title: Biology of N-methylpyrrole-N-methylimidazole hairpin polyamide.
abstract: Chemical substances that can recognize and bind DNA in a sequence-specific manner have enormous importance in modern biology and medicine. When covalently linked, hairpin polyamides made up of N-methylpyrrole (Py) and N-methylimidazole (Im) can bind to DNA in a sequence-specific manner. An Im opposite a Py recognizes and binds G:C from C:G, whereas a Py opposite an Im recognizes and binds to C:G. A Py-Py pair degenerately binds to T:A or A:T, whereas a hydroxypyrrole opposite a Py recognizes and binds to T:A from A:T, and vice versa. A variant in this recognition is the beta-alanine (beta-ala-beta-ala) pair, which also degenerately binds to A:T or T:A. The hairpin polyamides are cell permeable and bind to DNA at nanomolar concentrations, with binding coefficients similar to those of transcription factors. This review comprehensively discusses the current literature on using the sequence-specific recognition ability of the polyamides to study various DNA-protein interactions.
authors.affiliation: Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Surugadai, Kanda, Chiyoda-ku, Tokyo 101-0062, Japan.
authors.forename: Musti Sree Rama Chandra
authors.initials: MS
authors.lastname: Murty
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sugiyama
mesh_terms: D000478:Alkylation; D000818:Animals; D000970:Antineoplastic Agents / Q000494:pharmacology; D001665:Binding Sites; D001667:Binding, Competitive; D002478:Cells, Cultured; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D006801:Humans; D007093:Imidazoles / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D009757:Nylons / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D010539:Permeability; D011758:Pyrroles / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D014157:Transcription Factors / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics
chemical_list: D000970:Antineoplastic Agents; D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; D014157:Transcription Factors; D004247:DNA