ArticleBiophysical journal2006
Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers.
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Who cites it
140 citing papers in PubMed.
- Multivalent cations stabilize DNA duplexes beyond charge neutralization.Chemical science · 2026Article
- Protein crowders remodel RNA electrostatics, hydration, and dynamics: a challenge to steric crowding models.Nucleic acids research · 2026Article
- Tunable DNA Origami Nanosensors for Detection of Multiscale Spatial Ion Concentration Gradients.ACS sensors · 2026Article
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- Solid-state nanopore sensing reveals conformational changes induced by a mutation in a neuron-specific tRNAArg.Nucleic acids research · 2026Article
- Stability of non-canonical nucleic acid structure as a potential modulator of cell fate.Nucleic acids research · 2026Review
- A Simple and Fast Optical Clearing Method for Whole-Mount Fluorescence In Situ Hybridization (FISH) Imaging.Journal of biophotonics · 2025Article
- Tunable DNA Origami Nanosensors for Detection of Multiscale Spatial Ion Concentration Gradients.bioRxiv : the preprint server for biology · 2025Article
- RLDOCKScore: A Scoring Function for RNA-Ligand Docking and Small Molecule Virtual Screening.Journal of chemical theory and computation · 2025Article
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- Denaturation methods for reusable magnetic biosensors.Lab on a chip · 2025Article
- Structural Insights into an Antiparallel Chair-Type G-Quadruplex From the Intron of NOP56 Oncogene.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- DNA Sensing with Whispering Gallery Mode Microlasers.Nano letters · 2025Article
- Computational modeling of cotranscriptional RNA folding.Computational and structural biotechnology journal · 2025Review
- ThermoPlex: an automated design tool for target-specific multiplex PCR primers based on DNA thermodynamics.Biology methods & protocols · 2025Article
- SERS-based detection of DNA methylation for cancer diagnosis: Cation-mediated adsorption to silver nanoparticles.PloS one · 2025Article
- Understanding the relationship between sequences and kinetics of DNA strand displacements.Nucleic acids research · 2024Article
- Surface-Enhanced Raman Spectroscopy (SERS)-Based Sensors for Deoxyribonucleic Acid (DNA) Detection.Molecules (Basel, Switzerland) · 2024Review
- Article
- Ratiometric nonfluorescent CRISPR assay utilizing Cas12a-induced plasmid supercoil relaxation.Communications chemistry · 2024Article
80 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Metal ions play crucial roles in thermal stability and folding kinetics of nucleic acids. For ions (especially multivalent ions) in the close vicinity of nucleic acid surface, interion correlations and ion-binding mode fluctuations may be important. Poisson-Boltzmann theory ignores these effects whereas the recently developed tightly bound ion (TBI) theory explicitly accounts for these effects. Extensive experimental data demonstrate that the TBI theory gives improved predictions for multivalent ions (e.g., Mg2+) than the Poisson-Boltzmann theory. In this study, we use the TBI theory to investigate how the metal ions affect the folding stability of B-DNA helices. We quantitatively evaluate the effects of ion concentration, ion size and valence, and helix length on the helix stability. Moreover, we derive practically useful analytical formulas for the thermodynamic parameters as functions of finite helix length, ion type, and ion concentration. We find that the helix stability is additive for high ion concentration and long helix and nonadditive for low ion concentration and short helix. All these results are tested against and supported by extensive experimental data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.