Google News.