Triplet Anisotropy Decay Measurements of DNA Internal Motion

Michael Hogan, Johnny Wang, R. H. Austin

Research output: Chapter in Book/Report/Conference proceedingChapter


Triplet anisotropy decay techniques have been used to measure the internal flexibility and overall rotational motions of DNA over a time range of 15 ns to 200 μs. Nearly monodisperse DNA fragments with lengths varying from 65 to 600 base pairs were studied using the intercalating dye methylene blue as a triplet probe. The slow end-over-end tumbling of short DNA fragments (<165 base pairs) is as predicted for a rigid rod. As expected, a longer DNA fragment (600 base pairs) experiences slow segmental motions of its helix axis. At the earliest times, anisotropy decays more rapidly than expected for a rigid rod, suggesting that, when it is bound, methylene blue monitors fast internal motions of the helix. Since the rod-like end-over-end tumbling rules out fast bending motions (for short DNA fragments), the fast components of DNA anisotropy decay must be due to twisting motions of the helix, occurring with a time constant near 50ns. The same techniques were used to measure the conformational flexibility of DNA in the nucleosome. It is concluded that, when the DNA helix is wrapped to form a nucleosome, it experiences substantial internal flexibility, occurring with a time constant near 30 ns. The amplitude and time-scale of this motion appear to be similar to that seen in the uncomplexed DNA helix.

Original languageEnglish (US)
Title of host publicationCiba Foundation Symposium 93 - Mobility and Function in Proteins and Nucleic Acids
PublisherJohn Wiley and Sons Ltd
Number of pages20
ISBN (Electronic)9780470720752
ISBN (Print)0272796573, 9780272796573
StatePublished - May 30 2008

All Science Journal Classification (ASJC) codes

  • General Biochemistry, Genetics and Molecular Biology
  • General Medicine


  • Chromatin structure
  • Eukaryotic dna
  • High mobility group proteins
  • Histones
  • Nucleosome structure


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