Thermodynamics of drug-dna interactions

Batch calorimetry, differential scanning calorimetry (DSC), uv/vis absorption spectroscopy, fluorescence spectroscopy, and circular dichroism (CD), have been used to detect, monitor, and thermodynamically characterize the binding of daunomycin,dipyrandenium, dipyrandium, and netropsin to poly d(AT) and actinomycin D to salmon testes (ST) DNA. The following thermodynamic binding profiles have been obtained: All the poly d(AT) binding studies were done at 25°C while actinomycin binding to ST DNA was performed at 1°C to enhance drug solubility. These thermodynamic parameters are interpreted in terms of specific interactions that have been proposed as part of models for the binding of each drug. Temperature-dependent uv absorption spectroscopy and DSC were used to characterize the influence of each of these drugs on the thermally-induced melting behavior of the host DNA. At saturation, drug binding increases the thermal stability of poly d(AT) in the order: netropsin > daunomycin > dipyrandium >dipyrandenium. Below saturation, drug binding to poly d(AT) induces biphasic melting behavior in which the thermal resolution of the two subtransitions (domains) varies from drug to drug. In general, we find that the higher the binding constant for a drug the more it increases the thermal stability of the duplex and the more it thermally resolves the two drug-induced domains. A comparison of the van’t Hoff and the calorimetric transition enthalpies reveals that each drug has a different effect on the cooperativity of the duplex to single strand transition of poly d(AT). Specifically, we find that drugs which bind by modes which penetrate the helix (e.g. daunomycin and dipyrandium) significantly reduce the cooperativity of duplex melting. By contrast, dipyrandenium, which “outside” binds and induces an “alternating” helix structure actually increases the cooperativity of duplex melting.