Author
Elisa Tomita-Sudo, Konan Laboratory for Oligonucleotide Therapeutics
Junji Kawakami, Konan Laboratory for Oligonucleotide Therapeutics, Department of Nanobiochemistry, FIRST, Konan University
Keywords
Thermodynamics, Kinetics, Duplex formation, Analytical methods
Abstract
UV melting experiments provide thermodynamic information such as ΔH°,ΔS°,ΔG°, and melting temperature (Tm). Usually, these parameters are evaluated by means of UV melting experiment under the condition with a gentle temperature gradient (e.g., 0.5℃/min) to allow the reaction to reach equilibrium at each temperature. On the other hand, when the UV vs temperature curves are measured at fast temperature changes, differences, so-called hysteresis, may be observed in the profiles during the heating and cooling phases. In this study, we used the hysteresis behavior of UV absorbance to investigate a simple method to obtain kinetic information on DNA duplex formation. The activation energy was calculated from the kon and koff obtained from the kinetic analysis and compared with the enthalpy change (ΔH°) associated with duplex formation obtained from the thermodynamic analysis to examine the validity of this method. It is suggested that this approach enables us to consider the sequence dependence of the binding and dissociation rate constants easily.