Comparison of the patterns of DNA alkylation by phenol and amino seco-CBI-TMI compounds: use of a PCR method for the facile preparation of single end-labelled double-stranded DNA.

Both 5-hydroxy- and 5-amino-seco-CBI-TMI minor groove alkylators are very potent cytotoxins. The patterns of alkylation of the two enantiomers of both compounds were compared on a section of the gpt gene. All of the compounds alkylated only at adenines, with the amino compounds being slightly more selective. Consensus alkylation sequences for both S (natural) enantiomers were identical, but for the R (unnatural) enantiomers these varied slightly. The consensus sequences suggest that the S enantiomers bind lying in the 3'-->5' direction from the alkylated adenine, but there was no clear indication of which direction the R enantiomers lie on the DNA. Both S enantiomers were 10- to 100-fold more efficient alkylators than the R enantiomers, and the amino compounds were somewhat more efficient than the corresponding phenols. The S enantiomers were more cytotoxic then the R in both the phenol and amino series. The large amounts of end-labelled DNA required for this work was obtained by first end-labelling appropriate primer oligonucleotides, then amplifying by PCR. Compared with other methods in use, this is a simple and flexible one-step procedure for the preparation of labelled DNA of any sequence. An improvement in the synthesis of 5-hydroxy-seco-CBI-TMI is reported.