Sequence-dependent dynamics in duplex DNA

The submicrosecond bending dynamics of duplex DNA were measured at a single site, using a site-specific electron paramagnetic resonance active spin pr obe. The observed dynamics are interpreted in terms of the mean squared amp litude of bending relative to the end-to-end vector defined by the weakly b ending rod model. The bending dynamics monitored at the single site varied when the length and position of a repeated AT sequence, distant from the sp in probe, were changed. As the distance between the probe and the AT sequen ce was increased, the mean squared amplitude of bending seen by the probe d ue to that sequence decreased. A model for the sequence-dependent internal flexural motion of duplex DNA, which casts the mean squared bending amplitu des in terms of sequence-dependent bending parameters, has been developed. The best fit of the data to the model occurs when the (AT), basepairs are a ssumed to be 20% more flexible than the average of the basepairs within the control sequence. These findings provide a quantitative basis for interpre ting the kinetics of biological processes that depend on duplex DNA flexibi lity, such as protein recognition and chromatin packaging.