Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides

Continuous stacking hybridization of oligodeoxyribonucleotides with the stem of a preformed minihairpin structure of a DNA template was studied by thermal denaturation in solution. The thermodynamic parameters (DeltaHdegrees, DeltaSdegrees, and DeltaG(37)degrees) were determined for the formation of all 16 possible types of coaxial stackings (or cooperative interactions) (5)'X*pY(3)'/(5)'ZZ'(3)'(an asterisk stands for a nick) between the terminal complementary base pairs of two adjacent duplexes formed on a common DNA template. The maximum efficacy DeltaG(37)degrees of coaxial stacking (1 M NaCl, pH 7.4) was observed for the G*pC/GC interaction (-2.76 kcal mol(-1)), whereas the minimum efficacy was observed for the T*pA/TA interaction (-0.85 kcal mol-1). In the general case, the efficacy of the cooperative interaction at the X*pY/ZZ' junction does not correlate with the energy of formation of the corresponding unified XY/ZZ' dinucleotide pair in the structure of native DNA. The formation of a stack by the terminal oligonucleotide bases upon their continuous stacking hybridization makes the major and governing contribution to the energy of cooperative interaction.