ArticleNucleic acids research2016
Quantifying the ion atmosphere of unfolded, single-stranded nucleic acids using equilibrium dialysis and single-molecule methods.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 23 citations in OpenAlex.
- Structural Prediction of Coronavirus s2m Kissing Complexes and Extended Duplexes.ACS physical chemistry Au · 2025Article
- Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations.Scientific reports · 2024Article
- Recent advances and challenges in the interaction between myofibrillar proteins and flavor substances.Frontiers in nutrition · 2024Review
- Structural, Dynamical, and Entropic Differences between SARS-CoV and SARS-CoV-2 s2m Elements Using Molecular Dynamics Simulations.ACS physical chemistry Au · 2023Article
- 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
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Single-stranded nucleic acid elasticity arises from internal electrostatic tension.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Divalent ion competition reveals reorganization of an RNA ion atmosphere upon folding.Nucleic acids research · 2017Article
- The impact of base stacking on the conformations and electrostatics of single-stranded DNA.Nucleic acids research · 2017Article
- Counting the ions surrounding nucleic acids.Nucleic acids research · 2017Article
- Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension.Journal of molecular biology · 2016Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To form secondary structure, nucleic acids (NAs) must overcome electrostatic strand-strand repulsion, which is moderated by the surrounding atmosphere of screening ions. The free energy of NA folding therefore depends on the interactions of this ion atmosphere with both the folded and unfolded states. We quantify such interactions using the preferential ion interaction coefficient or ion excess: the number of ions present near the NA in excess of the bulk concentration. The ion excess of the folded, double-helical state has been extensively studied; however, much less is known about the salt-dependent ion excess of the unfolded, single-stranded state. We measure this quantity using three complementary approaches: a direct approach of Donnan equilibrium dialysis read out by atomic emission spectroscopy and two indirect approaches involving either single-molecule force spectroscopy or existing thermal denaturation data. The results of these three approaches, each involving an independent experimental technique, are in good agreement. Even though the single-stranded NAs are flexible polymers that are expected to adopt random-coil configurations, we find that their ion atmosphere is quantitatively described by rod-like models that neglect large-scale conformational freedom, an effect that we explain in terms of the competition between the relevant structural and electrostatic length scales.
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