Abstract

Equilibrium and kinetic studies on the interaction of daunorubicin, doxorubicin, and the beta-anomer of doxorubicin with B and Z form DNA were made using spectroscopic and fluorometric methods. The beta-anomer of doxorubicin binds more weakly to calf thymus DNA than do the parent compounds, with a binding constant over 2 orders of magnitude lower than that found for doxorubicin. The ionic strength dependence of the binding constant is identical for daunorubicin and the beta-anomer of doxorubicin, indicating that the electrostatic contribution to the binding free energy is the same for the two compounds. Rate constants for steps along the dissociation pathway are larger for the beta-anomer relative to the parent compounds, indicating a shorter lifetime for the beta-anomer-DNA complex. Daunorubicin and doxorubicin were equally effective as inhibitors of the rate of the B to Z transition of polydeoxyguanylic-deoxycytidylic acid (poly(dGdC] in 3.0 M NaCl. Both compounds bound cooperatively to poly (dGdC) under high salt conditions that initially favor the Z conformation. In contrast, the beta-anomer of doxorubicin did not inhibit the rate of the B to Z transition under these conditions, and would not bind to poly(dGdC) in 3.0 M NaCl. The beta-anomer did inhibit the rate of the transition of poly(dGm5dC) to the Z form in 50 mM NaCl, 2.5 mM MgCl2, although not as effectively as daunorubicin. Further, binding of the beta-anomer to poly(dGm5dC) under these conditions was cooperative, although the beta-anomer was clearly a less efficient allosteric effector on the B to Z transition than was daunorubicin. These results emphasize the importance of the stereochemistry of the daunosamine residue in the specific and preferential binding of anthracycline antibiotics to B form DNA.