Thermal perturbation differential spectra of ribonucleic acids. II. Nearest neighbour interactions.

Dinucleoside monophosphates are used here as models for studying sequence dependence of the hypochromic effect correlated with base stacking. It was shown that once the contribution due to the temperature dependent hydration change of the bases is substracted from the thermal perturbation difference spectra of dinucleoside monophosphates, the absorbance change of the dimer only due to unstacking of the bases could be obtained. In order to be able to use these corrected thermal perturbation difference spectra as models for studying nearest neighbour interactions in nucleic acids, it was necessary to normalize them to 100% unstacking of the bases. To perform this normalization, apparent thermodynamic parameters were extracted from the corrected transition curves by means of the two-state model.