Thermodynamic dependence of DNA/DNA and DNA/RNA hybridization reactions on temperature and ionic strength

The thermodynamics of 5′-ATGCTGATGC-3′ binding to its complementary DNA and RNA strands was determined in sodium phosphate buffer under varying conditions of temperature and salt concentration from isothermal titration calorimetry (ITC). The Gibbs free energy change, ΔG° of the DNA hybridization reactions increased by about 6 kJ mol− 1 from 20 °C to 37 °C and exhibited heat capacity changes of − 1.42 ±0.09 kJ mol− 1 K− 1 for DNA/DNA and − 0.87 ± 0.05 kJ mol− 1 K− 1 for DNA/RNA. Values of ΔG° decreased non-linearly by 3.5 kJ mol− 1 at 25 °C and 6.0 kJ mol− 1 at 37 °C with increase in the log of the sodium chloride concentration from 0.10 M to 1.0 M. A near-linear relationship was observed, however, between ΔG° and the activity coefficient of the water component of the salt solutions. The thermodynamic parameters of the hybridization reaction along with the heat capacity changes were combined with thermodynamic contributions from the stacking to unstacking transitions of the single-stranded oligonucleotides from differential scanning calorimetry (DSC) measurements, resulting in good agreement with extrapolation of the free energy changes to 37 °C from the melting transition at 56 °C.