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

Y. R. Yamada, Charles 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

Fingerprint

Look-ahead
Transcription
RNA
Error Rate
RNA Synthesis
Error Reduction
DNA
Error Correction
Reduction Method
Mathematical Analysis
Linkage
Template
Random walk
Error correction
Computer Simulation
Model
Distinct
Hydrolysis
Unknown
Integer

Keywords

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

ASJC Scopus subject areas

  • Modeling and Simulation

Cite this

The influence of look-ahead on the error rate of transcription. / Yamada, Y. R.; Peskin, Charles.

In: Mathematical Modelling of Natural Phenomena, Vol. 5, No. 3, 01.2010, p. 206-227.

Research output: Contribution to journalArticle

Yamada, Y. R. ; Peskin, Charles. / The influence of look-ahead on the error rate of transcription. In: Mathematical Modelling of Natural Phenomena. 2010 ; Vol. 5, No. 3. pp. 206-227.
@article{de860f814a1d432caf61d96c6f5703d4,
title = "The influence of look-ahead on the error rate of transcription",
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.",
keywords = "chemical master equation, elongation dynamics of transcription, error-correcting mechanisms, Gillespie simulation, transcription modeling",
author = "Yamada, {Y. R.} and Charles Peskin",
year = "2010",
month = "1",
doi = "10.1051/mmnp/20105313",
language = "English (US)",
volume = "5",
pages = "206--227",
journal = "Mathematical Modelling of Natural Phenomena",
issn = "0973-5348",
publisher = "EDP Sciences",
number = "3",

}

TY - JOUR

T1 - The influence of look-ahead on the error rate of transcription

AU - Yamada, Y. R.

AU - Peskin, Charles

PY - 2010/1

Y1 - 2010/1

N2 - 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.

AB - 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.

KW - chemical master equation

KW - elongation dynamics of transcription

KW - error-correcting mechanisms

KW - Gillespie simulation

KW - transcription modeling

UR - http://www.scopus.com/inward/record.url?scp=78349309327&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78349309327&partnerID=8YFLogxK

U2 - 10.1051/mmnp/20105313

DO - 10.1051/mmnp/20105313

M3 - Article

VL - 5

SP - 206

EP - 227

JO - Mathematical Modelling of Natural Phenomena

JF - Mathematical Modelling of Natural Phenomena

SN - 0973-5348

IS - 3

ER -