title: The application of fluorescence-conjugated pyrrole/imidazole polyamides in the characterization of protein-DNA complex formation.
abstract: N-Methylpyrrole (Py)-N-methylimidazole-(Im) polyamides are sequence-specific DNA-binding modules that are widely used for gene regulation, as synthetic transcriptional factors and as sequence-specific DNA alkylating agents. Recently, Py-Im polyamides have been conjugated with fluorophores, resulting in conjugates that are useful for the detection of specific DNA sequences. A Förster resonance energy transfer has been observed between Cy3- and Cy5-conjugated Py-Im polyamides on the nucleosome, indicating that fluorescence-conjugated Py-Im polyamides could possibly be used to characterise protein-DNA complexes. In this minireview, we discuss recent reports regarding fluorescence-conjugated Py-Im polyamides and their future application in the characterization of protein-DNA complex formation.
authors.affiliation: Institute for Integrated Cell-Materials Science (WPI-iCeMS), Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan. han.yongwoon.4u@kyoto-u.ac.jp hs@kuchem.kyoto-u.ac.jp harada.yoshie.4r@kyoto-u.ac.jp.
authors.forename: Yong-Woon
authors.initials: YW
authors.lastname: Han
authors.affiliation: Institute for Integrated Cell-Materials Science (WPI-iCeMS), Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan. han.yongwoon.4u@kyoto-u.ac.jp hs@kuchem.kyoto-u.ac.jp harada.yoshie.4r@kyoto-u.ac.jp and Department of Chemistry, Graduate School of Science, Kitashirakawa-oiwakecho, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sugiyama
authors.affiliation: Institute for Integrated Cell-Materials Science (WPI-iCeMS), Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan. han.yongwoon.4u@kyoto-u.ac.jp hs@kuchem.kyoto-u.ac.jp harada.yoshie.4r@kyoto-u.ac.jp and Graduate School of Biostudies, Yoshida Konoecho, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
authors.forename: Yoshie
authors.initials: Y
authors.lastname: Harada
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D005453:Fluorescence; D007093:Imidazoles / Q000737:chemistry*; D009707:Nucleosomes / Q000737:chemistry; D009757:Nylons / Q000737:chemistry*; D011758:Pyrroles / Q000737:chemistry*; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D007093:Imidazoles; D009707:Nucleosomes; D009757:Nylons; D011758:Pyrroles; D014157:Transcription Factors; D004247:DNA; C096654:N-methylpyrrole; C018100:1-methylimidazole