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Molecular drivers of RNA phase separation.

Vysakh Ramachandran¹, Davit A Potoyan^1,2,3

¹Department of Chemistry, Iowa State University, Ames, IA 50011.

Proceedings of the National Academy of Sciences of the United States of America

|November 4, 2025

Summary

RNA can form protein-free condensates influenced by magnesium ions, exhibiting base-specific phase transitions. This study reveals how ion concentration, sequence, and temperature control RNA condensate behavior.

Keywords:

RNA biomolecular condensates phase-separation

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Area of Science:

Biochemistry
Molecular Biology
Biophysics

Background:

RNA molecules are key in biomolecular condensate assembly and regulation.
RNA can phase-separate independently of proteins, forming unique condensates.
Magnesium ions critically influence RNA condensate dynamics and thermodynamics, leading to base-specific phase transitions.

Purpose of the Study:

To elucidate the molecular basis of sequence and ion-dependent phase behavior in RNA condensates.
To investigate the driving forces behind RNA condensate formation and stability under varying conditions.
To understand the role of magnesium ions and nucleotide chemistry in RNA phase separation.

Main Methods:

Atomistic simulations of RNA tetranucleotides and their analogs.
Mapping equilibrium thermodynamic profiles and structural ensembles.
Systematic analysis of sequence-, ion-, and temperature-dependent phase behaviors.

Main Results:

Magnesium ions induce disorder-order transitions, promoting lower critical solution temperatures (LCSTs) in RNA condensates.
RNA condensate thermal stability follows the order G > A > C > U, driven by base stacking and hydrogen bonding.
Base chemistry and the 2'hydroxyl group modulate the LCST response; nucleotide modifications fine-tune self-assembly thresholds.

Conclusions:

RNA condensate phase behavior is intricately controlled by magnesium ions, sequence composition, and temperature.
The findings provide molecular insights into RNA-driven phase separation and its regulation.
Nucleotide modifications offer a mechanism to precisely control RNA condensate formation and function.