Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants.

• 韓, 龍雲

• Matsumoto, Tomoko

• Yokota, Hiroaki

• Kashiwazaki, Gengo

• Morinaga, Hironobu

• Hashiya, Kaori

• Bando, Toshikazu

• Harada, Yoshie

• Sugiyama, Hiroshi

抄録

N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py-Im polyamides 1-5 with different number of Im rings were synthesized, and their binding behaviour was investigated with surface plasmon resonance assay. It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides. The structures of four-ring Py-Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller. As the minor groove of DNA has a helical structure, planar Py-Im polyamides need to change their conformation to fit it upon binding to the minor groove. The data explain that an increase in planarity of Py-Im polyamide induced by the incorporation of Im reduces the association rate of Py-Im polyamides. This fundamental knowledge of the binding of Py-Im polyamides to DNA will facilitate the design of hairpin Py-Im polyamides as synthetic DNA-binding modules.

収録刊行物

• Nucleic acids research

  Nucleic acids research 40 (22), 11510-11517, 2012-10-04

  Oxford University Press

詳細情報

• CRID: 1050001335756200576
• NII論文ID: 120005122357
• NII書誌ID: AA00760269
• ISSN: 03051048
• HANDLE: 2433/167748
• 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