A quantitative model of error accumulation during PCR amplification

E. Pienaar, M. Theron, M. Nelson, Hendrik J Viljoen

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

The amplification of target DNA by the polymerase chain reaction (PCR) produces copies which may contain errors. Two sources of errors are associated with the PCR process: (1) editing errors that occur during DNA polymerase-catalyzed enzymatic copying and (2) errors due to DNA thermal damage. In this study a quantitative model of error frequencies is proposed and the role of reaction conditions is investigated. The errors which are ascribed to the polymerase depend on the efficiency of its editing function as well as the reaction conditions; specifically the temperature and the dNTP pool composition. Thermally induced errors stem mostly from three sources: A + G depurination, oxidative damage of guanine to 8-oxoG and cytosine deamination to uracil. The post-PCR modifications of sequences are primarily due to exposure of nucleic acids to elevated temperatures, especially if the DNA is in a single-stranded form. The proposed quantitative model predicts the accumulation of errors over the course of a PCR cycle. Thermal damage contributes significantly to the total errors; therefore consideration must be given to thermal management of the PCR process.

Original languageEnglish (US)
Pages (from-to)102-111
Number of pages10
JournalComputational Biology and Chemistry
Volume30
Issue number2
DOIs
StatePublished - Apr 1 2006

Fingerprint

polymerase chain reaction
Polymerase Chain Reaction
Polymerase chain reaction
Amplification
Hot Temperature
DNA-Directed DNA Polymerase
DNA
deoxyribonucleic acid
editing
Damage
Deamination
Temperature
Model
Uracil
damage
Cytosine
Guanine
Nucleic Acids
DNA Damage
Research Design

Keywords

  • Cytosine deamination
  • Depurination
  • Polymerase chain reaction
  • Thermal damage

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Organic Chemistry
  • Computational Mathematics

Cite this

A quantitative model of error accumulation during PCR amplification. / Pienaar, E.; Theron, M.; Nelson, M.; Viljoen, Hendrik J.

In: Computational Biology and Chemistry, Vol. 30, No. 2, 01.04.2006, p. 102-111.

Research output: Contribution to journalArticle

Pienaar, E. ; Theron, M. ; Nelson, M. ; Viljoen, Hendrik J. / A quantitative model of error accumulation during PCR amplification. In: Computational Biology and Chemistry. 2006 ; Vol. 30, No. 2. pp. 102-111.
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