Requirement of β-alanine components in sequence-specific DNA alkylation by pyrrole–imidazole conjugates with seven-base pair recognition

To investigate the effect of incorporation of β-alanine in alkylating N-methylpyrrole (Py)–N-methylimidazole (Im) polyamide, seco-CBI conjugates 2–8 were synthesized by an Fmoc solid-phase method and subsequent coupling with an alkylating moiety. DNA-alkylating activities of conjugates 2–8 were evaluated by high-resolution denaturing gel electrophoresis with 202-base pair (bp) DNA fragments. Alkylation by conjugates 2 and 3, which have antiparallel pairings of β-alanine (β) opposite β (β/β) and Py/β, occurred mainly at the adenine (A) of the matching sequences, 5′-AGCTCCA-3′ (site 1) and 5′-AGCACCA-3′ (site 3). However, conjugate 4, with β/Py, did not show any DNA-alkylating activities. Similarly, conjugate 5, which possessed a Py/Py pair, weakly alkylated the matching sites at micromolar concentrations. Conjugates 6 and 7, which possessed β/β and Py/β pairs, respectively, alkylated at the A of the matching sequences, 5′-ACTACCA-3′ (site 2) and 5′-ACAACCA-3′ (site 4). In contrast, conjugated 8, with a Py/Py pair, showed lower activity and less alkylated DNA at sites 2 and 4 with mismatched alkylation at site 1 at a higher concentration than that of 6 and 7. These results demonstrate that incorporation of β-alanine is required for the sequence-specific alkylation by seco-CBI Py–Im conjugates with a seven-base pair sequence.

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