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Method offers new approach to DNA data storage

Origami and superresolution microscopy team up for digital data writing and reading

by Celia Henry Arnaud
April 29, 2021 | A version of this story appeared in Volume 99, Issue 16

Images of the patterns of dots generated using DNA origami.
Credit: Nat. Commun.
Super-resolution microscopy images are used to read data encoded in DNA origami. Shown are matrix designs for six of the origami. The scale bar is 20 nm.

DNA shows promise as a material for data storage because it resists degradation and can pack a lot of information into a small volume. But reading the stored data typically requires sequencing the DNA. Researchers now show that they can use DNA origami—a method that takes advantage of DNA’s complementary base pairs to create desired shapes—and superresolution microscopy to store and read data from arrays of glowing dots without the need for time-consuming sequencing (Nat. Commun. 2021, DOI: 10.1038/s41467-021-22277-y).

William L. Hughes and George D. Dickin­son of Boise State University and their colleagues designed DNA origami sequences that fold into a 2D carpet. Each carpet contains 48 sites that act as the bits—the ones and zeros—of stored data.

When the origami folds, some sites have a DNA strand sticking up and others don’t, representing one and zero, respectively. After adding fluorescently labeled DNA that is complementary to the strands that stick up, the researchers can take pictures with superresolution fluor­escence microscopy; the sites that glow are ones, and those that don’t are zeros.

The researchers encoded error-correction strategies into the origami, Hughes says, which was a key step because the synthesis of the DNA, the assembly of the origami, and the microscopy readout have intrinsic variability that can lead to mistakes. With the correction algorithm, the researchers were able to recover an encoded message with 100% accuracy.

“This is a very powerful way of reading information and highlights the power of superresolution spectroscopy,” says Robert Grass, who studies DNA data storage at the Swiss Federal Institute of Technology (ETH), Zurich. He thinks that scaling up the writing of the data could be challenging, so writing and reading DNA bar codes that are used for tagging and labeling products might be a more suitable application than large-scale data storage. In DNA bar coding, “speed and simplicity may be more important than cost and scalability,” Grass says.



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