Dynamics in isomerization of intramolecular DNA triplexes in supercoiled plasmids

Kinetic and thermodynamic nature of two isomers, H-y3 and H-y5, for an intramolecular Pyr.Pur.Pyr triplex in supercoiled plasmid was studied by a specific chemical probe. H-y3 was found to be more stable in terms of enthalpy change by 6 to 10 kcal/mol than H-y5, and the time constant for the conversion from H-y5 to H-y3 was 0.6 hr in the absence of Mg2+, while it was 6 hr in the presence of 50mM Mg2+. The transition probability from the duplex form to either two isomers was also measured: the kinetic barrier was higher for the transition to H-y3 than that to H-y5. These results indicated that Mg2+ acts to increase kinetic barriers of interconversion between H-y3 and H-y5 isomers.