New DNA computer assesses water quality
Genetic networks mimic electronic circuits to perform a range of logic functions
Date:
February 17, 2022
Source:
Northwestern University
Summary:
Synthetic biologists have developed a low-cost, easy-to-use,
hand-held device that can let users know -- within mere minutes
-- if their water is safe to drink. The new device works by using
powerful and programmable genetic networks, which mimic electronic
circuits, to perform a range of logic functions.
FULL STORY ========================================================================== Northwestern University synthetic biologists have developed a low-cost,
easy- to-use, hand-held device that can let users know -- within mere
minutes -- if their water is safe to drink.
==========================================================================
The new device works by using powerful and programmable genetic networks,
which mimic electronic circuits, to perform a range of logic functions.
Among the DNA-based circuits, for example, the researchers engineered
cell-free molecules into an analog-to-digital converter (ADC), a
ubiquitous circuit type found in nearly all electronic devices. In
the water-quality device, the ADC circuit processes an analog input (contaminants) and generates a digital output (a visual signal to inform
the user).
The research will be published on Feb. 17 in the journal Nature Chemical Biology.
Equipped with a series of eight small test tubes, the device glows green
when it detects a contaminant. The number of tubes that glow depend
upon how much contamination is present. If only one tube glows, then
the water sample has a trace level of contamination. But if all eight
tubes glow, then the water is severely contaminated. In other words,
the higher concentration of contamination leads to a higher signal.
"We programmed each tube to have a different threshold for
contaminations," said Northwestern's Julius B. Lucks, who led the
research. "The tube with the lowest threshold will light up all the
time. If all the tubes light up, then there is a big problem. Building
circuits and programmable DNA computing opens up many possibilities for
other types of smart diagnostics." Lucks is a professor of chemical and biological engineering in Northwestern's McCormick School of Engineering
and a member of the Center for Synthetic Biology. The paper's co-authors include Jaeyoung Jung, Chloe' Archuleta and Khalid Alam -- all from Northwestern.
==========================================================================
Meet ROSALIND The new system builds off work that Lucks and his team
published in Nature Biotechnology in July 2020. In that work, the team introduced ROSALIND (named after famed chemist Rosalind Franklin and
short for "RNA output sensors activated by ligand induction"), which
could sense 17 different contaminants in a single drop of water. When the
test detected a contaminant exceeding the U.S Environmental Protection
Agency's standards, it either glowed green or not to give a simple, easy-to-read positive or negative result.
To develop ROSALIND, Lucks and his team employed cell-free synthetic
biology.
With synthetic biology, researchers take molecular machinery -- including
DNA, RNA and proteins -- out of cells, and then reprogram that machinery
to perform new tasks. At the time, Lucks likened ROSALIND's inner workings
to "molecular taste buds." "We found out how bacteria naturally taste
things in their water," he said.
"They do so with little molecular-level 'taste buds.' Cell-free synthetic biology allows us to take those little molecular taste buds out and put
them into a test tube. We can then 're-wire' them to produce a visual
signal. It glows to let the user quickly and easily see if there's
a contaminant in the water." Molecular brainpower Now, in the new
version -- dubbed ROSALIND 2.0 -- Lucks and his team have added a
"molecular brain."
==========================================================================
"The initial platform was a bio-sensor, which acted like a taste
bud," Lucks said. "Now we have added a genetic network that works
like a brain. The bio- sensor detects contamination, but then the
output of the bio-sensor feeds into the genetic network, or circuit,
which works like a brain to perform logic." Researchers freeze-dried
the reprogrammed "molecular brains" to become shelf- stable and put
them into test tubes. Adding a drop of water to each tube sets off a
network of reactions and interactions, ultimately causing the freeze-
dried pellet to glow in the presence of a contaminant.
To test the new system, Lucks and his team demonstrated that it could successfully detect concentration levels of zinc, an antibiotic and
an industrial metabolite. Giving the level of contamination -- rather
than a simple positive or negative result -- is important for informing mitigation strategies, Lucks said.
"After we introduced ROSALIND, people said they wanted a platform that
could also give concentration amounts," he said. "Different contaminants
at different levels require different strategies. If you have a low level
of lead in your water, for example, then you might be able to tolerate
it by flushing your water lines ahead of using them. But if you have
high levels, then you need to stop drinking your water immediately and
replace your water line." Empowering individuals Ultimately, Lucks
and his team hope to empower individuals to test their own water on a
regular basis. With inexpensive, hand-held devices like ROSALIND, that
may soon become a reality.
"It's clear that we need to enable people with information to make
important, sometimes lifesaving decisions," Lucks said. "We're seeing
that with at-home tests for COVID-19. People need at-home tests because
they need that information quickly and regularly. It's similar with
water. There are many cases where water quality needs to be measured
routinely. It's not a one-time thing because contamination levels can
change over time." The study, "Programming cell-free biosensors with
DNA strand displacement circuits," was supported by the U.S. Department
of Defense, the National Science Foundation, the Crown Family Center
for Jewish and Israel Studies and the Searle Funds at The Chicago
Community Trust.
Video:
https://youtu.be/OAQCnDHzqaE ========================================================================== Story Source: Materials provided by Northwestern_University. Original
written by Amanda Morris. Note: Content may be edited for style and
length.
========================================================================== Journal Reference:
1. Jaeyoung K. Jung, Chloe' M. Archuleta, Khalid K. Alam, Julius
B. Lucks.
Programming cell-free biosensors with DNA strand displacement
circuits.
Nature Chemical Biology, 2022; DOI: 10.1038/s41589-021-00962-9 ==========================================================================
Link to news story:
https://www.sciencedaily.com/releases/2022/02/220217122339.htm
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