A Thermodynamic Investigation into the Stabilization of Poly(dA).[poly(dT)]2Triple Helical DNA by Various Divalent Metal Ions

Abstract

Effects of representative group II and transition metal ions on the stability of the <TEX>$poly(dA){\cdot}[poly(dT)]_2$</TEx> triplex were investigated by the van’t Hoff plot constructed from a thermal melting curve. The transition, <TEX>$poly(dA){\cdot}[poly(dT)]_2\;{\rightarrow}\;poly(dA){\cdot}poly(dT)\;+\;poly(dT)$</TEX>, was non-spontaneous with a positive Gibb’s free energy, endothermic (<TEX>${\Delta}H^{\circ}$</TEX> > 0), and had a favorable entropy change (<TEX>${\Delta}S^{\circ}$</TEX> > 0), as seen from the negative slope and positive y-intercept in the van’t Hoff plot. Therefore, the transition is driven by entropy change. The <TEX>$Mg^{2+}$</TEX> ion was the most effective at stabilization of the triplex, with the effect decreasing in the order of <TEX>$Mg^{2+}\;>\;Ca^{2+}\;>\;Sr^{2+}\;>\;Ba^{2+}$</TEX>. A similar stabilization effect was found for the duplex to single strand transition: <TEX>$poly(dA){\cdot}poly(dT)\;+\;poly(dT)\;→\;poly(dA)\;+\;2poly(dT)$</TEX>, with a larger positive free energy. The transition metal ions, namely <TEX>$Ni_{2+},\;Cu_{2+},\;and\;Zn_{2+}$</TEX>, did not exhibit any effect on triplex stabilization, while showing little effect on duplex stabilization. The different effects on triplex stabilization between group II metal ions and the transition metal ions may be attributed to their difference in binding to DNA; transition metals are known to coordinate with DNA components, including phosphate groups, while group II metal ions conceivably bind DNA via electrostatic interactions. The <TEX>$Cd_{2+}$</TEX> ion was an exception, effectively stabilizing the triplex and melting temperature of the third strand dissociation was higher than that observed in the presence of <TEX>$Mg_{2+}$</TEX>, even though it is in the same group with <TEX>$Zn_{2+}$</TEX>. The detailed behavior of the <TEX>$Cd_{2+}$</TEX> ion is currently under investigation.