The role of base excision repair in the repair of alkylation damage produced by 
a series of sequence specific oligopyrrole-containing analogues of distamycin A 
that tether benzoic acid mustard (BAM) has been examined. Whereas BAM alkylates 
and cross-links in the major groove of DNA, attachment to pyrrole units produces 
monoalkylations in the minor groove of DNA at AT tracts. Both sequence 
specificity of alkylation and cytotoxicity increase from one to three attached 
pyrrole units (compounds 1-3), and with 3 alkylation is selective for purine-N3 
in the sequence 5'-TTTTGPu (where Pu = guanine or adenine). In a model bacterial 
(Escherichia coli) system repair of the sequence specific minor groove 
alkylations produced by 2 and 3 does not appear to involve BER, since neither a 
formamidopyrimidine-DNA glycosylase repair deficient E. coli mutant (BH 20, fpg- 
mutant) nor a 3-methyladenine-DNA glycosylase repair deficient mutant (GC 4803, 
tag-alkA- mutant) showed increased cytotoxicity to 2 or 3 compared with the wild 
type, AB 1157. The monopyrrole compound 1 was, however, approximately 4-fold 
more cytotoxic to the GC 4803 mutant compared with wild type and BH 20, 
suggesting a role for the 3-methyladenine-DNA glycosylase in the recognition and 
excision of the adducts formed by 1. In contrast, increased sensitivity (> 
10-fold) was observed for the conventional nitrogen mustard BAM in the BH 20 
strain, suggesting a role for the formamidopyrimidine-DNA glycosylase in the 
repair of the lesions produced by the agent. In a cell-free system the E. coli 
3-methyladenine-DNA glycosylase (AlkA) was shown to remove alkylations at 
5'-TTTTGPu sequences. However, the efficiency in removing the adducts formed by 
the oligopyrrole compounds decreased dramatically from compound 1 to compound 3. 
Increasing the size of the DNA adduct formed in the minor groove therefore 
decreased the efficiency of recognition and removal of the adduct by the DNA 
glycosylase.