Kinetic and equilibrium studies of the interaction of amsacrine and anilino ring-substituted analogues with DNA.

The kinetic stability of complexes of the clinical antileukemic drug amsacrine and anilino ring-substituted analogues with DNA has been studied by using the surfactant sequestration technique in a stopped-flow spectrophotometer. In addition, viscometric measurements using covalently closed circular DNA and displacement measurements of DNA-bound ethidium have been performed to evaluate helix unwinding angles and association constants, respectively. Amsacrine and its analogues dissociate from DNA by a complex kinetic pathway which involves at least three discernible transiently bound forms of the drug. Dissociation time constants for amsacrine are found to range from less than 1 to 6 ms in buffer of ionic strength 0.1, and the biomolecular association rate constant is greater than 10(6) M-1 s-1. We find that amsacrine forms one of the weakest intercalation complexes among the compounds studied, as judged by the criteria of kinetic stability, affinity, and chromophore-base pair stacking interactions. Unlike other compounds of this broad class (intercalating chromophores bearing sterically-demanding side chains), addition of the bulky side chain has little effect on the kinetic stability of the drug-DNA complexes, suggesting that the acridinesulfonanilides may intercalate into DNA from the less sterically demanding major groove of the helix. Such a binding geometry would facilitate the formation of the previously proposed ternary complex between amsacrine, DNA, and gene-regulatory enzymes (e.g., topoisomerases and repressors) which are known to bind in the major groove.