National University of Singapore (NUS) Capturing Immense Potential of Microscopic DNA for Storage

In a world first, a ‘biological camera’ bypasses the constraints of current DNA storage methods, harnessing living cells and their inherent biological mechanisms to encode and store data.

Research team led by assoc prof. Poh Chueh Loo (right) has pioneered
innovative ‘biological camera’ that harnesses living cells and
their inherent biological mechanisms to encode and store data.

This represents a breakthrough in encoding and storing images directly within DNA, creating a new model for information storage reminiscent of a digital camera.

Led by principal investigator associate professor Poh Chueh Loo from the College of Design and Engineering, National University of Singapore, and the NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), the team’s findings, which could potentially shake up the storage industry, were published in Nature Communications on July 3, 2023.

New paradigm to address global data overload
As the world continues to generate data at an unprecedented rate, data has come to be seen as the ‘currency’ of the 21st century. Estimated to be 33ZB in 2018, it has been forecasted that the Global Datasphere will reach 175ZB by 2025. That has sparked a quest for a storage alternative that can transcend the confines of conventional data storage and address the environmental impact of resource-intensive data centres.

It is only recently that the idea of using DNA to store other types of information, such as images and videos, has garnered attention. This is due to DNA’s exceptional storage capacity, stability, and long-standing relevance as a medium for information storage.

“We are facing an impending data overload. DNA, the key biomaterial of every living thing on Earth, stores genetic information that encodes for an array of proteins responsible for various life functions. To put it into perspective, a single gram of DNA can hold over 215,000TB of data – equivalent to storing 45 million DVDs combined,” said Poh.

“DNA is also easy to manipulate with current molecular biology tools, can be stored in various forms at room temperature, and is so durable it can last centuries”, says Lim Cheng Kai, a graduate student working with Poh.

Despite its immense potential, current research in DNA storage focuses on synthesising DNA strands outside the cells. This process is expensive and relies on complex instruments, which are also prone to errors.

To overcome this bottleneck, Poh and his team turned to live cells, which contain an abundance of DNA that can act as a ‘data bank’, circumventing the need to synthesise the genetic material externally.

Through sheer ingenuity and clever engineering, the team developed ‘BacCam’ – a novel system that merges various biological and digital techniques to emulate a digital camera’s functions using biological components.

“Imagine the DNA within a cell as an undeveloped photographic film,” explained Poh. “Using optogenetics – a technique that controls the activity of cells with light akin to the shutter mechanism of a camera, we managed to capture ‘images’ by imprinting light signals onto the DNA ‘film’.”

Next, using barcoding techniques akin to photo labelling, the researchers marked the captured images for unique identification. Machine-learning algorithms were employed to organise, sort, and reconstruct the stored images. These constitute the ‘biological camera’, mirroring a digital camera’s data capture, storage, and retrieval processes.

The study showcased the camera’s ability to capture and store multiple images simultaneously using different light colours. More crucially, compared to earlier methods of DNA data storage, the team’s innovative system is easily reproducible and scalable.

Graduate student Lim Cheng Kai (left) worked with assoc. prof. Poh Chueh Loo (right)
to develop a novel system which captures and stores images directly into DNA.

“As we push the boundaries of DNA data storage, there is an increasing interest in bridging the interface between biological and digital systems,” said Poh. “Our method represents a major milestone in integrating biological systems with digital devices. By harnessing the power of DNA and optogenetic circuits, we have created the first ‘living digital camera,’ which offers a cost-effective and efficient approach to DNA data storage. Our work not only explores further applications of DNA data storage but also re-engineers existing data-capture technologies into a biological framework. We hope this will lay the groundwork for continued innovation in recording and storing information.”

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Article: A biological camera that captures and stores images directly into DNA

Nature Communications has published an article written by Cheng Kai Lim, Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore, Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore, Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore, and Integrative Sciences and Engineering Programme (ISEP), NUS Graduate School, National University of Singapore, Singapore, Singapore, Jing Wui Yeoh, Aurelius Andrew Kunartama, Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore, and Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore, Wen Shan Yew, Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore, Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore, and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore, and Chueh Loo Poh, Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore, and Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore.

Abstract: “The increasing integration between biological and digital interfaces has led to heightened interest in utilizing biological materials to store digital data, with the most promising one involving the storage of data within defined sequences of DNA that are created by de novo DNA synthesis. However, there is a lack of methods that can obviate the need for de novo DNA synthesis, which tends to be costly and inefficient. Here, in this work, we detail a method of capturing 2-dimensional light patterns into DNA, by utilizing optogenetic circuits to record light exposure into DNA, encoding spatial locations with barcoding, and retrieving stored images via high-throughput next-generation sequencing. We demonstrate the encoding of multiple images into DNA, totaling 1152 bits, selective image retrieval, as well as robustness to drying, heat and UV. We also demonstrate successful multiplexing using multiple wavelengths of light, capturing 2 different images simultaneously using red and blue light. This work thus establishes a ‘living digital camera’, paving the way towards integrating biological systems with digital devices.“