One tiny chemical difference between RNA and DNA may help explain how life began

Without cellular compartments, fragile RNA molecules would have faced major obstacles on the early Earth. They would have needed to encounter one another often enough to interact while also surviving a hot, acidic, and chemically challenging environment.

One possible solution is RNA's ability to gather into liquid-like droplets known as condensates. These structures do not have membranes, but they can concentrate RNA molecules in one place. That could have increased the chances for chemical interactions while also providing some protection from harsh surroundings.

Why RNA Forms Droplets So Easily

A new study led by the University at Buffalo is helping explain why RNA is especially good at forming these condensates. Published in Nature Communications under the journal's early access guidelines, the research shows that a very small chemical difference between RNA and DNA can strongly influence how readily RNA forms droplets as temperatures increase.

The same chemical feature also appears to make RNA condensates more likely to develop interconnected networks and shift from a fluid state into a more rigid, gel like structure.

"These findings reveal, for the first time, how remarkably small changes in molecular chemistry can control the emergence of much larger, self-organized biomolecular structures like RNA condensates," says lead corresponding author Priya R. Banerjee, PhD, Twentieth Century Club Professor in the UB Department of Physics. "They could allow us to eventually address even deeper questions, like whether these condensates helped bridge the gap between simple molecules and the earliest forms of life."

The study was conducted in collaboration with Jerelle Joseph, PhD, assistant professor of chemical and biological engineering at Princeton University. The research was supported by the National Institutes of Health, the National Science Foundation, and Hypothesis Fund.

Testing a Key Idea in RNA World Theory

The work is part of Banerjee's broader research into RNA world theory, which proposes that RNA played a central role in the emergence of life on Earth.

RNA is unusual because it can both store genetic information and help drive chemical reactions. Those abilities may have allowed early RNA molecules to carry out chemistry that eventually contributed to the emergence of DNA, proteins and the first cells.

However, RNA world theory has long faced major unanswered questions. RNA is relatively unstable, raising the issue of how it could have survived under harsh prebiotic conditions. Scientists also need to explain how enough RNA molecules could have gathered in the same place to interact before cell membranes existed.

RNA condensates may offer part of the answer.

A 2023 study led by Banerjee showed that RNA has a natural tendency to organize into liquid-like droplets at high temperatures. The new work builds on those findings by directly comparing RNA with single stranded DNA that contained essentially the same sequences.

RNA Condenses More Easily Than DNA

In laboratory experiments, the researchers found that RNA began forming droplets at temperatures about 10 degrees Celsius lower than the corresponding DNA. That indicated that RNA had a substantially stronger tendency to condense.

RNA molecules were also more likely to form connected networks inside the droplets. As those networks developed, the droplets changed from a more fluid material into something more gel-like. Such a transition could potentially have helped protect RNA under difficult environmental conditions.

The reason appears to come down to an extremely small difference in molecular structure.

RNA and DNA differ chemically by only one oxygen atom in each sugar unit. Every RNA sugar contains a chemical group called a 2′-hydroxyl (2′-OH), which DNA does not have.

One Tiny Chemical Difference Has a Big Effect

To understand how that feature changes RNA's behavior, the researchers used temperature controlled microscopy, small angle X ray scattering and molecular dynamics simulations performed by the Joseph group.

Their results suggest that the 2′-OH allows RNA to interact more strongly with magnesium ions. RNA also appears to hold fewer water molecules around its backbone than DNA.

Together, those differences make it easier for RNA molecules to approach one another and assemble as temperatures rise.

The team tested the importance of the 2′-OH even further by chemically changing it to 2′-Ome, similar to what's found in many natural RNA. That modification reduced RNA's tendency to form condensates and also changed whether the resulting structures remained fluid or transitioned into a gel-like state.

"This single oxygen-containing group on RNA's sugar has a surprisingly powerful effect on whether these molecules come together, remain dynamic or become arrested into a gel-like material," says first author Gable Wadsworth, PhD, a postdoc in Banerjee's lab who will join the University of Texas at El Paso as an assistant professor this fall.

Building RNA Compartments That Behave Like Cells

Banerjee's lab is now trying to take the findings a step further by engineering RNA droplets that can carry out some of the basic activities performed by cells, including biochemical reactions.

The researchers are working to program these droplets so they behave as active, dynamic, cell-sized compartments. If successful, the work could provide a foundation for creating synthetic cells made entirely from RNA.

It could also offer new insight into how simple molecules began organizing themselves into increasingly complex systems long before modern cells appeared.

"These kinds of self-organizing RNA compartments were possibly a step along the way to single-cell organisms," Banerjee says.