Identification of the specific sites of interaction between intercalating drugs and DNA

A number of intercalating drugs have been found capable of causing site-specific inhibition of nick-translation in a DNA template of known sequence. Compounds of the 4'-(9-acridinylamino) methanesulphonanilide (AMSA) series cause selective inhibition in regions of G-C base pairs. Other intercalating drugs including ethidium bromide, adriamycin and actinomycin D also exhibited a G-C base pair preference although bisantrene-induced inhibition tended to be in regions of A-T base pairs. Diacridine compounds were more effective in inhibiting polymerase action as the linker chain was increased from 4 to 8 carbons. Results with mitonafide , anthracene derivatives, mithramycin and distamycin A are also presented. Inhibition caused by a given drug varied significantly from site to site in the DNA but apart from a preference for G-C or A-T rich regions, there seemed no preference for certain base sequences per se. Rather, it was felt that secondary structures, such as hairpins, in DNA might be of importance. The hypothesis is advanced that inhibition of polymerase action in this in vitro system may provide a useful and biologically relevant measure of the strength of drug binding at various DNA sites.