Ion-mediated RNA structural collapse: effect of spatial confinement

TL;DR

This study investigates how spatial confinement in cellular environments enhances ion-mediated RNA folding, revealing that confinement significantly increases ion efficiency in promoting RNA structural collapse.

Contribution

The paper introduces a model showing that spatial confinement enhances ion effects on RNA folding, a novel insight into cellular RNA behavior.

Findings

Ion efficiencies are increased by confinement for Na+ and Mg2+.

Confinement reduces electrostatic free energy differences.

Enhanced ion effects promote RNA structural collapse.

Abstract

RNAs are negatively charged molecules residing in macromolecular crowding cellular environments. Macromolecular confinement can influence the ion effects in RNA folding. In this work, using the recently developed tightly bound ion model for ion fluctuation and correlation, we investigate the confinement effect on the ion-mediated RNA structural collapse for a simple model system. We found that, for both Na$^+$ and Mg$^{2+}$, ion efficiencies in mediating structural collapse/folding are significantly enhanced by the structural confinement. Such an enhancement in the ion efficiency is attributed to the decreased electrostatic free energy difference between the compact conformation ensemble and the (restricted) extended conformation ensemble due to the spatial restriction.