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

• Published in: Journal of the American Chemical Society Vol. 129; no. 17; pp. 5384 - 5390
• Main Authors: Minoshima, Masafumi, Bando, Toshikazu, Sasaki, Shunta, Shinohara, Ken-ichi, Shimizu, Tatsuhiko, Fujimoto, Jun, Sugiyama, Hiroshi
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 02.05.2007; Amer Chemical Soc
• Subjects: Alkylation; Antibiotics, Antineoplastic - chemistry; Base Sequence; Chemistry; Chemistry, Multidisciplinary; DNA - chemistry; Electrophoresis, Polyacrylamide Gel; Fluorescent Dyes; Imidazoles - chemistry; Indicators and Reagents; Indoles - chemistry; Magnetic Resonance Spectroscopy; Molecular Sequence Data; Nucleic Acid Conformation; Nucleic Acid Denaturation; Physical Sciences; Pyrroles - chemistry; Science & Technology; Solvents; Spectrometry, Mass, Electrospray Ionization; Surface Plasmon Resonance; Xanthenes; CPI CONJUGATE; SOLID-PHASE SYNTHESIS; HAIRPIN POLYAMIDES; AMINO-ACIDS; SIMPLIFIED ANALOG; ANTITUMOR-ACTIVITY; DUOCARMYCIN-A; BINDING; INTERSTRAND CROSS-LINKING; MINOR-GROOVE
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja065235a

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.