The roles of aromaticity in the structure of DNA and its intercalation complexes with quinones

Abstract

The X-ray crystallographic coordinate data of a 56 DNA double helical oligomers were examined, using the molecular modeling program STR3DI32.EXE, in order to ascertain the aromatic statuses of the Watson–Crick hydrogen bonded base pairs. Several oligomers that were intercalated with anthraquinoid molecules (like the daunomycin and nogalamycin aglycones) were also included in the study in order to evaluate the aromatic statuses of the intercalated entities. This study revealed that the base pairs were aromatic in their Watson–Crick hydrogen bonded double helices, whereas they are known to be non-aromatic in situations in which they are not involved in Watson–Crick hydrogen bonding. The resonance energy gained by the aromatization of these bases, while engaged in Watson–Crick hydrogen bonding, must contribute to the stability of these DNA double helices. The anthraquinoid intercalates were revealed to be in their radical anion form, having received an electron from one of the bases between which these intercalates were sited. These anthraquinoid intercalates are therefore “held” in position by ionic – charge transfer – interactions, as well as hydrogen bonding due to their glycosidic entities. These observations are also relevant to investigations of the electrical conductivity of DNA double helices that are similarly intercalated.