New study shows the potential of DNA-based data-structures systems


Date:
August 12, 2021
Source:
Newcastle University
Summary:
Engineers have created new dynamic DNA data structures able to store
and recall information in an ordered way from DNA molecules. They
also analyzed how these structures are able to be interfaced with
external nucleic acid computing circuits.



FULL STORY ========================================================================== Newcastle University research offers important insights into how we
could turn to DNA into a green-by-design data structure that organises
data like conventional computers.


==========================================================================
The team, led by researchers from Newcastle University's School of
Computing, created new dynamic DNA data structures able to store and
recall information in an ordered way from DNA molecules. They also
analysed how these structures are able to be interfaced with external
nucleic acid computing circuits.

Publishing their findings in the journal Nature Communications,the
scientists present an in vitro implementation of a stack data structure
using DNA polymers. Developed as a DNA chemical reaction system, the
stack system is able to record combinations of two different DNA signals
(0s and 1s), release the signals into solution in reverse order, and
then re-record.

The stack, which is a linear data structure which follows a particular
order in which the operations are performed, stores and retrieves
information (DNA signal strands) in a last-in first-out order by building
and truncating DNA "polymers" of single ssDNA strands. Such a stack
data structure may eventually be embedded in an in vivo context to store messenger RNAs and reverse the temporal order of a translational response, among other applications.

Professor Natalio Krasnogor, of Newcastle University's School of
Computing, who led the study explains: "Our civilisation is data
hungry and all that information processing thirst is having a strong environmental impact. For example, digital technologies pollute more
than the aviation industry, the top 7000 data centers in the world use
around 2% of global electricity and we all heard about the environmental footprint of some cryptocurrencies.

"In recent years DNA has been shown to be an excellent substrate to store
data and the DNA is a renewable, sustainable resource. At Newcastle we
are passionate about sustainability and thus we wanted to start taking
baby steps into green-by-design molecular information processing in DNA
and go beyond simply storing data. We wanted to be able to organise
it. In computer science, data structures are at the core of all the
algorithms that run our modern economy; this is so because you need a
way to have a unified and standardised way to operate on the data that
is stored. This is what data structures enable.

We are the first to demonstrate a molecular realisation of this crucial component of the modern information age." Study co-author, Dr Annunziata Lopiccolo, Research Associate at Newcastle University's Centre for
Synthetic Biology and the Bioeconomy, added: "If we start thinking about
data storage, immediately our minds picture electronic microchips, USB
drives and many other existing technologies. But over the last few years biologists challenged the data storage media sector demonstrating that
the DNA nature, as a highly stable and resilient media, can function
as a quaternary data storage, rather than binary. In our work we wanted
to demonstrate that it is possible to use the quaternary code to craft
readable inputs and outputs under the form of programmable signals,
with a linear and organised data structure. Our work expands knowledge
in the context of information processing at the nanoscale level."
Study co-author Dr Harold Fellermann, Lecturer at Newcastle University
School of Computing added: "Our biomolecular data structure, where both
data as well as operations are represented by short pieces of DNA, has
been designed with biological implementations in mind. In principle,
we can imagine such a device to be used inside a living cell, bacteria
for example. This makes it possible to bring computational power to
domains that are currently hard to access with traditional silicon-based, electronic computing. In the future, such data structures might be used
in environmental monitoring, bioremediation, green production, and even personalised 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 the DNA chemistry and to see good agreement with experimental results coming out
of the lab. The computational model allowed us to really get a handle on
the performance of the DNA stack data structure -- we could systematically explore its absolute limits and suggest future avenues for improvement."
The experimental DNA stack system constitutes proof-of principle that
a polymerising DNA chemistry can be used as a dynamic data structure to
store two types of DNA signal 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 enormous potential of this technology, and how it could help tackle the rapidly growing data demands.

========================================================================== Story Source: Materials provided by Newcastle_University. Note: Content
may be edited for style and length.


========================================================================== Journal Reference:
1. Annunziata Lopiccolo, Ben Shirt-Ediss, Emanuela Torelli, Abimbola
Feyisara Adedeji Olulana, Matteo Castronovo, Harold Fellermann,
Natalio Krasnogor. A last-in first-out stack data structure
implemented in DNA.

Nature Communications, 2021; 12 (1) DOI: 10.1038/s41467-021-25023-6 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/08/210812123103.htm

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