Sequence-dependent kinetic model for transcription elongation by RNA polymerase. Academic Article uri icon

Overview

abstract

  • We present a kinetic model for the sequence-dependent motion of RNA polymerase (RNAP) during transcription elongation. For each NTP incorporation, RNAP has a net forward translocation of one base-pair along the DNA template. However, this process may involve the exploration of back-tracked and forward-tracked translocation modes. In our model, the kinetic rates for the reaction pathway, calculated based on the stabilities of the transcription elongation complex (TEC), necessarily lead to sequence-dependent NTP incorporation rates. Simulated RNAP elongation kinetics is in good agreement with data from transcription gels and single-molecule studies. The model provides a kinetic explanation for well-known back-tracked pauses at transcript positions with unstable TECs. It also predicts a new type of pause caused by an energetically unfavorable transition from pre to post-translocation modes.

publication date

  • November 19, 2004

Research

keywords

  • DNA-Directed RNA Polymerases
  • Models, Biological
  • Peptide Chain Elongation, Translational
  • Transcription, Genetic

Identity

Scopus Document Identifier

  • 7444253928

Digital Object Identifier (DOI)

  • 10.1016/j.jmb.2004.08.107

PubMed ID

  • 15522289

Additional Document Info

volume

  • 344

issue

  • 2