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The Influence of Look-Ahead on the Error Rate ofTranscription

Published online by Cambridge University Press:  28 April 2010

Y. R. Yamada  and
C. S. Peskin
Y. R. Yamada*
Affiliation:
Department of Mathematics, University of Michigan, 48109-1043 Ann Arbor, MI, USA
C. S. Peskin
Affiliation:
Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
*
1 Corresponding author. E-mail: yryamada@umich.edu
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Abstract

In this paper we study the error rate of RNA synthesis in the look-ahead model for therandom walk of RNA polymerase along DNA during transcription. The model’s centralassumption is the existence of a window of activity in whichribonucleoside triphosphates (rNTPs) bind reversibly to the template DNA strand beforebeing hydrolyzed and linked covalently to the nascent RNA chain. An unknown, butimportant, integer parameter of this model is the window size w. Here, weuse mathematical analysis and computer simulation to study the rate at whichtranscriptional errors occur as a function of w. We find dramaticreduction in the error rate of transcription as w increases, especiallyfor small values of w. The error reduction method provided by look-aheadoccurs before hydrolysis and covalent linkage of rNTP to the nascent RNAchain, and is therefore distinct from error correction mechanisms that have previouslybeen considered.

Keywords

transcription modelingelongation dynamics of transcriptionerror-correcting mechanismsGillespie simulationchemical master equation
Type
Research Article
Information
Mathematical Modelling of Natural Phenomena , Volume 5 , Issue 3: Mathematical modeling in the medical sciences , 2010 , pp. 206 - 227
Copyright
© EDP Sciences, 2010

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