Stabilization of RNA Structure by Mg Ions

Laing, Lance G.; Gluick, Thomas C.; Draper, David E.

doi:10.1006/jmbi.1994.1256

Cited by 169 publications

(148 citation statements)

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“…Most formulations of the effects of Mg 2ϩ on RNA folding transitions have considered Mg 2ϩ as a ligand that binds stoichiometrically to sites in the folded forms of the RNA, e.g., I ϩ nMg 2ϩ º N⅐(Mg 2ϩ ) n (11)(12)(13). This approach oversimplifies the complex set of interactions taking place between RNA, Mg 2ϩ , monovalent cations, and anions (6).…”

Section: [1]mentioning

confidence: 99%

Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Grilley

Soto²,

Draper³

2006

Proc. Natl. Acad. Sci. U.S.A.

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119

184

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Mg 2؉ ions are very effective at stabilizing tertiary structures in RNAs. In most cases, folding of an RNA is so strongly coupled to its interactions with Mg 2؉ that it is difficult to separate free energies of Mg 2؉ -RNA interactions from the intrinsic free energy of RNA folding. To devise quantitative models accounting for this phenomenon of Mg 2؉ -induced RNA folding, it is necessary to independently determine Mg 2؉ -RNA interaction free energies for folded and unfolded RNA forms. In this work, the energetics of Mg 2؉ -RNA interactions are derived from an assay that measures the effective concentration of Mg 2؉ in the presence of RNA. These measurements are used with other measures of RNA stability to develop an overall picture of the energetics of Mg 2؉ -induced RNA folding. Two different RNAs are discussed, a pseudoknot and an rRNA fragment. Both RNAs interact strongly with Mg 2؉ when partially unfolded, but the two folded RNAs differ dramatically in their inherent stability in the absence of Mg 2؉ and in the free energy of their interactions with Mg 2؉ . From these results, it appears that any comprehensive framework for understanding Mg 2؉ -induced stabilization of RNA will have to (i) take into account the interactions of ions with the partially unfolded RNAs and (ii) identify factors responsible for the widely different strengths with which folded tertiary structures interact with Mg 2؉ .cations ͉ ion interaction coefficients ͉ Wyman linkage relations M g 2ϩ ions strongly stabilize RNA tertiary structures under conditions that only weakly affect RNA secondary structure stability, a phenomenon first studied in the folding of transfer RNA (1, 2). Although the sensitivity of RNA folding to Mg 2ϩ has been amply documented for many RNAs, it is still unknown how this sensitivity is quantitatively related to the strengths of Mg 2ϩ -RNA interactions. Thus, for most RNAs, the magnitude of the intrinsic RNA instability is unknown, nor is it known how much more favorably Mg 2ϩ interacts with the native RNA structure than with structures from which folding takes place. Lacking this fundamental overview of Mg 2ϩ -RNA interaction free energies, it has not been possible to carry out extensive evaluations of theoretical models that seek to explain Mg 2ϩ -induced RNA folding in terms of the underlying physical interactions (3, 4).In this article, we parse the tertiary folding of two different RNAs into the intrinsic free energy of folding in the absence of Mg 2ϩ and the free energies of Mg 2ϩ interactions with folded and partially folded states. To obtain the relevant free energies, we devised a practical experimental method for measuring the effect of RNA on Mg 2ϩ ion activities and derived the equations necessary for extracting Mg 2ϩ -RNA interaction free energies from the experimental data. The two RNAs have vastly different stabilities in the absence of Mg 2ϩ and correspondingly large differences in the favorable interactions of the native RNA structures with Mg 2ϩ . Clearly, different RNAs use different strategies ...

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Section: [1]mentioning

confidence: 99%

Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Grilley

Soto²,

Draper³

2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

119

184

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“…The greater sensitivity of tertiary interactions to divalent metal ions compared with secondary structure has been observed in many RNAs (e.g., see refs. [47][48][49]. What is unusual in this system is that the assembly of core helices (I C ) is separated by its Mg 2ϩ requirement from the formation of stable tertiary interactions (N).…”

Section: D Model Of the Azoarcus Ribozymementioning

confidence: 99%

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

Rangan

Masquida

Westhof

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

135

166

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Compact but non-native intermediates have been implicated in the hierarchical folding of several large RNAs, but there is little information on their structure. In this article, ribonuclease and hydroxyl radical cleavage protection assays showed that base pairing of core helices stabilize a compact state of a small group I ribozyme from Azoarcus pre-tRNA ile . Base pairing of the ribozyme core requires 10-fold less Mg 2؉ than stable tertiary interactions, indicating that assembly of helices in the catalytic core represents a distinct phase that precedes the formation of native tertiary structure. Tertiary folding occurs in <100 ms at 37°C. Such rapid folding is unprecedented among group I ribozymes and illustrates the association between structural complexity and folding time. A 3D model of the Azoarcus ribozyme was constructed by identifying homologous sequence motifs in rRNA. The model reveals distinct structural features, such as a large interface between the P4 -P6 and P3-P9 domains, that may explain the unusual stability of the Azoarcus ribozyme and the cooperativity of folding.RNA modeling ͉ RNA structure ͉ metal ions ͉ hydroxyl radical footprinting T he assembly of RNA into functional structures underlies many steps in gene expression and regulation. Recent work has outlined the Mg 2ϩ -dependent folding pathways of large ribozymes (1, 2). Experimental and theoretical results suggest that the initial association of divalent cations induces collapse of the extended RNA chain into more compact structures that favor formation of tertiary interactions (3-8). The structure of the compact intermediates and the extent to which these interactions lead to the native conformation are not yet characterized.On the one hand, individual domains of the Tetrahymena group I ribozyme and the catalytic domain of RNase P fold on a time scale (10-100 ms) similar to the initial collapse transitions of the ribozyme (6, 9, 10). On the other hand, nonspecific collapse results in an ensemble of native and non-native conformations. Many larger RNAs, such as the Tetrahymena group I and Bacillus subtilis RNase P ribozymes, fold slowly in vitro because a large fraction of the RNA population becomes trapped in misfolded intermediates (11,12). An important question is whether RNAs with a simpler 3D architecture are more likely to fold directly to the native structure, as expected from theoretical models (4). Furthermore, we want to know whether the likelihood of misfolding can be predicted from the specificity of counterion-induced collapse.We investigated the Mg 2ϩ -dependent equilibrium folding pathway and constructed a 3D model of the Azoarcus group I intron. The 205-nt group IC3 intron in the pre-tRNA ile of the Azoarcus bacterium is the smallest known self-splicing group I intron (13). It retains the conserved catalytic core common to all group I introns, but lacks the peripheral domains that stabilize folding intermediates of the larger Tetrahymena intron (14).We observed two macroscopic folding transitions in the Azoarcus ribozyme...

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“…36,37 Only the U to I transition was assumed to be cooperative with respect to Mg 2þ . Because the ions are responding to changes in the electrostatic field of the RNA rather than mass action, 38 the Hill constant reflects the relative stabilization of U, I and N by Mg 2þ , rather than the precise number of excess magnesium ions associated with the folded RNA. The urea dependence of the kinetics was fit to the linear extrapolation model: 39 where ½D is the concentration of urea, and the first two terms represent the urea-dependence of the native (N) and unfolded (U) states, respectively.…”

Section: Folding Kineticsmentioning

confidence: 99%

Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA

Rangan

Masquida

Westhof

et al. 2004

Journal of Molecular Biology

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Stabilization of RNA Structure by Mg Ions

Cited by 169 publications

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Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA

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Stabilization of RNA Structure by Mg Ions

Cited by 169 publications

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Mg 2+ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Mg 2+ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA

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Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures