NMR cross-correlated relaxation rates reveal ion coordination sites in DNA
Language English Country United States Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
21819145
DOI
10.1021/ja202397p
Knihovny.cz E-resources
- MeSH
- DNA chemistry MeSH
- Ions chemistry MeSH
- Nucleic Acid Conformation MeSH
- Models, Molecular MeSH
- Nuclear Magnetic Resonance, Biomolecular methods MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- DNA MeSH
- Ions MeSH
In this work, a novel NMR method for the identification of preferential coordination sites between physiologically relevant counterions and nucleic acid bases is demonstrated. In this approach, the NMR cross-correlated relaxation rates between the aromatic carbon chemical shift anisotropy and the proton-carbon dipolar interaction are monitored as a function of increasing Na(+), K(+), and Mg(2+) concentrations. Increasing the counterion concentration modulates the residence times of the counterions at specific sites around the nucleic acid bases. It is demonstrated that the modulation of the counterion concentration leads to sizable variations of the cross-correlated relaxation rates, which can be used to probe the site-specific counterion coordination. In parallel, the very same measurements report on the rotational tumbling of DNA, which, as shown here, depends on the nature of the ion and its concentration. This methodology is highly sensitive and easily implemented. The method can be used to cross-validate and/or complement direct but artifact-prone experimental techniques such as X-ray diffraction, NMR analysis with substitutionary ions, and molecular dynamics simulations. The feasibility of this technique is demonstrated on the extraordinarily stable DNA mini-hairpin d(GCGAAGC).
References provided by Crossref.org
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
