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 Im PyPy 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 indica ted that 8a exclusively alkylated the A of the 5'-TGTAAAA-3' within a simil ar to 400 bp DNA fragment. Similarly, alkylation by 8b occurred exclusively at the G of the 5'-AGTCAGA-3' sequence with efficiency at nanomolar concen tration. To better understand the structure of the alkylated DNA by these c onjugates, 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 an d selectively alkylate N3 of the purine bases of their target sequences.