Origins of netropsin binding affinity and specificity: correlations of thermodynamic and structural data

Abstract

We report complete thermodynamic profiles for netropsin binding to an oligomeric and to several polymeric DNA host duplexes. These data allow us to reach the following conclusions: netropsin binding by deep penetration into the minor groove is overwhelmingly enthalpy driven and exhibits a very high binding affinity (K approximately 10(9) at 25 degrees C); deep penetration into the minor groove is required to form those drug-DNA interactions responsible for the enthalpy-driven high binding affinity of netropsin; I-C base pairs form binding sites for netropsin that thermodynamically are equivalent to those formed by A-T base pairs; the positive binding entropies reflect entropic contributions from molecular events other than just water spine disruption; the thermodynamic binding data primarily reflect local netropsin-DNA interactions rather than long-range binding-induced conformational changes at regions distant from the binding site; the enhanced binding affinity associated with deep penetration of netropsin into the minor groove does not result from more favorable electrostatic interactions; the binding of netropsin to the central AATT core of the decamer duplex [d(GCGAATTCGC)]2 is thermodynamically modeled best by netropsin binding to the poly[d(AT)].poly[d(AT)] duplex rather than the poly(dA).poly(dT) duplex. We propose correlations between our thermodynamic data and specific molecular interactions defined by NMR and x-ray structural studies on similar and identical drug-DNA complexes.