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Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides

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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*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 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.

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  1. Novosibirsk Institute of Bioorganic Chemistry, 8 prosp. Akad. Lavrent"eva, 630090, Novosibirsk, Russian Federation

    D. V. Pyshnyi & E. M. Ivanova

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  1. D. V. Pyshnyi
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  2. E. M. Ivanova
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Pyshnyi, D.V., Ivanova, E.M. Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides. Russian Chemical Bulletin 51, 1145–1155 (2002). https://doi.org/10.1023/A:1020954307319

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