Thermodynamic comparison of PNA/DNA and DNA/DNA hybridization reactions at ambient temperature

The thermodynamics of 13 hybridization reactions between 10 base DNA sequences of design 5'-ATGCXYATGC-3' with X, Y = A, C, G, T and their complementary PNA and DNA sequences were determined from isothermal titration calorimetry (ITC) measurements at ambient temperature. For the PNA/DNA hybridization reactions, the binding constants range from 1.8 x 10(6) M-1 for PNA(TT)/DNA to 4.15 x 10(7) M-1 for PNA(GA)/DNA and the binding enthalpies range from -194 kJ mol(-1) for PNA(CG)/DNA to -77 kJ mol(-1) for PNA(GT)/DNA. For the corresponding DNA/ DNA binding reactions, the binding constants range from 2.9 x 10(5) M-1 for DNA(GT)/DNA to 1.9 x 10(7) M-1 for PNA(GA)/DNA and the binding enthalpies range from -223 kJ mol(-1) for DNA(CG)/DNA to -124 kJ mol(-1) for DNA(TT)/DNA. Most of the PNA sequences exhibited tighter binding affinities than their corresponding DNA sequences resulting from smaller entropy changes in the PNA/DNA hybridization reactions. van't Hoff enthalpies and extrapolated Delta G values determined from UV melting studies on the duplexes exhibited closer agreement with the ITC binding enthalpies and Delta G values for the, DNA/DNA duplexes than for the PNA/DNA duplexes.