Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4–P6 RNA by smFRET

Bisaria, Namita; Herschlag, Daniel

doi:10.1042/bst20140268

Cited by 21 publications

(30 citation statements)

References 50 publications

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“…63 The A225U P4–P6 folding equilibrium constant was the same, within experimental error, in the presence of NaCl, KCl, or RbF (at 2.5 M, K eq obs = 0.45 ± 0.13, 0.38 ± 0.03, and 0.48 ± 0.03 for NaCl, KCl, and RbF, respectively). However, the folding equilibrium constant was ∼5-fold lower in the presence of RbCl ( K eq obs = 0.09 ± 0.01 at 2.5 M).…”

Section: Resultsmentioning

confidence: 74%

Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere?

et al. 2016

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Electrostatics are central to all aspects of nucleic acid behavior, including their folding, condensation, and binding to other molecules, and the energetics of these processes are profoundly influenced by the ion atmosphere that surrounds nucleic acids. Given the highly complex and dynamic nature of the ion atmosphere, understanding its properties and effects will require synergy between computational modeling and experiment. Prior computational models and experiments suggest that cation occupancy in the ion atmosphere depends on the size of the cation. However, the computational models have not been independently tested, and the experimentally observed effects were small. Here, we evaluate a computational model of ion size effects by experimentally testing a blind prediction made from that model, and we present additional experimental results that extend our understanding of the ion atmosphere. Giambasu et al. developed and implemented a three-dimensional reference interaction site (3D-RISM) model for monovalent cations surrounding DNA and RNA helices, and this model predicts that Na+ would outcompete Cs+ by 1.8–2.1-fold; i.e., with Cs+ in 2-fold excess of Na+ the ion atmosphere would contain an equal number of each cation (Nucleic Acids Res.2015, 43, 8405). However, our ion counting experiments indicate that there is no significant preference for Na+ over Cs+. There is an ∼25% preferential occupancy of Li+ over larger cations in the ion atmosphere but, counter to general expectations from existing models, no size dependence for the other alkali metal ions. Further, we followed the folding of the P4–P6 RNA and showed that differences in folding with different alkali metal ions observed at high concentration arise from cation–anion interactions and not cation size effects. Overall, our results provide a critical test of a computational prediction, fundamental information about ion atmosphere properties, and parameters that will aid in the development of next-generation nucleic acid computational models.

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Section: Resultsmentioning

confidence: 74%

Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere?

et al. 2016

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“…The more favorable folding in Na + relative to Rb + (when each is present with its preferred anions) presumably reflects stabilization by specific Na + binding to the tetraloop/tetraloop receptor tertiary interaction in folded P4–P6. 65,81–83 …”

Section: Resultsmentioning

confidence: 99%

“…64 Charges were assigned using the PDB 2PQR routine 24 with the CHARMM parameter set. Nonlinear PB calculations were carried out using the Adaptive Poisson–Boltzmann Solver (version 1.4.1) 22 on a 405 × 405 × 578 Å 3 grid with a grid spacing of 1.8 Å and the ion size equal 4 Å (the approximated radius of the hydrated ions; 12,65 see also comment (66)). Varying the grid spacing in the range 1.5–2.5 Å and changing the box size by ±30% gave identical results within 1% relative error.…”

Section: Experimental Methodsmentioning

confidence: 99%

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

et al. 2015

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The ion atmosphere is a critical structural, dynamic, and energetic component of nucleic acids that profoundly affects their interactions with proteins and ligands. Experimental methods that “count” the number of ions thermodynamically associated with the ion atmosphere allow dissection of energetic properties of the ion atmosphere, and thus provide direct comparison to theoretical results. Previous experiments have focused primarily on the cations that are attracted to nucleic acid polyanions, but have also showed that anions are excluded from the ion atmosphere. Herein, we have systematically explored the properties of anion exclusion, testing the zeroth-order model that anions of different identity are equally excluded due to electrostatic repulsion. Using a series of monovalent salts, we find, surprisingly, that the extent of anion exclusion and cation inclusion significantly depends on salt identity. The differences are prominent at higher concentrations and mirror trends in mean activity coefficients of the electrolyte solutions. Salts with lower activity coefficients exhibit greater accumulation of both cations and anions within the ion atmosphere, strongly suggesting that cation–anion correlation effects are present in the ion atmosphere and need to be accounted for to understand electrostatic interactions of nucleic acids. To test whether the effects of cation–anion correlations extend to nucleic acid kinetics and thermodynamics, we followed the folding of P4–P6, a domain of the Tetrahymena group I ribozyme, via single-molecule fluorescence resonance energy transfer in solutions with different salts. Solutions of identical concentration but lower activity gave slower and less favorable folding. Our results reveal hitherto unknown properties of the ion atmosphere and suggest possible roles of oriented ion pairs or anion-bridged cations in the ion atmosphere for electrolyte solutions of salts with reduced activity. Consideration of these new results leads to a reevaluation of the strengths and limitations of Poisson–Boltzmann theory and highlights the need for next-generation atomic-level models of the ion atmosphere.

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“…Since its first demonstration in 1996, smFRET has been used to provide mechanistic answers in diverse areas of biological research. These studies unraveled molecular mechanisms of helicases and topoisomerases (40), DNA replication, DNA repair (41), transcription (42–44), translation (42,45,46), enzymatic function (47–49), molecular motors (50), membrane proteins (51), protein folding (52, 53), nucleic acids (54, 55), RNA folding (54, 56, 57), and ribozyme catalysis (58, 59). Because a short review cannot do justice to the large number and diversity of smFRET studies, we will discuss a few representative examples.…”

Section: A Brief Historical Overview Of Single-molecule Fret In Biochmentioning

confidence: 99%

“…Similarly, smFRET helped to elucidate the conformational dynamics, folding mechanisms, and function of RNA molecules (54–59). Not all genes code for proteins.…”

Section: A Brief Historical Overview Of Single-molecule Fret In Biochmentioning

confidence: 99%

Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer

Lerner

Cordes

Ingargiola

et al. 2018

Science

491

449

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Classical structural biology can only provide static snapshots of biomacromolecules. Single-molecule Förster resonance energy transfer (smFRET) paved the way for studying dynamics in macromolecular structures under biologically relevant conditions. Since its first implementation in 1996, smFRET experiments have confirmed previously hypothesized mechanisms and provided new insights into many fundamental biological processes, such as DNA maintenance and repair, transcription, translation, and membrane transport. We review 22 years of contributions of smFRET to our understanding of basic mechanisms in biochemistry, molecular biology, and structural biology. Additionally, building on current state-of-the-art implementations of smFRET, we highlight possible future directions for smFRET in applications such as biosensing, high-throughput screening, and molecular diagnostics.

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Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4–P6 RNA by smFRET

Cited by 21 publications

References 50 publications

Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere?

Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere?

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer

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