DNA Alkylation by Pyrrole−Imidazole seco-CBI Conjugates with an Indole Linker:  Sequence-Specific DNA Alkylation with 10-Base-Pair Recognition through Heterodimer Formation

The sequence-specific DNA alkylation by conjugates 4 and 5, which consist of N-methylpyrrole (Py)−N-methylimidazole (Im) polyamides and 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI) linked with an indole linker, was investigated in the absence or presence of partner Py−Im polyamide 6. High-resolution denaturing polyacrylamide gel electrophoresis revealed that conjugate 4 alkylates DNA at the sequences 5‘-(A/T)GCCT A -3‘ through hairpin formation, and alkylates 5‘-GGAAAGAAA A -3‘ through an extended binding mode. However, in the presence of partner Py−Im polyamide 6, conjugate 4 alkylates DNA at a completely different sequence, 5‘-AGGTTGTCC A -3‘. Alkylation of 4 in the presence of 6 was effectively inhibited by a competitor 7. Surface plasmon resonance (SPR) results indicated that conjugate 4 does not bind to 5‘-AGGTTGTCC A -3‘, whereas 6 binds tightly to this sequence. The results suggest that alkylation proceeds through heterodimer formation, indicating that this is a general way to expand the recognition sequence for DNA alkylation by Py−Im seco-CBI conjugates.