ArticleJournal of the American Chemical Society2007
Measurement of the effect of monovalent cations on RNA hairpin stability.
Article in Journal of the American Chemical Society, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Specific Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein Deduced from Hairpin Unfolding.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Exploring the Application of Nano-Differential Scanning Calorimetry in RNA Characterization.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The Unpaved Road of Non-Coding RNA Structure-Function Relationships: Current Knowledge, Available Methodologies, and Future Trends.Non-coding RNA · 2025Review
- Thermodynamic determination of RNA duplex stability in magnesium solutions.Biophysical journal · 2023Article
- RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations.The journal of physical chemistry. B · 2022Article
- Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts.Science advances · 2022Article
- Twisting DNA by salt.Nucleic acids research · 2022Article
- NaMicroscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada · 2022Article
- The nucleotide addition cycle of the SARS-CoV-2 polymerase.Cell reports · 2021Article
- The nucleotide addition cycle of the SARS-CoV-2 polymerase.bioRxiv : the preprint server for biology · 2021Article
- Single-Molecule Studies of Protein Folding with Optical Tweezers.Annual review of biochemistry · 2020Review
- Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix-Junction-Helix Systems.Journal of the American Chemical Society · 2018Article
- Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies.The journal of physical chemistry. B · 2018Article
- Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling.The journal of physical chemistry. B · 2017Article
- Physics-based all-atom modeling of RNA energetics and structure.Wiley interdisciplinary reviews. RNA · 2017Review
- Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA.The journal of physical chemistry. B · 2017Article
- Targeted binding of nucleocapsid protein transforms the folding landscape of HIV-1 TAR RNA.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Modeling of RNA nanotubes using molecular dynamics simulation.European biophysics journal : EBJ · 2014Article
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Authors and funding
4 authors.
Funding
Abstract
Using optical tweezers, we have measured the effect of monovalent cation concentration and species on the folding free energy of five large (49-124 nt) RNA hairpins, including HIV-1 TAR and molecules approximating A.U and G.C homopolymers. RNA secondary structure thermodynamics are accurately described by a model consisting of nearest-neighbor interactions and additive loop and bulge terms. Melting of small (<15 bp) duplexes and hairpins in 1 M NaCl has been used to determine the parameters of this model, which is now used extensively to predict structure and folding dynamics. Few systematic measurements have been made in other ionic conditions or for larger structures. By applying mechanical force, we measured the work required to fold and unfold single hairpins at room temperature over a range of cation concentrations from 50 to 1000 mM. Free energies were then determined using the Crooks fluctuation theorem. We observed the following: (1) In most cases, the nearest-neighbor model accurately predicted the free energy of folding at 1 M NaCl. (2) Free energy was proportional to the logarithm of salt concentration. (3) Substituting potassium ions for sodium slightly decreased hairpin stability. The TAR hairpin also misfolded nearly twice as often in KCl, indicating a differential kinetic response. (4) Monovalent cation concentration affects RNA stability in a sequence-dependent manner. G.C helices were unaffected by changing salt concentration, A.U helices were modestly affected, and the hairpin loop was very sensitive. Surprisingly, the U.C.U bulge of TAR was found to be equally stable in all conditions tested. We also report a new estimate for the elastic parameters of single-stranded RNA.
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