Equilibrium binding of benzo[a]pyrene tetrol to synthetic polynucleotides: sequence selectivity, thermodynamic properties, and ionic strength dependence

We have investigated the equilibrium binding of racemic 7r,8t,9t,10c-tetrahydroxy-7,8,9,10-tetrahydrobenzoa]pyrene to the double-stranded, synthetic polynucleotides polyd(A-T)], polyd(G-C)], and polyd(G-m5C)] at low binding ratios. Difference absorption spectroscopy shows a 10-nm red shift for binding to polyd(A-T)] and an 11-nm red shift for binding to either polyd(G-C)] or polyd(G-m5C)]. The value of delta epsilon for binding is approximately the same for all three hydrocarbon-polynucleotide complexes. Binding of this neutral polycyclic aromatic hydrocarbon derivative to these polynucleotides is dependent upon ionic strength and temperature. Analysis of complex formation employing polyelectrolyte theory shows a greater release of counterions associated with binding to polyd(A-T)] than with the other two polynucleotides (0.5 and ca. 0.36, respectively). Thus, sequence-selective binding of this hydrocarbon in DNA would be expected to change depending on salt concentration. The temperature dependence of binding was studied at 100 mM Na+ where the equilibrium binding constants for polyd(A-T)] and polyd(G-m5C)] are roughly equivalent and 6-fold greater than the binding affinity for polyd(G-C)]. The binding to polyd(A-T)] and polyd(G-C)] is characterized by a delta H omicron = -7.0 kcal/mol, and the large difference in affinity constants arises from differences in negative entropic contributions. Formation of hydrocarbon-polyd(G-m5C)] complexes is accompanied by a delta H = -9.1 kcal/mol. However, the affinity for polyd-(G-m5C)] is the same as that for polyd(A-T)] due to the much more negative entropy associated with binding to polyd(G-m5C)].