[Model of cytosine-, thymine-containing olygodeoxyribonucleotide protonation in solution]

In the present study, the experimental data on the pH-induced formation of the i-motif structure in the nucleotide sequence 5'-CCTTTCCTTTTCCTTTCC-3' (25oC, pH 3.3-8.9) obtained by spectroscopic techniques, such as UV molecular absorption and circular dichroism, has been analysed using the chemometric soft modelling-based MCR-ALS approach and the hard modelling-based matrix method. Soft modelling using 2 or 3 spectral species correctly reproduced spectral variations observed experimentally. The use of hard chemical modelling enabled us to propose the equilibrium model, which describes spectral changes as functions of solution acidity. Additionally, the intrinsic protonation constant Kin, and the cooperativity parameter w have been calculated from the fitting procedure of the circular dichroism as well as molecular absorption spectra. The results indicated that folding was accompanied by a cooperative process, i.e. the enhancement of protonated structure stability upon protonation.