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Biophys J, May 2000, p. 2560-2571, Vol. 78, No. 5
*Department of Chemistry University of Washington, Seattle,
Washington 98195-1700, and Department of Chemistry,
The Pennsylvania State University, University Park, Pennsylvania 16802 USA
The submicrosecond bending dynamics of duplex DNA were
measured at a single site, using a site-specific electron paramagnetic resonance active spin probe. The observed dynamics are interpreted in
terms of the mean squared amplitude of bending relative to the
end-to-end vector defined by the weakly bending rod model. The bending
dynamics monitored at the single site varied when the length and
position of a repeated AT sequence, distant from the spin probe, were
changed. As the distance between the probe and the AT sequence was
increased, the mean squared amplitude of bending seen by the probe due
to that sequence decreased. A model for the sequence-dependent internal
flexural motion of duplex DNA, which casts the mean squared bending
amplitudes in terms of sequence-dependent bending parameters, has been
developed. The best fit of the data to the model occurs when the
(AT)n basepairs are assumed to be 20% more flexible than
the average of the basepairs within the control sequence. These
findings provide a quantitative basis for interpreting the kinetics of
biological processes that depend on duplex DNA flexibility, such as
protein recognition and chromatin packaging.
Biophys J, May 2000, p. 2560-2571, Vol. 78, No. 5
© 2000 by the Biophysical Society 0006-3495/00/05/2560/12 $2.00
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