Genome complexity: DNA cellular interactions (Introduction)

by David Turell , Tuesday, June 30, 2020, 19:31 (1395 days ago) @ David Turell

Modeling of the 'bubbles' around the DNA:

https://phys.org/news/2020-06-burping-droplets-dna.html

"Liquid droplets formed from DNA display a peculiar response to enzymes. An international collaboration between LMU and UCSB has now been able to explain the mechanisms behind bubble formation.

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"Recent advances in cellular biology have found that the molecular components of living cells (such as DNA and proteins) can bind to 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.

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"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.

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"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."

Comment: The complexity of life includes physio-chemical reactions as well as molecular reactions. We haven't reached the end of unearthing the degree of complexity. It must be designed.