Supramolecular self-assembling cyanine and spermine binding to genomic DNA was a model for DNA-drug interactions during high throughput screening. Spermine competitively inhibited the self-assembly of cyanine upon DNA scaffolds as signaled by decreased fluorescence from the DNA-cyanine J-aggregate. The sequence of DNA exposure to cyanine or spermine was critical in determining the magnitude of inhibition. Methanol potentiated spermine inhibition by >10-fold. The IC(50) and association constant (K(a)) in 16% methanol were 0.35 +/- 0.03 microM and 2.86 x 10(6) M(-1) respectively, relative to 3.97 +/- 0.47 microM and 0.25 x 10(6) M(-1) respectively, in buffer. Increasing concentrations of cyanine overcame spermine inhibition, demonstrating the reversibility of DNA-drug interactions. LambdaDNA interacted similarly with spermine and cyanine, confirming system flexibility. The model drug, dye and methanol effects are discussed in detail. Cyanine might be a safer alternative to the mutagenic ethidium bromide for investigating DNA-drug interactions.