Genome complexity: physical DNA state (Introduction)

by David Turell , Wednesday, June 26, 2019, 00:12 (1765 days ago) @ David Turell

Its physical status is just right:

https://www.sciencedaily.com/releases/2019/06/190624173826.htm

"Inspired by ideas from the physics of phase transitions and polymer physics, researchers in the Divisions of Physical and Biological Sciences at UC San Diego set out specifically to determine the organization of DNA inside the nucleus of a living cell. The findings of their study, recently published in Nature Communications, suggest that the phase state of the genomic DNA is "just right" -- a gel poised at the phase boundary between gel and sol, the solid-liquid phase transition.

"Think of pudding, panna cotta -- or even porridge. The consistency of these delectables must be just right to be ideally enjoyed. Just as the "sol-gel" phase transition, according to the scientists, seems just right for explaining the timing of genomic interactions that dictate gene expression and somatic recombination.

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"By comparing experimental and simulated data, the scientists concluded that constrained motion is imposed by a network of cross-linked chromatin chains, or a mesh of bridges between the DNA strands that are characteristic of a gel phase. Yet, the amount of these cross-links is "just right" to poise the DNA near the sol phase -- a liquid phase describing a solution of uncross-linked chains.

"This pattern suggested to the scientists that a certain organizational principle of genomic DNA exists -- proximity to the sol-gel phase transition -- which explains how the genome can simultaneously possess stability and responsiveness within the nucleus.

"These results indicate that the packing pattern of DNA within a cell's nucleus has consequences for a cell's fate -- whether it becomes a live or diseased cell.

"'We have rigorous theories from physics -- abstract principles and mathematical equations. We have state-of-the-art experiments on biology -- innovative tracking of gene segments in live mammalian cell nuclei," noted Zhang. "It really amazes and excites me when the two aspects merge coherently into one story, where physics is not just a tool to describe the dynamics of gene segments, but helps to pinpoint the physical state of the genome, and further sheds light on the impact of the physical properties of this state on its biological function.''"

Comment: This precise physical status of DNA is a difficult state to achieve, and strongly suggests that it was designed to allow DNA a wide range of functions.