Site selectivity of daunomycin

We have reexamined the binding properties of the antitumor drug daunomycin using double-helical oligonucleotides 16 base pairs long that were designed to contain preferred binding sites for the drug. The preferred sites are contained in a six base pair core which is flanked on the 5' and 3' ends by tracts of adenines. The flanking sequences, which augment helix stability and reduce and effects, were chosen because daunomycin is known to bind poorly to poly(dA).poly(dT). Four major sequences were examined in the six base pair core: CGTACG, TAGCTG, TCATCC, and (TA)3 and compared with calf thymus DNA. A randomly generated 16 bp sequence containing no A tracts and a sequence containing only tracts of As and Ts were also used. Fluorometric, absorption, calorimetric, and stopped-flow techniques were used to examine the binding. The affinity of the drug for oligomers containing known binding sites was comparable to or enhanced relative to that for calf thymus bulk DNA. Association constants ranged from 1.0 x 10(8) to 3.0 x 10(7) M-1. The strongest core binding site found was CGTACG, but its affinity is only 2-fold larger than that of other core sequences. Appreciable binding to the flanking A tracts was observed. An oligonucleotide which incorporates the CGTACG sequence in a short hairpin helix binds an order of magnitude more weakly. Complex lifetimes measured by stopped flow generally increase with equilibrium stability; the kinetics confirm the existence of a set of weaker sites. The exothermic binding enthalpy for daunomycin with the CGTACG core sequence is more than twice as large as for the TATATA sequence. Binding to dA20.dT20 is endothermic, and a less exothermic component can be detected in the calorimetric binding curve of the oligomers containing flanking A tracts.