• New DNA computer assesses water quality

    From ScienceDaily@1:317/3 to All on Thu Feb 17 21:30:44 2022
    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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