Methylene Blue Binding to DNA with Alternating GC Base Sequence: A Modeling Study

摘要: Photoactive methylene blue is one of the most efficient singlet oxygen generating dyes. It binds to DNA and induces photosensitized reactions which can be used for sequence-specific cleavage backbone. Photophysical data obtained in complexes with indicate different binding modes dye depending on base sequences. In this study, a double-stranded decamer an alternating GC sequence has been investigated by structural modeling force field based energy calculations. Solvation desolvation effects have treated using electrostatic continuum model. For each three possible (intercalation minor major groove binding), search configurational space resulted six model structures were selected criterion lowest total energies. The differences estimated energies are only few kilocalories per mole, but suggest preference symmetric intercalation at 5‘-CpG-3‘ or ...