Calorimetric and spectroscoptc Investigation of drug - DNA Interactions. I. The binding of netropsin to poly d(AT)

Abstract

We report the first calorlmetric investigation of netropsin binding to poly d(AT). Temperature-dependent uv absorption, circular dichroism (CD), batch calorlmetry, and differential scanning calorimetry (DSC) were used to detect, monitor, and thermodynamically characterize the binding process. The following results have been obtained: 1) Netropsin groove binding is accompanied by a large exothermic enthalpy of 9.2 kcal/mol of drug bound at 25°C. This indicates that a large negative binding enthalpy may be a necessary but not a sufficient criterion for drug intercalation. We suggest that the exothermic binding might be correlated with specific H-bonding interactions. 2) From the difference in DSC transition enthalpies in the presence and absence of netropsin, we calculate a binding enthalpy of −10.7 kcal/mol of netropsin at 88°C. 3) We calculate a positive AS for netropsin binding to poly d(AT) at 25°C. This positive entropy change may reflect netropsln-induced release of condensed cations and/or bound water. 4) The netropsin-8aturated duplex monophasically melts 46°C higher than the free duplex. The unsaturated duplex melts through two thermally-resolved transitions that correspond to netropsin-free and netropsin-bound regions. These two regions interact dynamically with no substantial influence on the thermal stabilities of the separate domains. 5) Netropsin binding decreases the cooperativity of the duplex to single strand transition.