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I want to simulate transcription activation by a given transcription factor (TF) with known kinetics. The binding rate $k_{on}$ is given in $\mu M^{-1} s^{-1} $, describing a bimolecular reaction mechanism (second order reaction kinetics). However, what is the concentration of a specific promoter in a cell?

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In a diploid organism there are two copies of DNA which means two copies or "molecules" of promoter in the entire cell. The volume of a typical eukaryotic cell (HeLa) would be 2.25×10-12 litres (Zhao et al. 2007, BioNumbers).

$$\text{Concentration }(M)=\frac{\text{Molecules per cell}}{\text{Avogadro No.} \times \text{Volume of the cell }(l)}$$

This comes to around 1.4758×10-12 M for 2 molecules of promoter. Accordingly, you can calculate for a haploid cell, multiple alleles or prokaryotic cell.

You can also assume a 2-compartment model with nucleus and cytoplasm as two different compartments. In this case, the DNA would be localized in the nucleus and therefore its effective concentration would be higher in the nucleus. You can look up nuclear volume in BioNumbers and plug that in the above formula to obtain the effective concentration.


Zhao, L., et al. "Intracellular water‐specific MR of microbead‐adherent cells: the HeLa cell intracellular water exchange lifetime." NMR in Biomedicine 21.2 (2008): 159-164.

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