Abstract
The multistep kinetics through which DNA-binding proteins bind their targets are heavily studied, but relatively little attention has been paid to mechanisms of how proteins leave the double helix. Using single-DNA stretching and fluorescence detection, we recently demonstrated that the sequence-neutral DNA-binding proteins HU, NHP6A and Fis, readily exchange with each other and that the rate and degree of exchange is dependent on the concentration of solution-phase protein, regardless of protein species. We now examine the sequence dependence of binding and the exchange reactions investigated previously. Our results indicate an apparent disparity between biochemically measured sequence dependence and the sequence dependence in our single molecule approach. Additionally, we demonstrate a coarse-grained sequence dependence of the exchange reactions and correlate those results with our observed binding specificity.
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