Dynamics of backtracking long pauses of RNA polymerase

Abstract

The dynamics of backtracking long pauses by RNA polymerase is quantitatively studied based on our proposed model. Analytical formulas are obtained for the dependence of mean backtracking time and mean lifetime of backtracking long pauses on the binding affinity V 0 of RNAP to the DNA and RNA lattices, an important parameter for the transcription elongation complex. By comparison of the theoretically with experimentally obtained mean backtracking times, the value of binding affinity V 0 is predicted. Using the predicted V 0, the effects of external load on the mean backtracking time, on the lifetime of the backtracking long pauses and on the exit from the backtracking long pauses are studied. The results are in agreement with the available experimental data and, moreover, some predicted results are presented. In addition, using this V 0 we study the processivity of RNA polymerase under no and sideways forces.