Fig. 2: Calculation of ka and kd for Osym operator.
From: Anti-correlation of LacI association and dissociation rates observed in living cells
a First, r and γ are determined in a strain in which LacI is deleted (created in BioRender https://BioRender.com/q45e576). γ is determined by performing bulk RT-qPCR on the mVenusNB mRNA on samples taken at 2-min intervals following addition of rifampicin to halt transcription. Data points labeled “RIF” correspond to rifampicin-treated samples while points labeled “con” represent untreated samples. Error bars represent standard deviation of three biological replicates. r is determined by measuring mean mRNA expression μΔlacI in ΔlacI strains using mRNA FISH, and using the equation μΔlacI = r/γ. b Once r and γ are known, ka and kd are determined by measuring the mRNA copy number distribution in cells expressing LacI (created in BioRender https://BioRender.com/q45e576). From the distribution, the mean \(\mu\) and Fano factor F are computed. The Fano factor is corrected for the effect of RNAP copy number variation (see main text) to obtain the corrected Fano factor Fc, whereupon the appropriate values for \(\mu\), Fc, r, and γ are substituted in Eqs. (1) and (2), which are solved numerically for ka and kd. Source data are provided as a Source Data file.
