ArticleBiophysical journal2008
Electrostatic free energy landscapes for DNA helix bending.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Resonant Convergence: An Integrative Model for Electromagnetic Interactions in Biological Systems.International journal of molecular sciences · 2025Review
- The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations.Nucleic acids research · 2024Article
- Transcriptional control of mycobacterial DNA damage response by sigma adaptation.Science advances · 2021Article
- A pH-induced conformational switch in a tyrosine kinase inhibitor identified by electronic spectroscopy and quantum chemical calculations.Scientific reports · 2017Article
- Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling.Biophysical journal · 2017Article
- Predicting Molecular Crowding Effects in Ion-RNA Interactions.The journal of physical chemistry. B · 2016Article
- Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions.Biophysical journal · 2015Article
- Article
- Role of microscopic flexibility in tightly curved DNA.The journal of physical chemistry. B · 2014Article
- Many-body effect in ion binding to RNA.The Journal of chemical physics · 2014Article
- Exploring the electrostatic energy landscape for tetraloop-receptor docking.Physical chemistry chemical physics : PCCP · 2014Article
- Ion-mediated RNA structural collapse: effect of spatial confinement.Biophysical journal · 2012Article
- Quantitative analysis of the ion-dependent folding stability of DNA triplexes.Physical biology · 2011Article
- Salt contribution to RNA tertiary structure folding stability.Biophysical journal · 2011Article
- Importance of diffuse metal ion binding to RNA.Metal ions in life sciences · 2011Review
- Predicting ion binding properties for RNA tertiary structures.Biophysical journal · 2010Article
- Salt-dependent folding energy landscape of RNA three-way junction.Biophysical journal · 2010Article
- Predicting electrostatic forces in RNA folding.Methods in enzymology · 2009Article
- Salt dependence of nucleic acid hairpin stability.Biophysical journal · 2008Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Nucleic acids are highly charged polyanionic molecules; thus, the ionic conditions are crucial for nucleic acid structural changes such as bending. We use the tightly bound ion theory, which explicitly accounts for the correlation and ensemble effects for counterions, to calculate the electrostatic free energy landscapes for DNA helix bending. The electrostatic free energy landscapes show that DNA bending energy is strongly dependent on ion concentration, valency, and size. In a Na(+) solution, DNA bending is electrostatically unfavorable because of the strong charge repulsion on backbone. With the increase of the Na(+) concentration, the electrostatic bending repulsion is reduced and thus the bending becomes less unfavorable. In contrast, in an Mg(2+) solution, ion correlation induces a possible attractive force between the different parts of the helical strands, resulting in bending. The electrostatically most favorable and unfavorable bending directions are toward the major and minor grooves, respectively. Decreasing the size of the divalent ions enhances the electrostatic bending attraction, causing an increased bending angle, and shifts the most favorable bending to the direction toward the minor groove. The microscopic analysis on ion-binding distribution reveals that the divalent ion-induced helix bending attraction may come from the correlated distribution of the ions across the grooves in the bending direction.
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