Thermodynamics of Triple-Helix and Double-Helix Formations by Octamers of Deoxyriboadenylic and Deoxyribothymidylic Acids

Abstract

The triple-helix and double-helix formations by octamers of deoxyriboadenylic and deoxyribothymidylic acids, (dA)₈ and (dT)₈, have been studied energetically and dynamically by UV and CD measurements, a melting analysis, curve-fitting and nearest-neighbor calculations. The UV mixing curves and CD spectra showed that the triple-helix of (dA)₈·2(dT)₈ mainly existed in 0.05 mol dm⁻³ MgCl₂ buffer at a low temperature range, while the double helix of (dA)₈·(dT)₈ existed in 1 and 0.1 mol dm⁻³ NaCl buffers. The thermodynamic parameters for the triplex and duplex formations were obtained with analysis for the UV melting curves. The free-energy changes at 25 °C obtained from the melting temperature vs. oligomer concentration plots in the MgCl₂ buffer were −20.7 kJ mol⁻¹ for the triplex formation and −27.3 kJ mol⁻¹ for the duplex formation, respectively, which were consistent with the values obtained from the curve-fitting calculations. The free-energy changes for the duplex formation at 25 °C were −28.5 kJ mol⁻¹ in 1 mol dm⁻³ NaCl buffer, and −11.6 kJ mol⁻¹ in 0.1 mol dm⁻³ NaCl bufer, respectively. These values were discussed in comparison with the predicted values by the nearest-neighbor calculation.