Development of a fluorescent probe for the study of nucleosome assembly and dynamics

Jennie Bever, P. A. Liddell, R. Bash, D. LoVullo, T. K. Schiefer, M. Williams, D. C. Daniel, M. Thompson, A. K W Taguchi, D. Lohr, Neal Woodbury

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


To develop a probe for use in real-time dynamic studies of nucleosomes, core histones (from Drosophila) were conjugated to a DNA-intercalating dye, thiazole orange, by a reaction targeting Cys 110 of histone H3. In the absence of DNA, the conjugated histones are only very weakly fluorescent. However, upon reconstitution into nucleosomes by standard salt dialysis procedures, the probe fluoresces strongly, reflecting its ability to intercalate into the nucleosomal DNA. The probe is also sensitive to the nature of the DNA-histone interaction. Nucleosomes reconstituted by stepwise salt dialysis give a fluorescence signal quite different from that of the species formed when DNA and histones are simply mixed in low salt. In addition, changing either the DNA length or the type of sequence (nucleosome positioning sequences versus random DNA of the same size) used in the reconstitution alters the resulting fluorescence yield. The results are all consistent with the conclusion that a more rigid, less flexible nucleosome structure results in less fluorescence than a looser structure, presumably due to structural constraints on dye intercalation. This probe should be well suited to analyzing nucleosome dynamics and to following factor-mediated assembly and remodeling of nucleosomes in real time, particularly at the single-molecule level.

Original languageEnglish (US)
Pages (from-to)1-11
Number of pages11
JournalAnalytical Biochemistry
Issue number1
StatePublished - Jun 1 2003


  • Chromatin
  • Histone H3
  • Intercalating dye
  • Nucleosome exchange
  • Thiazole orange

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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