Intercalation and de-intercalation pathway of proflavine through the minor and major grooves of DNA: roles of water and entropy

DNA intercalation is a clinically relevant biophysical process due to its potential to inhibit the growth and survival of tumor cells and microbes through the arrest of the transcription and replication processes. Extensive kinetic and thermodynamic studies have followed since the discovery of the intercalative binding mode. However, the molecular mechanism and the origin of the thermodynamic and kinetic profile of the process are still not clear. Here we have constructed the free energy landscape of intercalation, de-intercalation and dissociation from both the major and minor grooves of DNA using extensive all-atom metadynamics simulations, capturing both the free energy barriers and stability in close agreement with fluorescence kinetic experiments. In the intercalated state, an alternate orientation of proflavine is found with an almost equal stability compared to the crystal orientation, however, separated by a 5.0 kcal mol−1 barrier that decreases as the drug approaches the groove edges. This study provides a comprehensive picture in comparison with experiments, which indicates that the intercalation and de-intercalation of proflavine happen through the major groove side, although the effective intercalation barrier increases because the path of intercalation goes through the stable (abortive) minor groove bound state, making the process a millisecond long one in excellent agreement with the experiments. The molecular origin of the higher barrier for the intercalation from the minor groove side is attributed to the desolvation energy of DNA and the loss of entropy, while the barrier from the major groove, in the absence of desolvation energy, is primarily entropic.