Rational design of sequence-specific DNA alkylating agents based on duocarmycin A and pyrrole-imidazole hairpin polyamides

Synthesis of novel conjugates between segment A of Duocarmycin A (Du) and N-methylimidazole (Im)-N-methylpyrrole (Py) hairpin polyamides and their DNA alkylation are described. The conjugates PyPyPy gamma ImPyPyDu (8a) and ImPyPy gamma ImPyPyDu (8b) were designed to alkylate the target sequences (A/T)G(A/T)(2)N(A/G) and (A/T)G(A/T)CN(AVG), respectively, according to Dervan's ring-pairing rule. High-resolution denaturing gel electrophoresis indicated that 8a exclusively alkylated the A of the 5'-TGTAAAA-3' within a similar to 400 bp DNA fragment. Similarly, alkylation by 8b occurred exclusively at the G of the 5'-AGTCAGA-3' sequence with efficiency at nanomolar concentration. To better understand the structure of the alkylated DNA by these conjugates, the alkylation of non-self-complementary duplex decanucleotides, ODN1 and ODN2, was investigated. HPLC and ESMS analyses of the reaction of these ODNs with 8a and 8b demonstrated that both conjugates efficiently and selectively alkylate N3 of the purine bases of their target sequences.