Ion-mediated RNA structural collapse: effect of spatial confinement

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.

22 pages, 5 figures

References in corpus (4)

• Size, shape, and flexibility of RNA structures
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• Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA
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• Flexibility of short DNA helices with finite-length effect: from base pairs to tens of base pairs
• RNA structure prediction: progress and perspective
• Potential of mean force between like-charged nanoparticles: Many-body effect
• Calculating potential of mean force between like-charged nanoparticles: a comprehensive study on salt effects