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RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA)strand which is complementary to a single-stranded DNA template. From theperspective of physicists, an RNAP is a molecular motor that utilizes chemicalenergy input to move along the track formed by a DNA. In many circumstances,which are described in this paper, a large number of RNAPs move simultaneouslyalong the same track; we refer to such collective movements of the RNAPs asRNAP traffic. Here we develop a theoretical model for RNAP traffic byincorporating the steric interactions between RNAPs as well as themechano-chemical cycle of individual RNAPs during the elongation of the mRNA.By a combination of analytical and numerical techniques, we calculate the ratesof mRNA synthesis and the average density profile of the RNAPs on the DNAtrack. We also introduce, and compute, two new measures of fluctuations in thesynthesis of RNA. Analyzing these fluctuations, we show how the level of {\itintrinsic noise} in mRNA synthesis depends on the concentrations of the RNAPsas well as on those of some of the reactants and the products of the enzymaticreactions catalyzed by RNAP. We suggest appropriate experimental systems andtechniques for testing our theoretical predictions.

Interacting RNA polymerase motors on DNA track: effects of traffic congestion and intrinsic noise on RNA synthesis