Figure 1

Elongation velocities on templates containing $N$-less cassettes. (a) Examples of single molecule traces of RNAP template position (relative to the promoter) vs time on a template containing a $U$-less cassette at two different NTP concentrations. The $U$-less cassette (287 bp) was located immediately before the runoff end. As expected, reduced UTP concentration slowed RNAP down on the upstream sequence but not on the $U$-less cassette. (b) Distributions of instantaneous velocities on all four $N$-less cassettes (top panel) and the corresponding upstream of the cassettes (bottom panel) at 1 mM NTPs. For each template, an instantaneous velocity histogram was generated from 30 single molecule traces. The means and the standard errors of the means (in $\mathrm{nt}/\mathrm{s}$) are $16.6\pm 0.3$ ($A$-less), $20.7\pm 0.3$ ($C$-less), $23.5\pm 0.4$ ($G$-less), $24.2\pm 0.5$ ($U$-less), and $20.6\pm 0.3$ (upstream sequence). For clarity, shown are Gaussian fits to histograms. For the $A$-less cassette, the original histogram is also shown.Reuse & Permissions

Figure 2

Elongation velocities at varied $A$, $U$, $G$, and $C$ concentrations, respectively, while maintaining the others at 1 mM. The template contained all four nucleotides. Each data point corresponds to an average of $\sim 15$ traces from transcription over at least a 400-bp range. The smooth curves are the corresponding fits using the model.Reuse & Permissions

Figure 3

Force-velocity measurements of transcription elongation and comparison with model predictions. Elongation velocity was measured under various forces at 1 mM all NTPs (black) or $200\mu \mathrm{M}$ UTP (arbitrarily chosen) with 1 mM A/C/GTP (gray). Each measured relation (dots with error bars) is compared with a prediction (smooth curve).Reuse & Permissions

Figure 4

Experimental (dots with error bars) [12] and predicted (smooth curves) probability density functions of the total dwell times at a 20-bp sequence surrounding the $\Delta tR2$ pause sequence under $+4$ (gray) and $+15\mathrm{pN}$ (black).Reuse & Permissions