Breakthrough in DNA Data Storage: Epigenetics Offers a New Approach

Edited by: @Tanurya Tanurya

In 2024, at least 149 zettabytes of data were created, captured, copied, or consumed, a number projected to more than double by 2028, according to Statista.

To address the exponential growth of information, scientists globally are racing to find more effective and sustainable storage solutions.

A promising idea emerges from biology: using DNA, the molecule that carries genetic instructions for all living beings, as a model for developing revolutionary storage technology.

A recent study published in the journal Nature introduced a novel approach based on epigenetics, promising to record information more quickly, economically, and stably than traditional methods.

DNA is known for its immense capacity to store data compactly and durably: one gram of this molecule can hold up to one trillion gigabytes of information, remaining intact for thousands of years under proper conditions.

The concept of using DNA as a digital repository was first proposed by physicist Richard Feynman in the 1950s.

Decades later, in 2012, geneticist George Church's team at Harvard University successfully encoded a 53,400-word book in DNA, demonstrating the concept's viability.

However, the method used, known as de novo synthesis, adds nucleotides—the letters of DNA: adenine (A), thymine (T), guanine (G), and cytosine (C)—one by one to create sequences representing binary data (0s and 1s).

This process is costly, time-consuming, and error-prone, limiting its large-scale application: only 1 bit (or one-eighth of a byte) can be added per nucleotide.

Importantly, the technology does not use a person's DNA for storage but rather laboratory-produced molecules designed exclusively for this purpose.

To overcome the limitations of de novo synthesis, a research team from China, Germany, and the United States developed an innovative method utilizing epigenetics—the branch of science studying chemical modifications to DNA that do not alter its sequence but affect its functionality.

The system created by the scientists records data through a process called methylation—the addition of small chemical groups called methyl to specific nucleotides of DNA. These modifications, known as epi-bits, represent the 0s and 1s of binary code.

Researchers used universal DNA templates and complementary fragments called mobile types—functioning like typographic pieces fitting into templates, allowing for precise data recording.

The enzyme DNMT1, which naturally performs methylation in living organisms, was adapted to print methylation patterns programmatically, turning DNA into a kind of 'data tape.'

In experiments, scientists recorded about 350 bits per reaction—a significant increase compared to the single bit from the de novo synthesis technique.

Additionally, this technology can record data in parallel, meaning multiple points of DNA can be modified simultaneously, contrasting with the traditional method that records data sequentially, making the process slower.

Data were retrieved with high precision through nanopore sequencing, a technology capable of detecting chemical changes in DNA and translating methylation patterns into digital information.

Moreover, scientists demonstrated that epi-bits remained stable even under adverse conditions, such as heating.

In a test called iDNAdrive, 60 volunteers without laboratory experience successfully used the system to record data, proving that the technique is accessible and can be applied in decentralized environments.

Despite advancements, barriers remain for widespread adoption of epigenetics-based technology.

One challenge is improving algorithms that detect methylation patterns, enhancing the accuracy and efficiency of the process. Another issue is the initial cost of necessary equipment, such as nanopore sequencing platforms, which are still expensive.

Nonetheless, the study's results are promising and suggest a future where DNA can meet the growing global data demands, with scalable potential for large-scale applications.

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