Goldilocks and RNA: where Mg2+ concentration is just right

Abstract

Magnesium, the most abundant divalent cation in cells, catalyzes RNA cleavage but also promotes RNA folding. Because folding can protect RNA from cleavage, we predicted a ‘Goldilocks landscape’, with local maximum in RNA lifetime at Mg2+ concentrations required for folding. Here, we use simulation and experiment to discover an innate and sophisticated mechanism of control of RNA lifetime. By simulation we characterized RNA Goldilocks landscapes and their dependence on cleavage and folding parameters. Experiments with yeast tRNAPhe and the Tetrahymena ribozyme P4–P6 domain show that structured RNAs can inhabit Goldilocks peaks. The Goldilocks peaks are tunable by differences in folded and unfolded cleavage rate constants, Mg2+ binding cooperativity, and Mg2+ affinity. Different folding and cleavage parameters produce Goldilocks landscapes with a variety of features. Goldilocks behavior allows ultrafine control of RNA chemical lifetime, whereas non-folding RNAs do not display Goldilocks peaks of protection. In sum, the effects of Mg2+ on RNA persistence are expected to be pleomorphic, both protecting and degrading RNA. In evolutionary context, Goldilocks behavior may have been a selectable trait of RNA in an early Earth environment containing Mg2+ and other metals.

Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations

“…While Mg 2+ is only found at concentrations of 10–30 mM in intracellular environments, most of the Mg 2+ tends to be bound to ribosomes, polynucleotides, and ATP . Still, RNA molecules are sensitive to the Mg 2+ concentration, where an optimal Mg 2+ concentration leads to a maximum lifetime of an RNA molecule . To analyze the rate at which Mg 2+ binds during our McMD simulations, we analyzed the reweighted structural ensemble and found that on average 14.65 Mg 2+ and 58.77 K + ions were bound simultaneously (i.e., within 5 Å) to the RNA, with the Mg 2+ binding density shown in Figure S8.…”

“… 44 Still, RNA molecules are sensitive to the Mg 2+ concentration, where an optimal Mg 2+ concentration leads to a maximum lifetime of an RNA molecule. 45 To analyze the rate at which Mg 2+ binds during our McMD simulations, we analyzed the reweighted structural ensemble and found that on average 14.65 Mg 2+ and 58.77 K + ions were bound simultaneously (i.e., within 5 Å) to the RNA, with the Mg 2+ binding density shown in Figure S8 . During the preparation of the system, 15 Mg and 106 K ions were added to the bulk solvent (randomly), suggesting that RNA is much more likely to bind to Mg 2+ than to bind to K + , and even higher concentrations of Mg 2+ might also be acceptable.…”

Natural soda lakes provide compatible conditions for RNA and membrane function that could have enabled the origin of life

“…S6 ), which is roughly consistent with previous estimates of ∼1% RNA degradation after 72 hours in 1 M K + and 5 mM Mg 2+ at pH 9.5 ( 36 ). The relatively low concentration of divalent cations may compensate for the high pH in lake water to keep the hydrolysis rate low ( 37 ). However, we also observed that fewer primers had been extended by at least three nucleotides after 72 hours in lake water, relative to standard laboratory conditions (Fig.…”

Optimizing Messenger RNA Analysis Using Ultra-Wide Pore Size Exclusion Chromatography Columns

“…In another investigation, we tested the effects of salts containing multivalent ions, such as magnesium ions [ 23 ]. It has previously been reported that multivalent ions (such as magnesium) can have a significant effect on nucleic acid structure (folding) [ 24 , 25 ]. For this reason, MgSO 4 and MgCl 2 were added to the mobile phase in small amounts (2 and 10 mM) as a higher concentration of Mg 2+ ions is known to impact negatively the structure of nucleic acids as reported elsewhere [ 24 , 25 ].…”

“…It has previously been reported that multivalent ions (such as magnesium) can have a significant effect on nucleic acid structure (folding) [ 24 , 25 ]. For this reason, MgSO 4 and MgCl 2 were added to the mobile phase in small amounts (2 and 10 mM) as a higher concentration of Mg 2+ ions is known to impact negatively the structure of nucleic acids as reported elsewhere [ 24 , 25 ]. The corresponding chromatograms are shown in Figure 2 and Figure S3 .…”