Promotion mechanism of triplex DNA formation by comb-type polycations: thermodynamic analyses of sequence specificity...

We have previously reported that in the presence of poly (L-lysine)-graft-Dextran (PLL-g-Dex) copolymer, the binding constant of the pyrimidine-motif triplex formation at neutral pH is about 100-times higher than that observed without any triplex stabilizer. Here, to explore the mechanism of the promotion effect of the PLL-g-Dex copolymer at neutral pH, the sequence specificity and the ionic strength dependence of the pyrimidine-motif triplex formation was examined in the absence or presence of the copolymer. The sequence specificity of the pyrimidine-motif triplex formation at neutral pH in the presence of copolymer was almost similar to that at acidic pH without the copolymer. As the concentration of magnesium cation increased, the binding constant of the pyrimidine-motif triplex formation without the copolymer increased. On the other hand, the binding constant of the pyrimidine-motif triplex formation in the presence of the copolymer decreased upon the increase in the concentration of magnesium cation. Considering these results in light of counterion condensation (CC) theory, we conclude that the copolymer does not hinder the sequence specificity of the triplex formation, and isolates the triplex formation from the CC effect, which may lead to a net increase in entropy change upon the triplex formation, providing a favorable component to binding constant of the triplex formation.