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.
Matsumoto
N
N
School of Pharmacy, Tokyo University of Pharmacy and Life Science, Japan.
Shimizu
M
M
Shindo
H
H
D001483:Base Sequence; D004278:DNA, Superhelical / Q000737:chemistry*; D004047:Diethyl Pyrocarbonate; D007536:Isomerism; D007700:Kinetics; D008274:Magnesium; D015335:Molecular Probes; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000737:chemistry*; D013816:Thermodynamics
D004278:DNA, Superhelical; D015335:Molecular Probes; D008274:Magnesium; D004047:Diethyl Pyrocarbonate