Dynamical Recrossing in the Intercalation Process of the Anticancer Agent Proflavine into DNA

Abstract

Intercalation into DNA is the interaction mode of some anthracycline antibiotics. Recently, the molecular mechanism of this process was explored using the static free energy landscape. Here we explore the dynamical effects in the intercalation of proflavine into DNA by calculating the transmission coefficient kappa-providing a measure of the departure from transition state theory for the reaction rate constant-by examination of the recrossing events at the transition state. For that purpose, we first found the accurate transition state of this complex system-as judged by a committor analysis-using a set of all-atom simulations of total length 6.3 ms. In a subsequent calculation of the transmission coefficient kappa in another extensive set of simulations the small value kappa = 0.1 was found, indicating a significant departure from TST. Comparison of this result with Grote-Hynes and Kramers theories shows that neither theory is able to capture this complex system's recrossing events; the source of this striking failure is discussed, as are related aspects of the mechanism. This study suggests that, for biomolecular processes similar to this, dynamical effects essential for the process are complex in nature and require novel approaches for their elucidation.