Imidazolyl-Naphthalenediimide-Based Threading Intercalators of DNA

Intercalation by threading is anticipated to feature in DNA-binding molecules for developing DNA-targeted diagnostics and therapeutics. We investigated the role of an imidazolyl moiety in threading intercalators of DNA by employing a number of imidazolyl-naphthalenediimide conjugates. Threading intercalation was studied by UV spectroscopy, competitive binding fluorescent dye displacement, circular dichroism, isothermal calorimetry, and computational analysis. NIm6 was found to be a strong candidate, with good half-life, as revealed by dissociation kinetic analysis. Computational studies supported intercalation of the naphthalene core between base pairs and binding of the imidazolyl moieties in the adjacent grooves (threading mechanism) through electrostatic and hydrogen-bonding interactions. The interaction of the positively charged imidazolium moieties with the negatively charged phosphate backbone of DNA contributed to the favorable enthalpy change, as revealed by the experimental and computational data. Threading intercalation by NIm6 caused significant retardation of DNA in an electrophoretic mobility shift assay. The biological significance of potent imidazolyl naphthalenediimide conjugates was demonstrated by the inhibition of topo- isomerase I activity and cytotoxicity against HeLa cells.