Alkylation of a human telomere sequence by heterotrimeric chlorambucil PI polyamide conjugates

We designed and synthesized human telomere alkylating N-methylpyrrole-N-methylimidazole (PI) polyamide conjugates (1–6). The C-type conjugates 1–3 possessed a chlorambucil moiety at the C terminus, whereas the N-type conjugates 4–6 had one of these moieties at the N terminus. The DNA alkylating activity of these conjugates was evaluated by high-resolution denaturing polyacrylamide gel electrophoresis using a 220 bp DNA fragment containing the human telomere repeat sequence 5′-(GGGTTA)₄-3′/5′-(TAACCC)₄-3′. C-type conjugates are designed to alkylate the G-rich-strand-containing 5′-GGGTTA-3′ and N-type conjugates were designed to alkylate the complementary C-rich strand-containing 5′-TAACCC-3′ sequence. The difference between conjugates 1–3 and 4–6 lies in the linker region between the polyamide moiety and chlorambucil. Conjugates 1 and 4 efficiently alkylated the 5′-GGTTAGGGTTA-3′ and 5′-CCCTAACCCTAA-3′ sequences, respectively, by recognizing 11 bp in the presence of distamycin A (Dist), in a heterotrimeric manner: one long alkylating polyamide conjugate (1–6) and two short partners (Dist).