Scientists have created a “living digital camera” that captures and stores images in DNA, the genetic code of all living things, reports a new study. The technique offers a novel approach to encoding digital information into biological material, an endeavor that has a host of potential future applications in computing and nanotechnology.
DNA, which stands for deoxyribonucleic acid, is a molecule that stores the genetic instructions for organisms using four nucleotides called adenine (A), thymine (T), guanine (G), and cytosine (C). In addition to providing a comprehensive guide to biological systems, the simple four-bit nature of DNA has attracted interest from scientists as a potential form of hardware for novel computing systems and data storage.
Now, researchers led by Cheng Kai Lim, a synthetic biologist at the National University of Singapore, have demonstrated that DNA can not only be used to take and store images, but that these pictures can later be retrieved via sequencing techniques.
By passing special 2D light through DNA samples, the researchers were able to create “a biological analogue to a digital camera” which they called BacCam, according to a study published last week in Nature Communications.
“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,” said Lim and his colleagues in the study. “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,” the team said. “This work thus establishes a ‘living digital camera’, paving the way towards integrating biological systems with digital devices.”
Scientists have been ruminating on the computational potential of DNA for decades, and the market for applications of DNA storage are expected to grow in the coming years. At this point, most efforts along these lines involve in-vitro synthesis of DNA, which means that scientists make synthetic strands of genetic material that can be manipulated to store information. Though this process is well-tested, it is also expensive, complicated, and often riddled with errors, according to Lim and his colleagues.
“While there have been substantial advances in accelerating this process…DNA synthesis remains a bottleneck in the adoption of DNA as a data storage medium,” the team said in the study. “There is thus significant interest in developing ways of encoding information into DNA that can either supersede or circumvent DNA synthesis in its current form.”
To that end, Lim and his colleagues came up with a new technique that sidesteps the need to synthesize DNA by working with living cells from the bacteria species Escherichia coli that contain so-called “optogenetic” circuits capable of recording the presence or absence of light within DNA.
The researchers projected simple 96-bit images—including a smiley face and the word “BacCam”—into specific sites of DNA of the bacterial culture using blue light. The images were successfully stored into the DNA, and could be retrieved with near-perfect accuracy by sequencing the encoded strands. Moreover, the team was able to use red light to project a separate image on the same segments of DNA, demonstrating that multiple images could be captured, stored, and deciphered from a single genetic sample.
“To scale this workflow beyond a single wavelength of light, we incorporated an additional wavelength of light, doubling the amount of data that can be stored in a single, simultaneous capture and demonstrating the multiplexing potential of the system,” Lim and his colleagues said. “The results imply that the number of different images that can be stored in a [DNA] pool and retrieved in a single run is between 100 and 1000.”
“As the field of DNA data storage continues to progress, there is an increasing interest in bridging the interface between biological and digital systems,” the team concluded. “Our work showcases further applications of DNA data storage that recreate existing information capture devices in a biological form, providing the basis for continued innovation in information recording and storage.”