Charge Density of Divalent Metal Cations Determines RNA Stability

Koculi, Eda; Hyeon, Changbong; Thirumalai, D.; Woodson, Sarah A.

doi:10.1021/ja068027r

Cited by 165 publications

(230 citation statements)

References 68 publications

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“…Moreover, recent studies have shown valence, size, and shape of counterions profoundly influence RNA folding. [147][148][149][150][151] Despite the complexity, it is possible to devise physics-based models that capture the essential aspects of RNA folding and dynamics. In order to provide a framework for understanding and anticipating the outcomes of increasingly sophisticated experiments involving RNA we have developed two classes of models.…”

Section: Rna Foldingmentioning

confidence: 99%

Minimal Models for Proteins and RNA: From Folding to Function

Pincus

Cho

Hyeon

et al. 2008

Progress in Molecular Biology and Translational Science

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We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key applications ranging from folding of proteins with disulfide bonds to functions of molecular machines. After presenting the theoretical basis that justifies the use of CG models, we explore the biophysical basis for the emergence of a finite number of folds from lattice models. The lattice model simulations of approach to the folded state show that non-native interactions are relevant only early in the folding process -a finding that rationalizes the success of structure-based models that emphasize native interactions. Applications of off-lattice C α and models that explicitly consider side chains (C α -SCM) to folding of β-hairpin and effects of macromolecular crowding are briefly discussed. Successful applications of a new class of off-lattice models, referred to as the Self- We also present two distinct models for RNA, namely, the Three Site Interaction (TIS) model and the SOP model, that probe forced unfolding and force quench refolding of a simple hairpin and Azoarcus ribozyme. The unfolding pathways of Azoarcus ribozyme depend on the loading rate, while constant force and constant loading rate simulations of the hairpin show that both forced-unfolding and force-quench refolding pathways are heterogeneous. The location of the transition state moves as force is varied. The predictions based on the SOP model show that force-induced unfolding pathways of the ribozyme can be dramatically changed by varying the loading rate. We conclude with a discussion of future prospects for the use of coarse-grained models in addressing problems of outstanding interest in biology.

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Section: Rna Foldingmentioning

confidence: 99%

Minimal Models for Proteins and RNA: From Folding to Function

Pincus

Cho

Hyeon

et al. 2008

Progress in Molecular Biology and Translational Science

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“…In the past decades, extensive experiments have been performed to investigate how metal ions promote RNA tertiary structural folding and stabilize tertiary structures; see Table 3 [16,19,32,[46][47][48][49][50][51][52][53][54][55][56][57][58][59][60]. These experiments have revealed several important roles of metal ions, especially Mg 2+ , in tertiary structural folding as shown below:…”

Section: Stabilization Of Tertiary Structuresmentioning

confidence: 99%

“…Native gel electrophoresis experiments [67] showed that higher [Mg 2+ ] and metal ions of higher charge density (charge/volume) would significantly stabilize the non-specific collapsed intermediates. The stabilization of the nonspecific collapsed state slows down the (productive) folding to the final native state which requires the formation and stabilization of specific native contacts [49,67]. In addition, a recent experiment showed that, depending on the ionic condition of the solution, the kinetic partitioning of the folding flux can be dependent on the initial conformational ensemble [68].…”

Section: Tetrahymenamentioning

confidence: 99%

3 Importance of Diffuse Metal Ion Binding to RNA

Tan¹,

Chen²

2015

Structural and Catalytic Roles of Metal Ions in RNA

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RNAs are highly charged polyanionic molecules. RNA structure and function are strongly correlated with the ionic condition of the solution. The primary focus of this article is on the role of diffusive ions in RNA folding. Due to the long-range nature of electrostatic interactions, the diffuse ions can contribute significantly to RNA structural stability and folding kinetics. We present an overview of the experimental findings as well as the theoretical developments on the diffuse ion effects in RNA folding. This review places heavy emphasis on the effect of magnesium ions. Magnesium ions play a highly efficient role in stabilizing RNA tertiary structures and promoting tertiary structural folding. The highly efficient role goes beyond the mean-field effect such as the ionic strength. In addition to the effects of specific ion binding and ion dehydration, ion-ion correlation for the diffuse ions can contribute to the efficient role of the multivalent ions such as the magnesium ions in RNA folding.

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“…As mentioned above, solution conditions (especially monovalent and divalent cation concentration) significantly alter the three-dimensional (3D) conformation of RNA (Heilman-Miller et al 2001a;Takamoto et al 2002Takamoto et al , 2004Koculi et al 2007). Chemical and enzymatic probes are often used to study the effects of solution conditions on the structure of RNA (Vary and Vournakis 1984b;Celander and Cech 1991;Mathews et al 1997;Uchida et al 2003;Takamoto et al 2004).…”

Section: Applications Example Use Casesmentioning

confidence: 99%

Sharing and archiving nucleic acid structure mapping data

Rocca-Serra

Bellaousov

Birmingham

et al. 2011

RNA

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Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the structure and/or dynamics of the nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed a standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments, or SNRNASMs. We propose a schema for sharing nucleic acid chemical probing data that uses generic public servers for storing, retrieving, and searching the data. We have also developed a consistent nomenclature (ontology) within the Ontology of Biomedical Investigations (OBI), which provides unique identifiers (termed persistent URLs, or PURLs) for classifying the data. Links to standardized data sets shared using our proposed format along with a tutorial and links to templates can be found at http:// snrnasm.bio.unc.edu.

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Charge Density of Divalent Metal Cations Determines RNA Stability

Cited by 165 publications

References 68 publications

Minimal Models for Proteins and RNA: From Folding to Function

Minimal Models for Proteins and RNA: From Folding to Function

3 Importance of Diffuse Metal Ion Binding to RNA

Sharing and archiving nucleic acid structure mapping data

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