A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide selection

Steve Viljoen, Mark A Griep, Michael Nelson, Hendrik J Viljoen

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

The enzymatically catalyzed template-directed extension of ssDNA/primer complex is an important reaction of extraordinary complexity. The DNA polymerase does not merely facilitate the insertion of dNMP, but it also performs rapid screening of substrates to ensure a high degree of fidelity. Several kinetic studies have determined rate constants and equilibrium constants for the elementary steps that make up the overall pathway. The information is used to develop a macroscopic kinetic model, using an approach described by Ninio [Ninio J., 1987. Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabilities. Proc. Natl. Acad. Sci. U.S.A. 84, 663-667]. The principle idea of the Ninio approach is to track a single template/primer complex over time and to identify the expected behavior. The average time to insert a single nucleotide is a weighted sum of several terms, including the actual time to insert a nucleotide plus delays due to polymerase detachment from either the ternary (template-primer-polymerase) or quaternary (+nucleotide) complexes and time delays associated with the identification and ultimate rejection of an incorrect nucleotide from the binding site. The passage times of all events and their probability of occurrence are expressed in terms of the rate constants of the elementary steps of the reaction pathway. The model accounts for variations in the average insertion time with different nucleotides as well as the influence of G + C content of the sequence in the vicinity of the insertion site. Furthermore the model provides estimates of error frequencies. If nucleotide extension is recognized as a competition between successful insertions and time delaying events, it can be described as a binomial process with a probability distribution. The distribution gives the probability to extend a primer/template complex with a certain number of base pairs and in general it maps annealed complexes into extension products.

Original languageEnglish (US)
Pages (from-to)101-110
Number of pages10
JournalComputational Biology and Chemistry
Volume29
Issue number2
DOIs
StatePublished - Apr 1 2005

Fingerprint

nucleotides
DNA-Directed DNA Polymerase
Kinetic Model
Nucleotides
Elongation
Fidelity
elongation
DNA
deoxyribonucleic acid
Insertion
primers
Template
Kinetics
kinetics
Pathway
insertion
templates
Rate Constant
inserts
Rate constants

Keywords

  • Biochemical engineering
  • Mathematical model
  • Molecular biology
  • Polymerase chain reaction

ASJC Scopus subject areas

  • Biochemistry
  • Structural Biology
  • Analytical Chemistry
  • Physical and Theoretical Chemistry

Cite this

A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide selection. / Viljoen, Steve; Griep, Mark A; Nelson, Michael; Viljoen, Hendrik J.

In: Computational Biology and Chemistry, Vol. 29, No. 2, 01.04.2005, p. 101-110.

Research output: Contribution to journalArticle

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