The search for a DNA target in the nucleus

The mean time TSTS for a transcription factor (TF) or a DNA-ligation enzyme, to find their target located on the molecule DNA is crucial for cell activation or survival. Using mean first passage time equations, we obtain here refined estimates for TSTS, based on the classical scenario in which the search process switches between a one-dimensional motion along the DNA molecule and a free Brownian motion in the nucleus. By considering the interaction potential between the TF and the DNA base pairs (bp), we find that the TF stays attached to the DNA molecule during an average time τDNA≈4.6 msτDNA≈4.6 ms. Between two consecutive attached periods, the TF diffuses freely inside the nucleus during τfree≈1.4 msτfree≈1.4 ms. In agreement with experimental data for the Lac-I TF, we find that τDNA≈3.2τfreeτDNA≈3.2τfree.