Titration of poly(dA-dT).poly(dA-dT) in solution at variable NaCl concentration

CD and uv absorption data showed that high molecular weight poly(dA-dT) poly(dA-dT),at 298 K, undergoes an acid-induced transition from B-double helix to random coil in NaCl solutions ofdifferent concentrations, ranging from 0.005 to 0.600M. Similarly, titration of the polynucleotide with astrong base causes duplex-to-single strands transition. The base- and acid-induced transitions were bothreversible by back-titration (with an acid or, respectively, with a base): the apparent pKa were the samein both directions. However, the number of protons per titratable site (adenine N1) required to reachhalf-denaturation was in great excess over the stoichiometric value; to a much larger extent, the sameeffect was observed also for the deprotonation of the N3H sites of thymine. Moreover, in the basicdenaturation experiments, at low salt concentrations ([NaCl] 0.300M) less acid than calculated wasneeded to back-titrate the base excess to half-denaturation. Both effects could be qualitatively justifiedon the basis of the counterion condensation theory of polyelectrolytes and considering the energy barriercreated by the negatively charged phosphodiester groups to the penetration of the OH ions inside thedouble helix and the screening effect of the Na ions on such charges, in the deprotonation experiments.