Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides

Abstract

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 (ΔH°, ΔS°, and ΔG°37) were determined for the formation of all 16 possible types of coaxial stackings (or cooperative interactions) 5"X*pY3"/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 ΔG°37 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.