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The dodecanucleotide d(CGCGATATCGCG) 2  was characterized by thermodynamic and UV-spectrophotometric measurements. A van’t Hoff enthalpy of ΔH uv  v.H. ~  - 190 kJ/mol was determined for the thermal transition using UV spectroscopy. This value was confirmed by differential scanning calorimetry (DSC). In addition we obtained the thermodynamic data ΔH DSC  = -405.1 kJ/mol, ΔS DSC  = -1290 J/mol·K and ΔG DSC  = -53.2 kJ/mol for the helix to coil transition of the dodecanucleotide. The association of berenil and the oligonucleotide was accompanied with a stabilization of the host duplex (increase in T m ) and an increase in the van’t Hoff enthalpy. The berenil binding parameters (ΔΔH DSC  = -32.6 kJ/mol, ΔΔS DSC  = -72 J/mol·K and ΔΔG DSC  = -11.1 kJ/mol) revealed significant differences compared to those of the pentamidine aggregation (ΔΔH DSC  = -23.7 kJ/mol, ΔΔS DSC  = -53 J/mol·K and ΔΔG DSC  = -7.8 kJ/mol). The transition of the pure oligonucleotide was characterized by a substantial amount of intermediate states (σ DSC  = 0.43) which decreased significantly upon binding of the drugs (σ DSC  ~ 0.80). The structural features of the complexes were analyzed by FT-IR spectroscopy. From these experiments we conclude that the configurations in the berenil and pentamidine complexes are different.

Thermodynamic and Spectroscopic Characterization of the Berenil and Pentamidine Complexes with the Dodecanucleotide d(CGCGATATCGCG) 2