ArticleNucleic acids research2012
Non-specific binding of Na+ and Mg2+ to RNA determined by force spectroscopy methods.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Single-molecule insights into SAM-I riboswitch ligand binding using scaled magnetic force spectroscopy with comparison to conventional biophysical methods.RNA biology · 2026Article
- Counterintuitive DNA destabilization by monovalent salt at high concentrations due to overcharging.Nature communications · 2025Article
- Stacking correlation length in single-stranded DNA.Nucleic acids research · 2024Article
- Universal cold RNA phase transitions.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability.ACS omega · 2024Article
- Exploring the conformational dynamics of the SARS-CoV-2 SL4 hairpin by combining optical tweezers and base analogues.Nanoscale · 2024Article
- Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time.Nucleic acids research · 2023Article
- Thermodynamic determination of RNA duplex stability in magnesium solutions.Biophysical journal · 2023Article
- Unravelling How Single-Stranded DNA Binding Protein Coordinates DNA Metabolism Using Single-Molecule Approaches.International journal of molecular sciences · 2023Review
- Temperature-dependent elastic properties of DNA.Biophysical reports · 2022Article
- Measurement of the specific and non-specific binding energies of MgBiophysical journal · 2022Article
- Nucleic Acid Thermodynamics Derived from Mechanical Unzipping Experiments.Life (Basel, Switzerland) · 2022Review
- Folding Free Energy Determination of an RNA Three-Way Junction Using Fluctuation Theorems.Entropy (Basel, Switzerland) · 2022Article
- Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways.The journal of physical chemistry letters · 2022Article
- Stem-loop formation drives RNA folding in mechanical unzipping experiments.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers.International journal of molecular sciences · 2021Article
- A Synthetic Riboswitch to Regulate Haloarchaeal Gene Expression.Frontiers in microbiology · 2021Article
- Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics.Journal of the American Chemical Society · 2020Article
- Theory and simulations for RNA folding in mixtures of monovalent and divalent cations.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Structural accommodations accompanying splicing of a group II intron RNP.Nucleic acids research · 2018Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of monovalent and multivalent ions on RNA stability, and the thermodynamic parameters for secondary structure prediction have only been derived at 1M [Na(+)]. Here, by mechanically unfolding and folding a 20 bp RNA hairpin using optical tweezers, we study the RNA thermodynamics and kinetics at different monovalent and mixed monovalent/Mg(2+) salt conditions. We measure the unfolding and folding rupture forces and apply Kramers theory to extract accurate information about the hairpin free energy landscape under tension at a wide range of ionic conditions. We obtain non-specific corrections for the free energy of formation of the RNA hairpin and measure how the distance of the transition state to the folded state changes with force and ionic strength. We experimentally validate the Tightly Bound Ion model and obtain values for the persistence length of ssRNA. Finally, we test the approximate rule by which the non-specific binding affinity of divalent cations at a given concentration is equivalent to that of monovalent cations taken at 100-fold concentration for small molecular constructs.
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