title: Studying RNAP-promoter interactions using atomic force microscopy.
abstract: The most fundamental step in gene expression is transcription, during which DNA is transcribed to a corresponding RNA strand by the action of RNA polymerases (RNAPs). Over the past two decades, atomic force microscopy (AFM) has been used as one of the key tools in the investigation of transcriptional events at the single-molecule level. AFM studies have provided significant insights into the structure-function relationships of RNAP-DNA complexes in different stages of transcription. Here, we begin by illustrating the basic setup of AFM, followed by an introduction of the applications of AFM techniques, including high-speed AFM (HS-AFM) imaging, to investigate RNAP-DNA interactions with a special focus on promoter-search processes and open promoter formations. The combination of AFM with a newly developed experimental technique, DNA origami nanotechnology, will also be described.
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan. Electronic address: ysuzuki79@kuchem.kyoto-u.ac.jp.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan; CREST, Japan Science and Technology Agency (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan. Electronic address: endo@kuchem.kyoto-u.ac.jp.
authors.forename: Masayuki
authors.initials: M
authors.lastname: Endo
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan; CREST, Japan Science and Technology Agency (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan. Electronic address: hs@kuchem.kyoto-u.ac.jp.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sugiyama
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000648:ultrastructure; D015870:Gene Expression; D018625:Microscopy, Atomic Force; D036103:Nanotechnology; D011401:Promoter Regions, Genetic; D014158:Transcription, Genetic
chemical_list: D012321:DNA-Directed RNA Polymerases
keywords: Atomic force microscopy; DNA origami; Promoter; RNA polymerase; Transcription