Abstract
The binding of eight ethidium derivatives to short ( ∼ 35 base-pair), random sequence DNA has been investigated using 1H-NMR. At 35°C, all drugs cause upfield shifts of the DNA imino proton resonances characteristic of intercalative binding to DNA, but the line shapes vary significantly with the nature of the drug. The results confirm our previous proposal that removal of the amino group at position-3, but not at position-8, on the parent ethidium shortens the lifetime of the intercalative state (less than 1–2 ms at 35°C). These results suggest that hydrogen-bonding interactions with the 3-NH 2 group are involved in stabilization of the drug-DNA complex or that changes in charge distribution that accompany removal of the 3-NH 2 group reduce the complex stability. The magnitude of the shift of the drug-DNA spectra indicates a slight preference for binding of the drugs adjacent to G·C base-pairs.
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