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Title: Construction and characterization of Cy3- or Cy5-conjugated hairpin pyrrole–imidazole polyamides binding to DNA in the nucleosome
Authors: Han, Yong-Woon
Tsunaka, Yasuo
Yokota, Hiroaki
Matsumoto, Tomoko
Kashiwazaki, Gengo
Morinaga, Hironobu
Hashiya, Kaori
Bando, Toshikazu  kyouindb  KAKEN_id
Sugiyama, Hiroshi  kyouindb  KAKEN_id  orcid (unconfirmed)
Harada, Yoshie
Author's alias: 韓, 龍雲
Issue Date: 24-Oct-2013
Publisher: Royal Society of Chemistry (RSC)
Journal title: Biomaterials Science
Volume: 2
Issue: 3
Start page: 297
End page: 307
Abstract: Sequence-specific DNA-binding modules, N-methylpyrrole (Py)-N-methylimidazole-(Im) polyamides have been recently conjugated with fluorophores, and some of these conjugates could be used for the detection of specific DNA sequences. In this study, we synthesized two Py–Im polyamides 1 and 2, which interact with the 145-bp nucleosome positioning sequence 601. We conjugated the cyanine dye Cy3 or Cy5 with 1 or 2. In the absence of target DNA, the fluorescent conjugate of a Py–Im polyamide had lower fluorescence intensity compared with Cy3 or Cy5 alone. In the presence of either the target DNA or the nucleosome, the fluorescence intensity of the conjugates increased. Furthermore, we observed a Förster resonance energy transfer between the Cy3–Py–Im polyamide and the Cy5–Py–Im polyamide on the nucleosome. These results open up the possibilities that fluorescent conjugates of Py–Im polyamides can be used for characterization of the dynamic interactions within protein–DNA complexes.
Rights: This journal is © The Royal Society of Chemistry 2014
This is not the published version. Please cite only the published version.
DOI(Published Version): 10.1039/C3BM60202H
PubMed ID: 32481858
Appears in Collections:Journal Articles

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