Evidence for sequence preferences in the intercalative binding of ethidium bromide to dinucleoside monophosphates

Abstract

The formation of solution complexes of ethidium bromide with the self-complementary ribodinucleoside monophosphates, as well as ethidium complexes with mixtures of complementary and non-complementary ribodinucleoside monophosphates, has been monitored by circular dichroism, fluorescence, nuclear magnetic resonance, and visible spectroscopic techniques. Although ethidium bromide will form a complex with all of the dinucleoside monophosphates used in this study, it does exhibit a definite preference for binding to dinucleosides that have a pyrimidine (3′-5′) purine sequence when compared to their isomeric purine (3′-5′) pyrimidine sequence dinucleosides. The pyrimidine-purine sequence dinucleoside monophosphate complexes with ethidium exhibit fluorescence, circular dichroism, and visible spectra that closely resemble the spectra observed for the ethidium complexes with double-stranded nucleic acids. An analysis of the nuclear magnetic resonance spectra of the same ethidium-dinucleoside monophosphate solutions used for the optical experiments shows that complexation results in the formation of a miniature double-helical complex in which the phenanthridinium ring of ethidium bromide is intercalated between the adjacent base-pairs of a miniature double-helical complex. The formation of a double-helical complex is also indicated by the observation of the hydrogen-bonded guanine ring NH resonance in a complex of ethidium bromide with CpG dissolved in an aqueous solution. The combination of the optical spectroscopies and the nuclear magnetic resonance experiments on these model systems thus provides direct evidence for the intercalation model for the binding of ethidium bromide to double-stranded nucleic acids. The fact that ethidium preferentially interacts with dinucleoside monophosphate sequence isomers suggests that it binds to the various base sequences available as intercalation sites on DNA and RNA with significantly different binding constants.