Thermodynamics of berenil binding to poly[d(AT)]center dot poly[d(AT)] andpoly[d(A)]center dot poly[d(T)] duplexes

Thermodynamics of berenil binding to poly[d(AT)].poly[d(AT)] and poly[d(A)] .poly[d(T)] duplexes in neutral buffer solutions was studied using a combin ation of calorimetric and spectroscopic techniques. By titration calorimetr y we found that at 25 degreesC the enthalpies of berenil binding to poly[d( AT)].poly[d(AT)] and poly[d(A)].poly[d(T)] are -20.4 and 10.3 kJ/mol of bou nd drug, respectively. Our CD results show that berenil binding to both dup lexes is at low berenil/DNA ratios slightly positively cooperative whereas at higher binding densities it is characterized by a constant affinity and a binding site size, n, of 4 base pairs/berenil molecule. Berenil binding t o both polynucleotides was also followed by performing UV titrations of ber enil solutions with DNA solutions at 25 degreesC and by measuring the UV me lting curves at different berenil/DNA molar ratios. From Scatchard plots th e best fit of experimental data with the predictions of the neighbor exclus ion model was obtained with K = 1.3.10(7) and n = 3.5 for poly[d(AT)].poly[ d(AT)] and K = 1.5.10(7) and n = 3.8 for poly[d(A)].poly[d(T)]. UV melting experiments showed for both polynucleotides that above their saturation wit h bound berenil they exhibit monophasic melting accompanied by a large incr ease in T-m, whereas at low drug/base pair ratios their melting is biphasic . Berenil binding constants determined at 25 degreesC using the T-m data an d the neighbor exclusion model are K = 2.3.10(7) for poly[d(AT)].poly[d(AT) ] and K = 7.4.10(6) for poly[d(A)].poly[d(T)]. From these K values the stan dard free energies of binding were determined and combined with the measure d enthalpies of binding to obtain the corresponding entropies of binding. T he resulting thermodynamic binding profiles show that berenil binding to po ly[d(AT)].poly[d(AT)] is governed by about equal enthalpic and entropic for ces whereas its binding to poly[d(A)].poly[d(T)] is overwhelmingly entropy driven.