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North Carolina State University researchers have created a tool addressing a long-standing DNA data storage problem. It allows users to preview stored files, such as thumbnail images.
DNA data storage is a popular technology. It can store large amounts of data in a compact package and for an extended period, and it’s energy-efficient. It was not possible to view the data stored in DNA files. You had to open the file to see what it was.
Our technique has the advantage of being more efficient in terms of time and money,” Kyle Tomek, a lead author on the paper and a Ph.D. student from NC State, says. You only need to sequence every possible file if you are sure which contains the desired data. You can instead sequence smaller parts of the DNA files as previews.
This is a brief overview of how it works.
Users can “name” data files by attaching primer-binding sequences (DNA sequences) to the ends of DNA strands containing information. Most systems use polymerase chain reactions (PCR) to identify and extract files. They use a small DNA primer to match the primer-binding sequence to identify the DNA strands that contain the file. After making many copies of the relevant DNA sequences, the system uses PCR to sequence the whole sample. The process creates many copies of the targeted DNA strands. This makes it easier to identify the sequence and then read the file.
One problem that DNA data storage researchers have had to deal with is that PCR can accidentally copy parts of multiple files if they have the same file names. Users must give files distinct names to avoid messy data.
Albert Keung, assistant professor of chemical, biomolecular, and engineering at NC State, said, “At some stage, it occurred to us that we might be able to use non-specific interactions as tools rather than seeing it as a problem.”
The researchers devised a method that uses similar file names to allow them to open an entire file or just a subset. The researchers use a particular naming convention to name a file or a subset of files. You can control several parameters of the PCR process, such as the temperature, DNA concentration, and types of reagents, so they can decide whether to open the whole file or just the preview.
James Tuck, the paper’s coauthor and computer engineering professor at NC State, said, “our technique makes the system more complicated.” This means we must be more careful when managing file-naming conventions as well as conditions of PCR. This makes the system more data-efficient but also significantly more user-friendly.
Researchers demonstrated their method by saving large JPEG files in DNA data storage and retrieving thumbnails and full-resolution files.
Although we only store image files, this technology can be used with many other file types. It also offers this new functionality without additional cost,” said Kevin Volkel, coauthor and NC State Ph.D. student.
The “file preview” technology is compatible with the DENSe (DNA Enrichment and Nested Separation) system, which researchers created to make DNA data storage more feasible. DENSe made DNA storage systems more flexible by providing improved data file labeling, retrieval, and retrieval methods.
Keung states that the paper will be published in Nature Communications today. Elaine Indermaur was a former student at NC State and coauthored the paper.
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