Predicting Monovalent Ion Correlation Effects in Nucleic Acids

Sun, Li‐Zhen; Zhou, Yuanzhe; Chen, Shijie

doi:10.1021/acsomega.9b01689

Cited by 6 publications

(9 citation statements)

References 87 publications

(200 reference statements)

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“…Though the MCTBI model (Eqs. 8 and 9) currently focuses on correlation effects (many-body ion distribution) for divalent ions, correlation effects for monovalent ions can be studied using a similar approach (95). However, because the correlation effect for monovalent ions is weak compared with that for multivalent ions, the MCTBI theory for a monovalent ions solution can give the same result as the nonlinear Poisson-Boltzmann equation.…”

Section: [Seq] From the 3d Conformational Ensemblementioning

confidence: 99%

Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability

Zhao

Zhang

Jiang

et al. 2020

Biophysical Journal

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The ability to accurately predict RNA hairpin structure and stability for different loop sequences and salt conditions is important for understanding, modeling, and designing larger RNA folds. However, traditional RNA secondary structure models cannot treat loop-sequence and ionic effects on RNA hairpin folding. Here, we describe a general, three-dimensional (3D) conformation-based computational method for modeling salt concentration-dependent conformational distributions and the detailed 3D structures for a set of three RNA hairpins that contain a variable, 15-nucleotide loop sequence. For a given RNA sequence, the new, to our knowledge, method integrates a Vfold2D two-dimensional structure folding model with IsRNA coarse-grained molecular dynamics 3D folding simulations and Monte Carlo tightly bound ion estimations of ion-mediated electrostatic interactions. The model predicts free-energy landscapes for the different RNA hairpin-forming sequences with variable salt conditions. The theoretically predicted results agree with the experimental fluorescence measurements, validating the strategy. Furthermore, the theoretical model goes beyond the experimental results by enabling in-depth 3D structural analysis, revealing energetic mechanisms for the sequenceand salt-dependent folding stability. Although the computational framework presented here is developed for RNA hairpin systems, the general method may be applied to investigate other RNA systems, such as multiway junctions or pseudoknots in mixed metal ion solutions.

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Section: [Seq] From the 3d Conformational Ensemblementioning

confidence: 99%

Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability

Zhao

Zhang

Jiang

et al. 2020

Biophysical Journal

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“…[356] Importantly, for Mg 2 + ions bound to RNA, the cationmediated effects go beyond pure electrostatics, and include polarisation and charge transfer. [353] Along these lines, the [347] and [348]). (b) Condensation and charge inversion of DNA molecules induced by ion-ion-correlation.…”

Section: Structural Stabilisation By Cationsmentioning

confidence: 94%

“…[353] A clear prediction for structural changes of RNA in the presence of cations is challenging, and clear differences exist between the structure of RNA in KCl and MgCl 2 solutions. [347] Interestingly, for both salts, the RNA structure deviates also significantly from the assumed canonical A-form of RNA. [347] Interestingly and potentially counterintuitively, quasi-elastic neutron scattering (QENS) measurements have shown RNA folding to go along with an increased flexibility of its backbone as is reflected, inter alia, in an increased mean-squared displacement and mobile atom fraction.…”

Section: Structural Stabilisation By Cationsmentioning

confidence: 95%

“…[347] Interestingly, for both salts, the RNA structure deviates also significantly from the assumed canonical A-form of RNA. [347] Interestingly and potentially counterintuitively, quasi-elastic neutron scattering (QENS) measurements have shown RNA folding to go along with an increased flexibility of its backbone as is reflected, inter alia, in an increased mean-squared displacement and mobile atom fraction. [360] The authors of Ref.…”

Section: Structural Stabilisation By Cationsmentioning

confidence: 95%

“…[346] Recent computer simulations for cations around DNA and RNA suggest that tighly bound divalent Mg 2 + ions can occur in two different surface areas with different binding distances, as opposed to tight binding of monovalent ions in one broad population. [347] Figure 6 shows a schematic representation of ion binding to a DNA molecule as well as condensation and charge inversion of DNA molecules induced by ion-ion correlation effects.…”

Section: Local Picture: Ion Distribution and Bindingmentioning

confidence: 99%

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Multivalent ions and biomolecules: Attempting a comprehensive perspective

2020

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Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self‐organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca2+, to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the “atomistic/molecular” local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico‐chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.

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Spontaneous Condensation of RNA into Nanoring and Globular Structures

et al. 2022

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The effect of polyvalent cations, like spermine, on the condensation of DNA into very well-defined toroidal shapes has been well studied and understood. A great effort has been made to obtain similar condensed structures from RNA molecules, but so far, it has been elusive. In this work, we show that single-stranded RNA (ssRNA) molecules can easily be condensed into nanoring and globular structures on a mica surface, where each nanoring structure is formed mostly by a single RNA molecule. The condensation occurs in a concentration range of different cations, from monovalent to trivalent, but at a higher concentration, globular structures appear. RNA nanoring structures were observed on mica surfaces by atomic force microscopy (AFM). The samples were observed in tapping mode and were prepared by drop evaporation of a solution of RNA in the presence of one type of the different cations used. As far as we know, this is the first time that nanorings or any other well-defined condensed RNA structures have been reported in the presence of simple salts. The RNA nanoring formation can be understood by an energy competition between the hydrogen bonding forming hairpin stems—weakened by the salts—and the hairpin loops. This result may have an important biological relevance since it has been proposed that RNA is the oldest genome-coding molecule, and the formation of these structures could have given it stability against degradation in primeval times. Even more, the nanoring structures could have the potential to be used as biosensors and functionalized nanodevices.

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Predicting Monovalent Ion Correlation Effects in Nucleic Acids

Cited by 6 publications

References 87 publications

Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability

Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability

Multivalent ions and biomolecules: Attempting a comprehensive perspective

Spontaneous Condensation of RNA into Nanoring and Globular Structures

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