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Issue 3, 2014
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Construction and characterization of Cy3- or Cy5-conjugated hairpin pyrrole–imidazole polyamides binding to DNA in the nucleosome

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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.

Graphical abstract: Construction and characterization of Cy3- or Cy5-conjugated hairpin pyrrole–imidazole polyamides binding to DNA in the nucleosome

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Publication details

The article was received on 26 Aug 2013, accepted on 07 Oct 2013 and first published on 24 Oct 2013


Article type: Paper
DOI: 10.1039/C3BM60202H
Biomater. Sci., 2014,2, 297-307

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    Construction and characterization of Cy3- or Cy5-conjugated hairpin pyrrole–imidazole polyamides binding to DNA in the nucleosome

    Y. Han, Y. Tsunaka, H. Yokota, T. Matsumoto, G. Kashiwazaki, H. Morinaga, K. Hashiya, T. Bando, H. Sugiyama and Y. Harada, Biomater. Sci., 2014, 2, 297
    DOI: 10.1039/C3BM60202H

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