The future of data storage is double-helical, research indicates
The Information Age needs a new data storage powerhouse. With an expanded molecular alphabet and a 21st century twist, DNA may just fit the bill.

Date:
March 3, 2022
Source:
Beckman Institute for Advanced Science and Technology
Summary:
Researchers added seven new letters to DNA's molecular alphabet
and developed a precise, letter-perfect sequencing method. These
innovations helped transform the double helix into a robust,
sustainable data storage platform fit for the Information Age and
built to last well beyond the 21st century.



FULL STORY ========================================================================== Imagine Bach's "Cello Suite No. 1" played on a strand of DNA.


==========================================================================
This scenario is not as impossible as it seems. Too small to withstand
a rhythmic strum or sliding bowstring, DNA is a powerhouse for storing
audio files and all kinds of other media.

"DNA is nature's original data storage system. We can use it to store any
kind of data: images, video, music -- anything," said Kasra Tabatabaei,
a researcher at the Beckman Institute for Advanced Science and Technology
and a coauthor on this study.

Expanding DNA's molecular makeup and developing a precise new sequencing
method enabled a multi-institutional team to transform the double helix
into a robust, sustainable data storage platform.

The team's paper appeared in Nano Letters in February 2022.

In the age of digital information, anyone brave enough to navigate
the daily news feels the global archive growing heavier by the
day. Increasingly, paper files are being digitized to save space and
protect information from natural disasters.



==========================================================================
From scientists to social media influencers, anyone with information
to store stands to benefit from a secure, sustainable data lock box --
and the double helix fits the bill.

"DNA is one of the best options, if not the best option, to store archival
data especially," said Chao Pan, a graduate student at the University
of Illinois Urbana-Champaign and a coauthor on this study.

Its longevity rivaled only by durability, DNA is designed to weather
Earth's harshest conditions -- sometimes for tens of thousands of years
-- and remain a viable data source. Scientists can sequence fossilized
strands to uncover genetic histories and breathe life into long-lost landscapes.

Despite its diminutive stature, DNA is a bit like Dr. Who's infamous
police box: bigger on the inside than it appears.

"Every day, several petabytes of data are generated on the internet. Only
one gram of DNA would be sufficient to store that data. That's how dense
DNA is as a storage medium," said Tabatabaei, who is also a fifth-year
Ph.D. student.



========================================================================== Another important aspect of DNA is its natural abundance and near-infinite renewability, a trait not shared by the most advanced data storage system
on the market today: silicon microchips, which often circulate for just
decades before an unceremonious burial in a heap of landfilled e-waste.

"At a time when we are facing unprecedented climate challenges,
the importance of sustainable storage technologies cannot be
overestimated. New, green technologies for DNA recording are emerging
that will make molecular storage even more important in the future,"
said Olgica Milenkovic, the Franklin W.

Woeltge Professor of Electrical and Computer Engineering and a co-PI on
the study.

Envisioning the future of data storage, the interdisciplinary team
examined DNA's millennia-old MO. Then, the researchers added their own 21st-century twist.

In nature, every strand of DNA contains four chemicals -- adenine,
guanine, cytosine, and thymine -- often referred to by the initials A,
G, C, and T. They arrange and rearrange themselves along the double
helix into combinations that scientists can decode, or sequence, to
make meaning.

The researchers expanded DNA's already broad capacity for information
storage by adding seven synthetic nucleobases to the existing four-letter lineup.

"Imagine the English alphabet. If you only had four letters to use, you
could only create so many words. If you had the full alphabet, you could produce limitless word combinations. That's the same with DNA. Instead of converting zeroes and ones to A, G, C, and T, we can convert zeroes and
ones to A, G, C, T, and the seven new letters in the storage alphabet," Tabatabaei said.

Because this team is the first to use chemically modified nucleotides for information storage in DNA, members innovated around a unique challenge:
not all current technology is capable of interpreting chemically modified
DNA strands. To solve this problem, they combined machine learning and artificial intelligence to develop a first-of-its-kind DNA sequence
readout processing method.

Their solution can discern modified chemicals from natural ones, and differentiate each of the seven new molecules from one another.

"We tried 77 different combinations of the 11 nucleotides, and our method
was able to differentiate each of them perfectly," Pan said. "The deep
learning framework as part of our method to identify different nucleotides
is universal, which enables the generalizability of our approach to many
other applications." This letter-perfect translation comes courtesy
of nanopores: proteins with an opening in the middle through which a
DNA strand can easily pass. Remarkably, the team found that nanopores
can detect and distinguish each individual monomer unit along the DNA
strand -- whether the units have natural or chemical origins.

"This work provides an exciting proof-of-principle demonstration of
extending macromolecular data storage to non-natural chemistries,
which hold the potential to drastically increase storage density in non-traditional storage media," said Charles Schroeder, the James Economy Professor of Materials Science and Engineering and a co-PI on this study.

DNA literally made history by storing genetic information. By the looks
of this study, the future of data storage is just as double-helical.

Additional UIUC collaborators include Aleksei Aksimentiev, the Center
for Biophysics and Quantitative Biology; and Alvaro Hernandez, the
Roy J. Carver Biotechnology Center. Partner institutions include the
University of Massachusetts at Amherst and Stanford University. For a
full list of collaborators and their affiliations, please consult the
published work.

========================================================================== Story Source: Materials provided by Beckman_Institute_for_Advanced_Science_and_Technology.

Original written by Jenna Kurtzweil. Note: Content may be edited for
style and length.


========================================================================== Journal Reference:
1. S. Kasra Tabatabaei, Bach Pham, Chao Pan, Jingqian Liu, Shubham
Chandak,
Spencer A. Shorkey, Alvaro G. Hernandez, Aleksei Aksimentiev,
Min Chen, Charles M. Schroeder, Olgica Milenkovic. Expanding the
Molecular Alphabet of DNA-Based Data Storage Systems with Neural
Network Nanopore Readout Processing. Nano Letters, 2022; DOI:
10.1021/acs.nanolett.1c04203 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/03/220303162030.htm

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