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 calledRNA polymerase (RNAP). It also uses the template as a track on which it moves as amotor, utilizing chemical energy input. The time it spends at each successive monomer ofDNA is random; we derive the exact distribution of these ‘dwell times’ in our model. Theinverse of the mean dwell time satisfies a Michaelis–Menten-like equation and is alsoconsistent with a general formula derived earlier by Fisher and Kolomeisky for molecularmotors with unbranched mechano-chemical cycles. Often many RNAP motors movesimultaneously on the same track. Incorporating the steric interactions among the RNAPsin our model, we also plot the three-dimensional phase diagram of our model for RNAPtraffic using an extremum current hypothesis.