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Interacting RNA polymerase motors on a DNA track: effects of traffic congestion and intrinsic noise on RNA synthesis.
- Source :
-
Physical review. E, Statistical, nonlinear, and soft matter physics [Phys Rev E Stat Nonlin Soft Matter Phys] 2008 Jan; Vol. 77 (1 Pt 1), pp. 011921. Date of Electronic Publication: 2008 Jan 25. - Publication Year :
- 2008
-
Abstract
- RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input to move along the track formed by DNA. In many circumstances, which are described in this paper, a large number of RNAPs move simultaneously along the same track; we refer to such collective movements of the RNAPs as RNAP traffic. Here we develop a theoretical model for RNAP traffic by incorporating the steric interactions between RNAPs as well as the mechanochemical cycle of individual RNAPs during the elongation of the mRNA. By a combination of analytical and numerical techniques, we calculate the rates of mRNA synthesis and the average density profile of the RNAPs on the DNA track. We also introduce, and compute, two different measures of fluctuations in the synthesis of RNA. Analyzing these fluctuations, we show how the level of intrinsic noise in mRNA synthesis depends on the concentrations of the RNAPs as well as on those of some of the reactants and the products of the enzymatic reactions catalyzed by RNAP. We suggest appropriate experimental systems and techniques for testing our theoretical predictions.
- Subjects :
- Binding Sites
Computer Simulation
Models, Statistical
Motion
Nucleic Acid Conformation
Protein Binding
DNA chemistry
DNA ultrastructure
DNA-Directed RNA Polymerases chemistry
DNA-Directed RNA Polymerases ultrastructure
Models, Chemical
Models, Molecular
Molecular Motor Proteins chemistry
Molecular Motor Proteins ultrastructure
Subjects
Details
- Language :
- English
- ISSN :
- 1539-3755
- Volume :
- 77
- Issue :
- 1 Pt 1
- Database :
- MEDLINE
- Journal :
- Physical review. E, Statistical, nonlinear, and soft matter physics
- Publication Type :
- Academic Journal
- Accession number :
- 18351890
- Full Text :
- https://doi.org/10.1103/PhysRevE.77.011921