RNA Polymerase interactions and elongation rate.

@article{Belitsky2019RNAPI,
  title={RNA Polymerase interactions and elongation rate.},
  author={Vladimir Belitsky and Gunter M. Sch{\"u}tz},
  journal={Journal of theoretical biology},
  year={2019},
  volume={462},
  pages={
          370-380
        }
}

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References

SHOWING 1-10 OF 42 REFERENCES

RNA polymerase motor on DNA track: effects of interactions, external force and torque

TLDR
A theoretical model is developed by incorporating the steric interactions of the RNAPs and their mechanochemical cycles which explicitly captures the cyclical shape changes of each motor and explains not only the dependence of the average velocity of a RNAP on the externally applied load force, but also predicts a nonmotonic variation of theaverage velocity on external torque.

A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases

TLDR
The torque mechanism is incorporated into a stochastic model and simulated transcription and results suggest that the torsional interaction of RNAPs is an important mechanism in maintaining fast transcription times, and that transcription should be viewed as a cooperative group effort by multiple polymerases.

Synergistic action of RNA polymerases in overcoming the nucleosomal barrier

TLDR
The data indicate that histone-DNA interactions dictate RNAP pausing behavior, and alleviation of nucleosome-induced backtracking by multiple polymerases may prove to be a mechanism for overcoming the nucleosomal barrier in vivo.

Sequence-dependent kinetic model for transcription elongation by RNA polymerase.

Cooperation Between RNA Polymerase Molecules in Transcription Elongation

TLDR
It is demonstrated that most transcriptional delays disappear if more than one RNAP molecule initiates from the same promoter, which explains why elongation is still fast and processive in vivo even without anti-arrest factors.

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

TLDR
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.

Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models.

RNA polymerase II (Pol II) is an essential enzyme that catalyzes transcription with high efficiency and fidelity in eukaryotic cells. During transcription elongation, Pol II catalyzes the nucleotide

Pausing and Backtracking in Transcription Under Dense Traffic Conditions

RNA polymerases transcribe the genetic information from DNA to RNA. They move along the DNA by stochastic single-nucleotide steps that are interrupted by pauses. Here we use a variant of driven

Trigger loop folding determines transcription rate of Escherichia coli’s RNA polymerase

TLDR
Single molecule experiments with the WT and two TL-tip mutants of the Escherichia coli enzyme reveal that tip mutations modulate RNAP’s pause-free velocity, identifying TL conformational changes as one of two rate-determining steps in elongation.