Fig. 4.

Kinetics of elongation and pausing. (a) The pause density (pauses/nt, for pauses >1 second) as a function of temperature. The fit to eqn 2 (solid line, R²= 0.9) suggests a kinetic competition between the elongation and pausing pathways and gives an activation energy of 1.29 ± 0.05 kcal/mol for entry into a pause. Error bars represent the standard error of the mean. (b) Simplest kinetic In this model k_e is a convolution of the rate constants of all the processes that take the enzyme from n to n+1, including all reversible and irreversible steps, making k_e an effective rate of transcription. The same way, k_p is the effective rate for pause entry. Once in a pause, pauses are well described by diffusion in a 1D energy potential backwards along the DNA. The inset shows this diffusion schematically, where k_f and k_b are the forward and backwards rates, respectively; ΔG_f^† and ΔG_b^† are the corresponding activation energies. The active site is represented by 1. (c) Elongation (k_e) and pausing rates (k_p) vs. temperature plotted using the Arrhenius equation and the values obtained for ΔG_e^†, k_eo,ΔG_p^† and k_po, as described in the text. The elongation rate increases more rapidly than the pausing rate due to its increased activation energy. The starting force for all traces was 2 pN (5 pN for 21°C). All runs go up to their arrest force.