Molecular Dynamics Simulations of Binding Modes between Methylene Blue and DNA with Alternating GC and AT Sequences

The understanding of interactions between small molecules and DNA is crucial to design new anticancer drugs targeted to DNA. Methylene blue (MB) is a phenothiazinium dye that has shown promising results in photodynamic therapy treatment. The noncovalent binding of methylene blue to DNA was experimentally and theoretically analyzed in the past, but certain features of the binding mode are still not clear. In this work, force field molecular dynamics simulations were performed to simulate the binding of methylene blue to alternating GC and AT sequences at two different ionic strengths. External, intercalative, minor groove, and major groove binding modes are discussed based on energetic and structural analyses. External and major groove complexes were found to be unstable structures, although for poly(dA-dT) the major groove binding mode cannot be discarded, especially at high ionic strengths. Minor groove and intercalative binding leads to stable adducts. The most energetically favorable orientation of the dye inside the minor groove is different for the two DNA sequences because of the different balances between the DNA deformation energy and the dye/DNA interaction energy. The intercalative binding is the most important interaction mode. The dye undergoes rotational transitions inside the intercalative pocket for both DNA sequences giving rise to three dye/DNA adducts that have different energetic and structural features. This rotational motion explains the different behavior found in experiments for the GC and AT nucleic acids at different ionic strengths.