The influence of look-ahead on the error rate of transcription

Y. R. Yamada, C. S. Peskin

Research output: Contribution to journalArticle

Abstract

In this paper we study the error rate of RNA synthesis in the look-ahead model for the random walk of RNA polymerase along DNA during transcription. The model's central assumption is the existence of a window of activity in which ribonucleoside triphosphates (rNTPs) bind reversibly to the template DNA strand before being hydrolyzed and linked covalently to the nascent RNA chain. An unknown, but important, integer parameter of this model is the window size w. Here, we use mathematical analysis and computer simulation to study the rate at which transcriptional errors occur as a function of w. We find dramatic reduction in the error rate of transcription as w increases, especially for small values of w. The error reduction method provided by look-ahead occurs before hydrolysis and covalent linkage of rNTP to the nascent RNA chain, and is therefore distinct from error correction mechanisms that have previously been considered.

Original languageEnglish (US)
Pages (from-to)206-227
Number of pages22
JournalMathematical Modelling of Natural Phenomena
Volume5
Issue number3
DOIs
StatePublished - Jan 2010

Keywords

  • Gillespie simulation
  • chemical master equation
  • elongation dynamics of transcription
  • error-correcting mechanisms
  • transcription modeling

ASJC Scopus subject areas

  • Modeling and Simulation
  • Applied Mathematics

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