Study by 23Na-NMR, 1H-NMR, and ultraviolet spectroscopy of the thermal stability of an 11-basepair oligonucleotide

Na-23-NMR, H-1-NMR, and ultraviolet (UV) spectroscopy have been used to study the thermal stability of the double helix structure of an 11-basepair oligonucleotide. The denaturation curves obtained by Na-23-NMR and UV are analyzed using a two-state model. The melting temperature and Delta H-0 obtained are identical within experimental error, suggesting that modifications in the ionic atmosphere, probed by 23Na-NMR, and the modifications in the basepair stacking, probed by UV, occur at the same temperature. Additional dynamical information on the denaturation process has been obtained by H-1-NMR: slow exchange is observed between the thymine methyl resonances, and the disappearance of imino protons shows that a single basepair opening does not contribute significantly to proton exchange.