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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 30, Number 11
BKCSDE 30(11)
November 20, 2009 

A Thermodynamic Investigation into the Stabilization of Poly(dA)·[poly(dT)]2 Triple Helical DNA by Various Divalent Metal Ions
Byung Hoon Choi, Ga Young Yeo, Jinah Jung, Bae Wook Lee, Sung Wook Han, Tae Sub Cho*
Triplex DNA, Divalent ions, Thermodynamics, Enthalpy, Entropy
Effects of representative group II and transition metal ions on the stability of the poly(dA)·[poly(dT)]2 triplex were investigated by the van’t Hoff plot constructed from a thermal melting curve. The transition, poly(dA)·[poly(dT)]2 → poly(dA)·poly(dT) + poly(dT), was non-spontaneous with a positive Gibb’s free energy, endothermic (ΔHo > 0), and had a favorable entropy change (ΔSo > 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 Mg2+ ion was the most effective at stabilization of the triplex, with the effect decreasing in the order of Mg2+ > Ca2+ > Sr2+ > Ba2+. A similar stabilization effect was found for the duplex to single strand transition: poly(dA)·poly(dT) + poly(dT) → poly(dA) + 2poly(dT), with a larger positive free energy. The transition metal ions, namely Ni2+, Cu2+, and Zn2+, 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 Cd2+ 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 Mg2+, even though it is in the same group with Zn2+. The detailed behavior of the Cd2+ ion is currently under investigation.
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