The motors can sense chemical information in their environment, process
that information, and then respond accordingly, mimicking some basic properties of living cells.

Date:
April 7, 2022
Source:
Emory University
Summary:
Chemists integrated computer functions into rolling DNA-based
motors, opening a new realm of possibilities for miniature,
molecular robots.

These DNA-based motors combine computational power with the ability
to burn fuel and move in an intentional direction.



FULL STORY ========================================================================== Chemists integrated computer functions into rolling DNA-based motors,
opening a new realm of possibilities for miniature, molecular
robots. Nature Nanotechnology published the development, the first
DNA-based motors that combine computational power with the ability to
burn fuel and move in an intentional direction.


==========================================================================
"One of our big innovations, beyond getting the DNA motors to perform
logic computations, is finding a way to convert that information into
a simple output signal -- motion or no motion," says Selma Piranej,
an Emory University PhD candidate in chemistry, and first author of the
paper. "This signal can be read by anyone holding a cell phone equipped
with an inexpensive magnifying attachment." "Selma's breakthrough removes major roadblocks that stood in the way of making DNA computers useful and practical for a range of biomedical applications," says Khalid Salaita,
senior author of the paper and an Emory professor of chemistry at Emory University. Salaita is also on the faculty of the Wallace H.

Coulter Department of Biomedical Engineering, a joint program of Georgia
Tech and Emory.

The motors can sense chemical information in their environment, process
that information, and then respond accordingly, mimicking some basic
properties of living cells.

"Previous DNA computers did not have directed motion built in,"
Salaita says.

"But to get more sophisticated operations, you need to combine both
computation and directed motion. Our DNA computers are essentially
autonomous robots with sensing capabilities that determine whether they
move or not." The motors can be programmed to respond to a specific
pathogen or DNA sequence, making them a potential technology for medical testing and diagnostics.



========================================================================== Another key advance is that each motor can operate independently, under different programs, while deployed as a group. That opens the door for
a single massive array of the micron-sized motors to carry out a variety
of tasks and perform motor-to-motor communication.

"The ability for the DNA motors to communicate with one another is a
step towards producing the kind of complex, collective action generated
by swarms of ants or bacteria," Salaita says. "It could even lead to
emergent properties." DNA nanotechnology takes advantage of the natural affinity for the DNA bases A, G, C and T to pair up with one another. By
moving around the sequence of letters on synthetic strands of DNA,
scientists can get the strands to bind together in ways that create
different shapes and even build functioning machines.

The Salaita lab, a leader in biophysics and nanotechnology, developed
the first rolling DNA-based motor in 2015. The device was 1,000 times
faster than any other synthetic motor, fast-tracking the burgeoning
field of molecular robotics. Its high speed allows a simple smart phone microscope to capture its motion through video.

The motor's "chassis" is a micron-sized glass sphere. Hundreds of DNA
strands, or "legs" are allowed to bind to the sphere. These DNA legs
are placed on a glass slide coated with the reactant RNA, the motor's
fuel. The DNA legs are drawn to the RNA, but as soon as they set foot
on it they erase it through the activity of an enzyme that is bound to
the DNA and destroys only RNA. As the legs bind and then release from
the substrate, they keep guiding the sphere along.



==========================================================================
When Piranej joined the Salaita lab in 2018, she began working on a
project to take the rolling motors to the next level by building in
computer programming logic.

"It's a major goal in the biomedical field to take advantage of DNA for computation," Piranej says. "I love the idea of using something that's
innate in all of us to engineer new forms of technology." DNA is like
a biological computer chip, storing vast amounts of information.

The basic units of operation for DNA computation are short strands of
synthetic DNA. Researchers can change the "program" of DNA by tweaking
the sequences of AGTC on the strands.

"Unlike a hard, silicon chip, DNA-based computers and motors can function
in water and other liquid environments," Salaita says. "And one of the
big challenges in fabricating silicon computer chips is trying to pack
more data into an ever-smaller footprint. DNA offers the potential to run
many processing operations in parallel in a very small space. The density
of operations you could run might even go to infinity." Synthetic DNA
is also biocompatible and cheap to make. "You can replicate DNA using
enzymes, copying and pasting it as many times as you want," Salaita says.

"It's virtually free." Limitations remain, however, in the nascent field
of DNA computation. A key hurdle is making the output of the computations easily readable. Current techniques heavily rely on tagging DNA with fluorescent molecules and then measuring the intensity of emitted light
at different wavelengths. This process requires expensive, cumbersome equipment. It also limits the signals that can be read to those present
in the electromagnetic spectrum.

Although trained as a chemist, Piranej began learning the basics of
computer science and diving into bioengineering literature to try to
overcome this hurdle. She came up with the idea of using a well-known
reaction in bioengineering to perform the computation and pairing it
with the motion of the rolling motors.

The reaction, known as toehold-mediated strand displacement, occurs on
duplex DNA -- two complementary strands. The strands are tightly hugging
one another except for one loose, floppy end of a strand, known as the
toe hold. The rolling motor can be programmed by coating it with duplex
DNA that is complementary to a DNA target -- a sequence of interest.

When the molecular motor encounters the DNA target as it rolls along
its RNA track, the DNA target binds to the toe hold of the duplex DNA,
strips it apart, and anchors the motor into place. The computer read
out becomes simply "motion" or "no motion." "When I first saw this
concept work during an experiment, I made this really loud, excited
sound," Piranej recalls. "One of my colleagues came over and asked,
'Are you okay?' Nothing compares to seeing your idea come to life like
that. That's a great moment." These two basic logic gates of "motion" or
"no motion" can be strung together to build more complicated operations, mimicking how regular computer programs build on the logic gates of
"zero" or "one." Piranej took the project even further by finding a way
to pack many different computer operations together and still easily read
the output. She simply varied the size and materials of the microscopic
spheres that form the chassis for the DNA-based rolling motors. For
instance, the spheres can range from three to five microns in diameter
and be made of either silica or polystyrene.

Each alteration provides slightly different optical properties that can
be distinguished through a cell phone microscope.

The Salaita lab is working to establish a collaboration with scientists at
the Atlanta Center for Microsystems Engineered Point-of-Care Technologies,
an NIH- funded center established by Emory and Georgia Tech. They are
exploring the potential for the use of the DNA-computing technology for
home diagnostics of COVID-19 and other disease biomarkers.

"Developing devices for biomedical applications is especially rewarding
because it's a chance to make a big impact in people's lives," Piranej
says. "The challenges of this project have made it more fun for me,"
she adds.


========================================================================== Story Source: Materials provided by Emory_University. Original written
by Carol Clark. Note: Content may be edited for style and length.


========================================================================== Related Multimedia:
*
The_high_speed_of_the_rolling_DNA-based_motor_allows_a_simple_smart_phone
microscope_to_capture_its_motion_through_video ========================================================================== Journal Reference:
1. Selma Piranej, Alisina Bazrafshan, Khalid
Salaita. Chemical-to-mechanical
molecular computation using DNA-based motors with onboard
logic. Nature Nanotechnology, 2022; DOI: 10.1038/s41565-022-01080-w ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/04/220407161939.htm

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