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Title: Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants.
Authors: Han, Yong-Woon  KAKEN_id
Matsumoto, Tomoko
Yokota, Hiroaki
Kashiwazaki, Gengo
Morinaga, Hironobu
Hashiya, Kaori
Bando, Toshikazu  kyouindb  KAKEN_id
Harada, Yoshie  KAKEN_id
Sugiyama, Hiroshi  kyouindb  KAKEN_id  orcid (unconfirmed)
Author's alias: 韓, 龍雲
Issue Date: 4-Oct-2012
Publisher: Oxford University Press
Journal title: Nucleic acids research
Volume: 40
Issue: 22
Start page: 11510
End page: 11517
Abstract: 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.
Rights: © The Author(s) 2012. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License.
DOI(Published Version): 10.1093/nar/gks897
PubMed ID: 23042247
Appears in Collections:Journal Articles

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