RNA polymerase motors: dwell time distribution, velocity and dynamical phases

Abstract

Polymerization of RNA from a template DNA is carried out by a molecular machine called RNA polymerase (RNAP). It also uses the template as a track on which it moves as a motor, utilizing chemical energy input. The time it spends at each successive monomer of DNA is random; we derive the exact distribution of these 'dwell times' in our model. The inverse of the mean dwell time satisfies a Michaelis-Menten-like equation and is also consistent with a general formula derived earlier by Fisher and Kolomeisky for molecular motors with unbranched mechano-chemical cycles. Often many RNAP motors move simultaneously on the same track. Incorporating the steric interactions among the RNAPs in our model, we also plot the three-dimensional phase diagram of our model for RNAP traffic using an extremum current hypothesis.