Magnesium effect on premelting transitions in nucleic acids: DNA duplex and RNA hairpin models

The effect of magnesium ions on the conformational changes in the temperature region below the melting transition (premelting transitions) of a DNA duplex and an RNA hairpin was studied by difference Raman spectroscopy. The chosen model systems were the polynucleotide poly(dA)–poly(dT) duplex and the apical hairpin of the trans-activation response (TAR) element of HIV-1. Magnesium effect was displayed by differences of Raman spectra measured at various temperatures with and without magnesium ions. Our results have revealed that magnesium ions influence measurably the premelting transitions in both cases; the extent of the effect and its character is though quite different. In the case of the B′ → B premelting transition of the polynucleotide poly(dA)–poly(dT) duplex, magnesium binds to the minor groove of the B but not of the B′ form and acts again the rearrangement in the vicinity of the thymidine keto-groups. On the other hand, the magnesium effect on the TAR hairpin premelting consists in a weak support of the premelting structural change via more effective electrostatic shielding.