Physics: Bubbling and burping droplets of DNA

Date:
July 6, 2020
Source:
Ludwig-Maximilians-Universita"t Mu"nchen
Summary:
Liquid droplets formed from DNA display a peculiar response
to enzymes.

An international collaboration has now been able to explain the
mechanisms behind bubble formation.



FULL STORY ========================================================================== Liquid droplets formed from DNA display a peculiar response to enzymes. An international collaboration between Ludwig-Maximilians-Universitaet
(LMU) in Munich and UCSB has now been able to explain the mechanisms
behind bubble formation.


==========================================================================
A watched pot never boils ... but researchers from Ludwig-Maximilians University (LMU), Munich, and University of California in Santa Barbara
(UCSB) and found that's not the case when watching liquids formed from
DNA. Recent advances in cellular biology have found that the molecular components of living cells (such as DNA and proteins) can bind each other
and form liquid droplets that appear similar to oil droplets in shaken
salad dressing. These cellular droplets interact with other components
to carry out basic processes critical to life, yet little is known about
how those interactions function. To gain insight into this fundamental
process, the LMU/UCSB team used modern methods of nanotechnology to
engineer a model system, a liquid droplet formed from particles of DNA,
and watched those droplets as they interacted with a DNA- cleaving enzyme.

Surprisingly, they found, in certain cases, addition of the enzyme would
cause the DNA droplets to suddenly start bubbling, appearing just like
boiling water.

"The bizarre thing about the bubbling DNA is that we didn't heat the
system - - it's as if a pot of water started boiling even though you
forgot to turn on the stove," says Professor Omar Saleh from UCSB,
co-leader of the project.

However, the bubbling behavior didn't always occur -- sometimes adding
the enzyme would cause the droplets to smoothly shrink away, and it was
unclear why one response or the other would occur.

To get to the bottom of this mystery, the team carried out a rigorous
set of precision experiments quantifying the shrinking and bubbling
behaviors. They found that there were two types of shrinking behavior,
the first cause by enzymes cutting the DNA only on the droplet surface,
and the second caused by enzymes penetrating inside the droplet. "This observation was critical to unraveling the behavior, as it put it into
our heads that the enzyme could start nibbling away at the droplets from
the inside," notes co-leader Tim Liedl, Professor at the LMU, where the experiments were conducted.

By comparing the droplet response to the DNA particle design, the
team cracked the case: they found that bubbling and penetration-based
shrinking occurred together, and only happened when the DNA particles
were only lightly bound together, whereas strongly-bound DNA particles
would keep the enzyme on the outside. Saleh notes: "It's like trying
to walk through a crowd -- if the crowd is tightly holding hands, you
wouldn't be able to get through." The bubbles, then, happen only in the lightly-bound systems, when the enzyme can get through the crowded DNA particles to the interior of the droplet, and begin to eat away at the
droplet from the inside. The chemical fragments created by the enzyme
lead to an osmotic effect, where water is drawn in from the outside,
causing a swelling phenomenon that produces the bubbles. The bubbles
grow, reach the droplet surface, then release the fragments in a burp-
like gaseous outburst. "It is quite striking to watch, as the bubbles
swell and pop over and over," says Liedl.

The work demonstrates a complex relationship between the basic material properties of a biomolecular liquid, and its interactions with external components. The team believes the insight gained from studying the
bubbling process will lead to both better models of living processes,
and enhanced abilities to engineer liquid droplets for use as synthetic bioreactors.

The research was enabled by an award to Professor Saleh from the Alexander
von Humboldt Foundation, which enabled him to visit Munich and work
directly with Tim Liedl on this project. "These types of international collaborations are extremely productive," says Saleh.


========================================================================== Story Source: Materials provided by
Ludwig-Maximilians-Universita"t_Mu"nchen. Note: Content may be edited
for style and length.


========================================================================== Journal Reference:
1. Omar A. Saleh, Byoung-jin Jeon, Tim Liedl. Enzymatic degradation of
liquid droplets of DNA is modulated near the phase
boundary. Proceedings of the National Academy of Sciences, 2020;
202001654 DOI: 10.1073/ pnas.2001654117 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/07/200706140845.htm

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