title: Sequence-specific DNA alkylation targeting for Kras codon 13 mutation by pyrrole-imidazole polyamide seco-CBI conjugates.
abstract: Hairpin N-methylpyrrole-N-methylimidazole polyamide seco-CBI conjugates 2-6 were designed for synthesis by Fmoc solid-phase synthesis, and their DNA-alkylating activities against the Kras codon 13 mutation were compared by high-resolution denaturing gel electrophoresis with 225 base pair (bp) DNA fragments. Conjugate 5 had high reactivity towards the Kras codon 13 mutation site, with alkylation occurring at the A of the sequence 5'-ACGTCACCA-3' (site 2), including minor 1 bp-mismatch alkylation against wild type 5'-ACGCCACCA-3' (site 3). Conjugate 6, which differs from conjugate 5 by exchanging one Py unit with a β unit, showed high selectivity but only weakly alkylated the A of 5'-ACGTCACCA-3' (site 2). The hairpin polyamide seco-CBI conjugate 5 thus alkylates according to Dervan's pairing rule with the pairing recognition which β/β pair targets T-A and A-T pairs. SPR and a computer-minimized model suggest that 5 binds to the target sequence with high affinity in a hairpin conformation, allowing for efficient DNA alkylation.
authors.affiliation: Department of Chemistry, Kyoto University, Kitashirakawa-Oiwaketyo, Sakyo, Kyoto, 606-8502 (Japan), Fax: (+81) 75-753-3670.
authors.forename: Rhys Dylan
authors.initials: RD
authors.lastname: Taylor
authors.forename: Sefan
authors.initials: S
authors.lastname: Asamitsu
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Takenaka
authors.forename: Makoto
authors.initials: M
authors.lastname: Yamamoto
authors.forename: Kaori
authors.initials: K
authors.lastname: Hashiya
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Kawamoto
authors.forename: Toshikazu
authors.initials: T
authors.lastname: Bando
authors.forename: Hiroki
authors.initials: H
authors.lastname: Nagase
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sugiyama
mesh_terms: D000409:Alanine / Q000235:genetics / Q000378:metabolism; D000478:Alkylation; D020029:Base Pairing; D001483:Base Sequence; D003062:Codon; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D007093:Imidazoles / Q000737:chemistry*; D008958:Models, Molecular; D009154:Mutation; D009757:Nylons / Q000138:chemical synthesis / Q000737:chemistry*; D011758:Pyrroles / Q000737:chemistry*; D018631:ras Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D003062:Codon; D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; D004247:DNA; D018631:ras Proteins; C096654:N-methylpyrrole; D000409:Alanine; C018100:1-methylimidazole
keywords: Kras codon 13 mutation; PAGE analysis; adenine alkylation; pyrrole-imidazole polyamides; sequence specificity