Comparative Analysis of DNA-Binding Selectivity of Hairpin and Cyclic Pyrrole-Imidazole Polyamides Based on Next-Generation Sequencing

HANDLE オープンアクセス
  • 柏﨑, 玄伍
    Department of Chemistry, Graduate School of Science, Kyoto University
  • 朝光, 世煌
    Department of Chemistry, Graduate School of Science, Kyoto University
  • 橋谷, かおり
    Department of Chemistry, Graduate School of Science, Kyoto University
  • 板東, 俊和
    Department of Systems Science, Graduate School of Informatics, Kyoto University
  • 杉山, 弘
    Department of Chemistry, Graduate School of Science, Kyoto University
  • Sawatani, Yoshito
    Department of Chemistry, Graduate School of Science, Kyoto University
  • Hashiya, Kaori
    Department of Chemistry, Graduate School of Science, Kyoto University
  • Bando, Toshikazu
    Department of Chemistry, Graduate School of Science, Kyoto University
  • Sugiyama, Hiroshi
    Department of Chemistry, Graduate School of Science, Kyoto University, ・Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University

抄録

Many long pyrrole-imidazole polyamides (PIPs) have been synthesized in the search for higher specificity, with the aim of realizing the great potential of such compounds in biological and clinical areas. Among several types of PIPs, we designed and synthesized hairpin and cyclic PIPs targeting identical sequences. Bind-n-Seq analysis revealed that both bound to the intended sequences. However, adenines in the data analyzed by the previously reported Bind-n-Seq method appeared to be significantly higher in the motif ratio than thymines, even though the PIPs were not expected to distinguish A from T. We therefore examined the experimental protocol and analysis pipeline in detail and developed a new method based on Bind-n-Seq motif identification with a reference sequence (Bind-n-Seq-MR). High-throughput sequence analysis of the PIP-enriched DNA data by Bind-n-Seq-MR presented A and T comparably. Surface plasmon resonance assays were performed to validate the new method.

収録刊行物

  • ChemBioChem

    ChemBioChem 17 (18), 1752-1758, 2016-09-15

    Wiley-VCH Verlag

キーワード

詳細情報 詳細情報について

  • CRID
    1050282810834184832
  • NII論文ID
    120006460111
  • ISSN
    14394227
  • HANDLE
    2433/230876
  • 本文言語コード
    en
  • 資料種別
    journal article
  • データソース種別
    • IRDB
    • CiNii Articles

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