Fig. 3: The synthesis rate of nascent proteins by coupled gene expression machines on single DNA molecules.

a Exemplary trace with an accumulation of fluorescent protein signal on a single DNA molecule. b Histogram of the accumulation (drift) as computed from linear fits to protein synthesis spots for multiple (top panel) and single (bottom panel) anchor site/s with a 2021 nt-long C-terminal extension. Black lines indicate Gaussian estimates to guide the eye. c Schematic depiction of transcription-induced supercoiling. d TIRFM images of nascent protein synthesis spots from DNA at two rifampicin (rif) levels with the longest C-terminal extension (1980 nt). Scale bar, 10 µm. e Scheme of transcriptional-driven protein synthesis model with nascent proteins (with events of HT folding, dye binding, elongation, and bleaching) produced from DNA via co-transcribing RNAPs in transcriptional (Tx) bursts. f Autocorrelation curve (ACF) for HT fused with different C-terminal extensions and fit to mono-exponential decays (solid lines). The inverse amplitude, G(0)⁻¹, and correlation time \({\tau }_{C}\) of the ACF for two different concentrations of the fluorogenic dye and four C-terminal extension lengths. A linear trend is shown for both quantities as a gray line. Experiments were replicated with increasing C-terminal extension for n = 2,2,4,2 at 50 nM and n = 2,2,2 at 250 nM fluorogenic dye (small circles) to obtain the average values (large circles). The error bars are given as SD. g ACF for different rifampicin levels with the C-terminal extension of 1,980 nt. The inverse amplitude, G(0)⁻¹, followed a binding model between rifampicin and E. coli RNAP (solid line). The correlation time \({\tau }_{C}\) was extracted from the mono-exponential fit to the ACF. Experiments were replicated with increasing rif concentration for n = 3,2,2,2 (small circles) to obtain average values (large circles) with error bars as SD. Source data are provided as a Source Data file.