ArticleBiochemistry2007
Quantitative analysis of monovalent counterion binding to random-sequence, double-stranded DNA using the replacement ion method.
Article in Biochemistry, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 58 citations in OpenAlex.
- Effect of Internal and Bulge Loops on the Thermal Stability of Small DNA Duplexes.The journal of physical chemistry. B · 2024Article
- Site-Specific Binding of Non-Site-Specific Ions.Biophysical journal · 2019Article
- Predicting Ion Effects in an RNA Conformational Equilibrium.The journal of physical chemistry. B · 2017Article
- Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations.Journal of chemical theory and computation · 2016Article
- Flanking A·T basepairs destabilize the B(∗) conformation of DNA A-tracts.Biophysical journal · 2015Article
- Structure, stability and behaviour of nucleic acids in ionic liquids.Nucleic acids research · 2014Review
- Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate.Scientific reports · 2014Article
- DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations.Biochemistry · 2013Article
- Ion-mediated RNA structural collapse: effect of spatial confinement.Biophysical journal · 2012Article
- Predicting ion-nucleic acid interactions by energy landscape-guided sampling.Journal of chemical theory and computation · 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
- Predicting ion binding properties for RNA tertiary structures.Biophysical journal · 2010Article
- Salt-dependent folding energy landscape of RNA three-way junction.Biophysical journal · 2010Article
- Effect of the matrix on DNA electrophoretic mobility.Journal of chromatography. A · 2009Review
- Monovalent cation binding in the minor groove of DNA A-tracts.Biochemistry · 2009Article
- Predicting electrostatic forces in RNA folding.Methods in enzymology · 2009Article
- Electrostatic free energy landscapes for DNA helix bending.Biophysical journal · 2008Article
- Monovalent cation binding by curved DNA molecules containing variable numbers of a-tracts.Biophysical journal · 2008Article
- Do zwitterions contribute to the ionic strength of a solution?Analytical biochemistry · 2008Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
A variation of affinity capillary electrophoresis, called the replacement ion (RI) method, has been developed to measure the binding of monovalent cations to random sequence, double-stranded (ds) DNA. In this method, the ionic strength is kept constant by gradually replacing a non-binding ion in the solution with a binding ion and measuring the mobility of binding and non-binding analytes as a function of binding ion concentration. The method was validated by measuring the binding of Li+ ions to adenosine nucleotides; the apparent dissociation constants obtained by the RI method are comparable to literature values obtained by other methods. The binding of Tris+, NH4+, Li+, Na+, and K+ to dsDNA was then investigated. The apparent dissociation constants observed for counterion binding to a random-sequence 26-base pair (bp) oligomer ranged from 71 mM for Tris+ to 173 mM for Na+ and K+. Hence, positively charged Tris buffer ions will compete with other monovalent cations in Tris-buffered solutions. The bound cations identified in this study may correspond to the strongly correlated, tightly bound ions recently postulated to exist as a class of ions near the surface of dsDNA (Tan, Z.-J., and Chen, S.-J. (2006) Biophys. J. 91, 518-536). Monovalent cation binding to random-sequence dsDNA would be expected to occur in addition to any site-specific binding of cations to A-tracts or other DNA sequence motifs. Single-stranded DNA oligomers do not bind the five tested cations under the conditions investigated here.
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