Spectroscopic study of protonation of oligonucleotides containing adenine and cytosine

Acidobasic properties of purine and pyrimidine bases (adenine, cytosine) and relevant nucleosides (adenosine, cytidine) were studied by means of glass-electrode potentiometry and the respective dissociation constants were determined under given experimental conditions ( I = 0.1 M (NaCl), t = (25.0 ± 0.1) °C): adenine (p K HL = 9.65 ± 0.04, p K H2L = 4.18 ± 0.04), adenosine (p K H2L = 3.59 ± 0.05), cytosine (p K H2L = 4.56 ± 0.01), cytidine (p K H2L = 4.16 ± 0.02). In addition, thermodynamic parameters for bases: adenine (Δ H 0 = (−17 ± 4) kJ mol −1 , Δ S 0 = (23 ± 13) J K −1 mol −1 ), cytosine (Δ H 0 = (−22 ± 1) kJ mol −1 , Δ S 0 = (13 ± 5) J K −1 mol −1 ) were calculated. Acidobasic behavior of oligonucleotides (5′CAC-CAC-CAC3′ = (CAC) 3 , 5′AAA-CCC-CCC3′ = A 3 C 6 , 5′CCC-AAA-CCC3′ = C 3 A 3 C 3 ) was studied under the same experimental conditions by molecular absorption spectroscopy. pH-dependent spectral datasets were analyzed by means of advanced chemometric techniques (EFA, MCR-ALS) and the presence of hemiprotonated species concerning (C + -C) a non-canonical pair ( i -motif) in titled oligonucleotides was proposed in order to explain experimental data obtained according to literature.