Doxorubicin, a member of the anthracycline family, is a commonly known anti-tumor agent. It is a small molecule with a cyclic sugar attached to a planar anthraquinone chromophore ring structure. The ring structure intercalates between two adjacent base pairs of the helix, with its sugar moiety binding in the minor groove, however the exact mechanism by which doxorubicin binds to DNA is unknown. Kinetic profiles of doxorubicin association and dissociation with two types of synthetic DNA (poly(dA-dT) and poly(dG-dC)) and one naturally occurring DNA (calf-thymus) were calculated using stopped-flow fluorescence spectroscopy. Activation entropies and enthalpies were calculated from Arrhenius data collected at several different temperatures. Poly(dA-dT) association and dissociation were both fit to single exponentials as well as poly(dG-dC) dissociation. Calf-thymus association and dissociation were both fit with double exponentials as was poly(dG-dC) association. For both association and dissociation for all three DNA types, DS‡ was negative. DH‡ was positive for both association and dissociation of poly(dA-dT) and poly(dG-dC) as well as dissociation with calf-thymus. Calf-thymus association however had a negative change in enthalpy. These results indicate that DNA sequence plays a role in binding and dissociation mechanisms. A series of density-functional energy minimization calculations were conducted in order to deduce possible transition states along the binding pathway, which were then compared to the experimental values. Through these calculations, we were able to construct an energetic profile of the transition from free drug and DNA to a bound complex using a 3’cytosine-adenine-adenine-thymine5’ DNA sequence.

Activation properties of the association and dissociation of doxorubicin and DNA

251st National Meeting (2016)

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