Thermal Stability of PNA/DNA and DNA/DNA Duplexes by Differential Scanning Calorimetry
M C. Chakrabarti, Frederick P. Schwarz
Thermodynamic quanties describing the hybridizatin reactions for 8mer PNA/DNA duplexes and the corresponding 8mer DNA/DNA duplexes were determined by isothermal titation calorimetry measurements at ambient temperatures. Values of δGb for the DNA/DNA duplexes were found to be in good agreement with values extrapolated from UV melting measurements on the dissociation of the duplexes at high temperature and with δGb values predicted from the nearest-neighbor Watson-Crick pair assignments at 310K. Apparently, contributions to δGb from any conformational differences between the 8mer single strand sequences had little effect on the extrapolated and predicted values of δGb . This is contrary to what was observed previously with the longer 10mer duplexes where these conformational differences contributed significantly to the thermodynamic parameters of PNA/DNA and DNA/DNA duplex formation. This is attributed to a higher probability of random-coil strand state formation with the shorter sequences. Values of δHb , however, did not exhibit good agreement with their values extrapolated from the UV melting measurements and values predicted from the model. The agreement exhibited by the δGb values in contrast to the non-agreement exhibited by the of δHb values is attributed to enthalpy-entropy compensation, which results in little variation in δGb by compensating large differences in the binding enthalpy with commensurate changes in the binding entropy.