title: Inhibition of transcription at a coding sequence by alkylating polyamide.
abstract: Transcription from DNA sequence-specifically alkylated by a hairpin polyamide (ImPyPy-gamma-ImPyLDu86, 1) was investigated. High-resolution polyacrylamide gel electrophoresis demonstrated that conjugate 1 alkylated a 993-bp DNA fragment, in accordance with the Py-Im recognition rule, predominantly at the one match site on the GFP-encoding strand and at four sites (I'-IV') on the noncoding strand. Alkylation of DNA inhibited the formation of full-length mRNA and caused the transcription of truncated mRNA. Polyacrylamide gel electrophoresis demonstrated that the length of the truncated mRNA was consistent with the alkylated site on the coding strand. Complete inhibition of full-length mRNA synthesis was observed in the presence of 50 nM 1. In clear contrast, the hydrolyzed derivative of 1, designated 2, produced no truncated mRNA, nor did it significantly retard transcription: >80% transcription of full-length mRNA was observed at 50 nM. These results clearly indicate that inhibition of transcription can be achieved with alkylating Py-Im polyamide even in the coding regions of genes.
authors.affiliation: Division of Biofunctional Molecules, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental Univ., Chiyoda, Tokyo 101-0062, Japan.
authors.forename: Takanori
authors.initials: T
authors.lastname: Oyoshi
authors.forename: Wakana
authors.initials: W
authors.lastname: Kawakami
authors.forename: Akihiko
authors.initials: A
authors.lastname: Narita
authors.forename: Toshikazu
authors.initials: T
authors.lastname: Bando
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sugiyama
mesh_terms: D000478:Alkylation; D004247:DNA / Q000737:chemistry / Q000187:drug effects* / Q000235:genetics* / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D007093:Imidazoles / Q000737:chemistry / Q000494:pharmacology; D009757:Nylons / Q000737:chemistry* / Q000494:pharmacology*; D011758:Pyrroles / Q000737:chemistry / Q000494:pharmacology; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D014157:Transcription Factors / Q000737:chemistry / Q000494:pharmacology; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; D012333:RNA, Messenger; D014157:Transcription Factors; D004247:DNA; C096654:N-methylpyrrole; C018100:1-methylimidazole