Scientists discover a ‘Goldilocks’ zone for DNA organization, opening new doors for drug development

PolyP and magnesium are involved in many biological processes. Thus, the findings could lead to new methods for tuning cellular responses, which could have impactful applications in translational medicine.

The ensuing study, published in Nature Communications on October 26, 2024, reveals a delicate “Goldilocks” zone — a specific magnesium concentration range — where DNA wraps around polyP-magnesium ion condensates. Similar to a thin eggshell covering a liquid-like interior, this seemingly simple structure may help cells organize and protect their genetic material.

This work began as a collaboration between co-senior authors Associate Professor Lisa Racki, PhD, and Professor Ashok Deniz, PhD, both in the Department of Integrative Structural and Computational Biology at Scripps Research. Racki had been studying these structures in bacterial cells, while Deniz’s next-door lab was exploring the physical chemistry of biomolecular condensates for the past decade. Collaboration, they realized, was the only way to unlock these ancient interactions.

“We knew that DNA was in close proximity to the magnesium-rich polyP condensates in cells, but we were totally surprised by the beautiful spheres of DNA that lit up under the microscope,” says Racki.

“Being molecular detectives, seeing these structures raised exciting questions for us about the physics and mathematics of the DNA shells and whether they influenced the polyP condensates,” adds Deniz.

Their microscopy images revealed that DNA wraps itself around a condensate, creating a thin eggshell-like barrier. This shell could affect molecule transportation and also slow down fusion: the process where two condensates merge into one. Without DNA shells, polyP-magnesium ion condensates readily fused — like how oil drops and vinegar fuse in a salad dressing bottle when shook.

However, careful examination showed that fusion overall slowed to varying extents, depending on DNA length. Longer DNA, the researchers suspected, caused greater entanglement on condensate surfaces — similar to how long hair tangles more than short hair.

DNA is more than 1,000 times thinner in diameter than condensates, making molecular details hard to visualize. Fortunately, infrastructure to capture such imaging has been developed by two other faculty members at Scripps Research: Assistant Professor Danielle Grotjahn, PhD, and Scripps Fellow Donghyun Raphael Park, PhD.

Teaming with Park, with help from Grotjahn, the researchers used cryo-electron tomography to closely examine the condensate surfaces. Using electrons instead of light, this technique captures three-dimensional, high-resolution images of samples that were rapidly frozen to preserve their structures. The new images revealed that DNA forms filaments protruding from condensate surfaces, resembling tangled hairs.

Another crucial discovery: DNA shell formation only occurred within a specific magnesium concentration range — too much or too little, and the shell wouldn’t materialize. This “Goldilocks” effect highlights how cells can regulate condensate structure, size and function simply by tuning control parameters.

“Although we think of cellular interfaces as boundaries, they also create a new landscape by providing a surface for molecules to organize,” notes Racki. “DNA may not actually be a tangled mess at the surface and is instead organized by these condensates.”

In this context, Deniz and Racki are particularly interested in understanding DNA supercoiling — how DNA twists like a spring to fit inside cells.

“Cells have to manage their DNA curls,” explains Racki. “Interestingly, the mathematics of DNA supercoiling results in ‘action-at-a-distance’ effects — like how twisting a rope can create coils far from where you’re holding it.”

The researchers suspect that DNA interactions with polyP condensates in cells might propagate local changes in DNA supercoiling over long distances, resulting in broader changes in gene expression and cell function. Investigating this effect is one of the team’s next goals.

“We’re excited by the prospects of leveraging these discoveries to develop new tools for cellular control — potentially simpler, more cost-effective approaches to manage biomatter for biomedicine,” says Deniz.

In addition to Deniz, Racki, Grotjahn and Park, authors of the study, “Reentrant DNA shells tune polyphosphate condensate size,” include co-first authors Ravi Chawla and Jenna K. A. Tom, and Tumara Boyd, Nicholas H. Tu and Tanxi Bai of Scripps Research.

This work was supported by funding from the National Institutes of Health (NIGMS Grant R35 GM130375, Grant DP2-GM-739-140918 and S10OD032467), Scripps Research start-up funds, a Postdoctoral Fellowship from the American Heart Association (Award #903967) and the Pew Scholars Program.