Molecular drivers of RNA phase separation.

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.