A method of using modified xanthine molecules as a binding agent is disclosed. Xanthine molecules with at least one substitution of a methyl group at the N1, N3, N7, or N9 position bind to intercalating molecules efficiently. This method can be applied to inhibiting intercalating molecules from binding to nucleic acids, as well as removing intercalating molecules that have been bound to nucleic acids. This method can also be applied to synthesize an efficient drug delivery system for compounds that have low solubility in aqueous media, including anti-neoplastic agents. The method can also be applied to flurosecently labeling nucleic acids.