Effect of netropsin on one-electron oxidation of duplex DNA

The effect of netropsin on the oxidative reactions of duplex DNA was examined. One-electron oxidation of DNA creates a radical cation that migrates through duplex DNA and reacts primarily at GG steps. Netropsin is a dication that specifically binds primarily by hydrogen bonding in the minor groove at sites that have four or more contiguous A.T base pairs. We showed that the oxidation potential of netropsin is less than that of any of the four nucleobases. We find that netropsin quenches the oxidative reactions of DNA independent of whether it is specifically bound. Within the Perrin model of static quenching, a netropsin within a rather large fixed volume around the DNA is an effective quencher.