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Nucleic Acids Research, 1982, Vol. 10, No. 2 749-762
© 1982

CHEMISTRY

Binding of ethidium derivatives to natural DNA: a 300 MHz 1H NMR study{dagger}

J. Feigon, W. Leupin, W.A. Denny{ddagger} and D.R. Kearns*

Department of Chemistry, University of California at San Diega La Jolla, CA 92093, USA

*To whom correspondence should be addressed

Received September 3, 1981. Revised November 24, 1981. Accepted November 24, 1981.

The binding of three ethidium derivatives, ethidium (1), des-3-amino ethidium (2) and des-8-amino ethidium (3), to short (–35 base pairs), random sequence DNA has been investigated using 300 MHz proton NNR. At 35°C all three drugs cause upfield shifts of the resonances from the exchangeable imino protons, as expected for Intercalative binding to DNA. However, the lineshapes vary significantly with the nature of the drug. The temperature dependence of the spectra of the DNA shows that differences between spectra observed at 35°C with ethidius and with des-3-amino ethidius are primarily due to differences in the drug binding kinetics rather than to differences in mode of binding. Removal of the emino group at position 3, but not at position 8, on the parent ethidius shortens the lifetime of the intercalative state; this implies that the 3-NH2 group is involved in stabilization of the drug-DNA complex. Analysis of the drug-DNA spectra indicates that there is a preference for binding of the drugs adjacent to G·C base pairs.

{dagger}A preliminary account of this work has been presented in part at the 25th Annual Meeting of the Biophysical Society, Denver, Colorado, Feb. 23–25, 1981.

{ddagger}Cancer chemotherapy Research Laboratory, University of Auckland, School of Medicine, Private Bag, Auckland, New Zealand.


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