Ribose-Water Interactions Stabilize RNA Structures

Ribonucleic acid (RNA) is a biological molecule that plays an important part in organismal genetics as well as the creation and development of life. With a composition comparable to DNA, RNA may perform a range of biological functions depending on its spatial conformation or how the molecule folds in on itself.

A study published in the journal Proceedings of the National Academy of Sciences (PNAS) shows for the first time how the process of RNA folding at low temperatures could offer new insights into primordial biochemistry and the evolution of life on Earth.

Professor Fèlix Ritort of the Faculty of Physics and the Institute of Nanoscience and Nanotechnology (IN2UB) at the University of Barcelona leads the study, which is also signed by UB experts Paolo Rissone, Aurélien Severino, and Isabel Pastor.

New Biochemistry for RNA at Low Temperatures

RNA is generated by connecting ribose (a monosaccharide) molecules with phosphate groups that attach to four types of nitrogenous bases: adenine (A), guanine (G), cytosine (C), and uracil(U). Both the sequence of bases and the three-dimensional structure of RNA play important roles in the molecule's wide range of activities.

The scientists employed the mechanical unfolding of RNA to gain a detailed understanding of the many shapes that RNA takes when folded in on itself.

The folded structures of biological molecules, from DNA to RNA and proteins, determine their biological action. Without structure there is no function, and without function there is no life.”

Fèlix Ritort, Head, Small Biosystem Lab, Department of Condensed Matter Physics, University of Barcelona

The study found that RNA sequences that form hairpin structures began to adopt new, compact forms below 20 °C.

Ritort added, “All the RNA molecules studied share unexpected novel structures at low temperatures. We identified a range of temperatures between +20°C and -50°C. Below +20°C, ribose-water interactions start to become important, and a maximum of RNA stability is reached at +5°C, where the density of water is maximal. Below 5ºC, the new RNA stability is determined by ribose-water interactions until -50ºC, when the RNA unfolds again, leading to the phenomenon of cold denaturation”

The study hypothesizes that this temperature range is universal and shared by all RNA molecules. However, it is influenced by sequence and other environmental factors such as medium salt and acidity levels.

These RNA ranks are basic structures sustained by the creation of complementary base pairs: adenine binds to uracil (A-U), and guanine binds to cytosine.

The researchers believe that these new structures “are created due to the formation of hydrogen bonds between ribose and water that weigh as much or more than the interactions between complementary bases in RNA (A-U and G-C).”

Ritort added, “In fact, this phenomenon is only observed in RNA, whereas it is not observed in DNA, where the proton at the 2’ position of deoxyribose does not form hydrogen bonds with water”

To obtain its results, the scientists used optical tweezer force spectroscopy, a delicate and accurate method for assessing molecule thermodynamics. This approach has allowed researchers to evaluate entropy changes and heat capacity during the folding of various RNAs.

As a result, it detects a drop in the heat capacity of the folded state at 20°C, suggesting a reduction in the folded RNA's degrees of freedom (most likely owing to the effect caused by the ribose-water bonds).

Beyond the Traditional View of RNA

But what are the ramifications of this phenomenon for RNA biochemistry and biological function? To begin, the dominance of ribose-water interactions alters the previously established laws that govern how RNA biochemistry is maintained by A-U and G-C pairing, as well as base-to-base stacking pressures.

Ritort stated, “this new altered biochemistry that we define in the article has implications for organisms that inhabit cold regions of the Earth (psychrophiles), from alpine regions to the deep waters of the oceans and arctic territories, at temperatures below 10ºC in the eutectic phase of saline water”

Beyond the specific A-U and G-C pairing rules, “the new RNA biochemistry determined by ribose-water interactions indicates the existence of a primitive, coarse biochemistry based on ribose and other sugars that predates that of RNA itself, which we have called the sweet-RNA world. This primitive biochemistry possibly began to evolve in cold environments in vast outer space, most likely on celestial bodies close to stars and subject to thermal cycles of heat and cold”, concluded Ritort.