New Study Shows the Potential of DNA-Based Data Structures

DNA

A double-stranded DNA fragment. Credit: Vcpmartin/Wikimedia/CC BY-SA 4.0

Newcastle University research provides important insights into how we can transform DNA into a green-by-design data structure that organizes data like conventional computers.

The team, led by researchers from Newcastle University’s School of Computing, created new dynamic DNA data structures capable of storing and retrieving information from DNA molecules in an ordered manner. They also analyzed how these structures can be linked to external nucleic acid computer circuits.

Publish their findings in the journal nature communication, the scientists present an in vitro implementation of a stack data structure using DNA polymers. Developed as a chemical DNA reaction system, the stacking system is capable of recording combinations of two different DNA signals (0s and 1s), resolving the signals in reverse order, and then re-recording them.

The stack, a linear data structure that follows a particular order in which the operations are performed, stores and retrieves information (DNA signal strands) in an order from last to first by building DNA “polymers” from single ssDNA and strands to be cut off. Such a stack data structure can ultimately be embedded in an in vivo context to, among other things, store messenger RNAs and reverse the temporal order of a translational response.

Professor Natalio Krasnogor, from Newcastle University’s School of Computing, who led the study, explains: “Our civilization is hungry for data and all that thirst for information processing has a strong impact on the environment. For example, digital technologies pollute more than the aviation industry, the top 7000 data centers in the world consume about 2% of global electricity and we have all heard about the carbon footprint of some cryptocurrencies.

“In recent years, DNA has been shown to be an excellent substrate to store data and DNA to be a renewable, sustainable resource. At Newcastle, we are passionate about sustainability, so we wanted to take small steps towards green-by-design molecular information in DNA and go beyond just storing data. We wanted to be able to organize it. In computer science, data structures are at the heart of all the algorithms that run our modern economy, this is because you need a way to create a unified and standardized way to work with the data stored. This is what data structures enable. We are the first to demonstrate a molecular realization of this critical part of the modern information age.”

Information processing at the nanoscale level

Co-author of the study, Dr. Annunziata Lopiccolo, research associate at Newcastle University’s Center for Synthetic Biology and the Bioeconomy, added: “When we start thinking about data storage, we immediately envision electronic microchips, USB drives and many other existing technologies. But recently For years, biologists have challenged the data storage media sector by showing that DNA nature, as a highly stable and resilient medium, can function as a quaternary data store rather than binary. In our work, we wanted to demonstrate that it is possible to use the “quaternary code to create readable inputs and outputs in the form of programmable signals, with a linear and organized data structure. Our work extends knowledge in the context of nanoscale information processing.”

Study co-author Dr. Harold Fellermann, lecturer at Newcastle University School of Computing, added: “Our biomolecular data structure, in which both data and operations are represented by short pieces of DNA, was designed with biological implementations in mind. In principle we can imagine that such a device can be used in a living cell, e.g. bacteria computing power to domains that are currently difficult to access with traditional silicon-based electronic computers. In the future, such data structures could be used in environmental monitoring, bioremediation, green manufacturing and even personalized nanomedicine.”

Study co-author, Dr. Benjamin Shirt-Ediss, Research Associate, Newcastle University School of Computing, said: “It was really interesting to develop a computational model of DNA chemistry and to see good agreement with experimental results coming out of the lab. allowed us to really get to grips with the performance of the DNA stack’s data structure – we were able to systematically explore its absolute limits and make suggestions for future opportunities for improvement.”

The experimental DNA stack system is proof of the principle that a polymerizing DNA chemistry can be used as dynamic data structure to store two types of DNA signals in a last-in-first-out order. While more research is needed to determine the best possible way to archive and access DNA-based data, the study highlights the tremendous potential of this technology and how it can help meet the rapidly growing demand for data. to grab.


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More information:
Annunziata Lopiccolo et al, A last-in first-out stack data structure implemented in DNA, nature communication (2021). DOI: 10.1038/s41467-021-25023-6

Quote: New Study Shows the Potential of DNA-based Data Structures Systems (2021, Aug. 13) Retrieved Aug. 13, 2021 from https://phys.org/news/2021-08-potential-dna-based-data-structures.html

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