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Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo

Figure 2

Recombinant HSF binds HSEs with picomolar affinity in vitro.

A and B) The mobility of the constant 200 attomole HSE probe shifts into a trimeric-HSF:HSE complex as increasing HSF is added. There is no HSF in the left-most lane, the right-most lane contains 3 nM HSF (1 nM trimeric HSF), and the intervening lanes contain two-fold serial dilutions of HSF. C) A hyperbolic curve based on the Kd equation (see Methods) was modeled using the band shift data, indicating a Kd of 42.6 pM (95% confidence interval of 36.8–49.4 pM). D) A hyperbolic curve based on the Kd equation (see Methods) was modeled using the band shift data, indicating a Kd of 224 pM (95% confidence interval of 181–276 pM). E) The intensity of each isolated HSE in the Drosophila genome is transformed to an absolute Kd using the absolute Kds calculated from band shift data in panels A and B. The Kd values range from 40–400 pM.

Figure 2

doi: https://doi.org/10.1371/journal.pgen.1002610.g002