A fundamental study of the PCR amplification of GC-rich DNA templates

T. G. Mamedov, E. Pienaar, S. E. Whitney, J. R. TerMaat, G. Carvill, R. Goliath, Anuradha Subramanian, Hendrik J Viljoen

Research output: Contribution to journalArticle

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Abstract

A theoretical analysis is presented with experimental confirmation to conclusively demonstrate the critical role that annealing plays in efficient PCR amplification of GC-rich templates. The analysis is focused on the annealing of primers at alternative binding sites (competitive annealing) and the main result is a quantitative expression of the efficiency (η) of annealing as a function of temperature (TA), annealing period (tA), and template composition. The optimal efficiency lies in a narrow region of TA and tA for GC-rich templates and a much broader region for normal GC templates. To confirm the theoretical findings, the following genes have been PCR amplified from human cDNA template: ARX and HBB (with 78.72% and 52.99% GC, respectively). Theoretical results are in excellent agreement with the experimental findings. Optimum annealing times for GC-rich genes lie in the range of 3-6 s and depend on annealing temperature. Annealing times greater than 10 s yield smeared PCR amplified products. The non-GC-rich gene did not exhibit this sensitivity to annealing times. Theory and experimental results show that shorter annealing times are not only sufficient but can actually aid in more efficient PCR amplification of GC-rich templates.

Original languageEnglish (US)
Pages (from-to)452-457
Number of pages6
JournalComputational Biology and Chemistry
Volume32
Issue number6
DOIs
StatePublished - Dec 1 2008

Fingerprint

Annealing
Amplification
Template
DNA
Polymerase Chain Reaction
Temperature
Genes
Gene
Complementary DNA
Binding Sites
Binding sites
CDNA
Theoretical Analysis
Sufficient
Alternatives
Experimental Results
Chemical analysis

Keywords

  • Annealing time
  • GC-rich
  • Mathematical model
  • PCR

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Organic Chemistry
  • Computational Mathematics

Cite this

A fundamental study of the PCR amplification of GC-rich DNA templates. / Mamedov, T. G.; Pienaar, E.; Whitney, S. E.; TerMaat, J. R.; Carvill, G.; Goliath, R.; Subramanian, Anuradha; Viljoen, Hendrik J.

In: Computational Biology and Chemistry, Vol. 32, No. 6, 01.12.2008, p. 452-457.

Research output: Contribution to journalArticle

Mamedov TG, Pienaar E, Whitney SE, TerMaat JR, Carvill G, Goliath R et al. A fundamental study of the PCR amplification of GC-rich DNA templates. Computational Biology and Chemistry. 2008 Dec 1;32(6):452-457. https://doi.org/10.1016/j.compbiolchem.2008.07.021
Mamedov, T. G. ; Pienaar, E. ; Whitney, S. E. ; TerMaat, J. R. ; Carvill, G. ; Goliath, R. ; Subramanian, Anuradha ; Viljoen, Hendrik J. / A fundamental study of the PCR amplification of GC-rich DNA templates. In: Computational Biology and Chemistry. 2008 ; Vol. 32, No. 6. pp. 452-457.
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