Influence of PCR reagents on DNA polymerase extension rates measured on real-time PCR instruments

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Publication Type pre-print
School or College School of Medicine
Department Pathology
Creator Wittwer, Carl T.
Other Author Montgomery, Jesse L.
Title Influence of PCR reagents on DNA polymerase extension rates measured on real-time PCR instruments
Date 2014-01-01
Description BACKGROUND: Radioactive DNA polymerase activity methods are cumbersome and do not provide initial extension rates. A simple extension rate assay would enable study of basic assumptions about PCR and define the limits of rapid PCR. METHODS: A continuous assay that monitors DNA polymerase extension using noncovalent DNA dyes on common real-time PCR instruments was developed. Extension rates were measured in nucleotides per second per molecule of polymerase. To initiate the reaction, a nucleotide analog was heat activated at 95 °C for 5 min, the temperature decreased to 75 °C, and fluorescence monitored until substrate exhaustion in 30-90 min. RESULTS: The assay was linear with time for over 40% of the reaction and for polymerase concentrations over a 100-fold range (1-100 pmol/L). Extension rates decreased continuously with increasing monovalent cation concentrations (lithium, sodium, potassium, cesium, and ammonium). Melting-temperature depressors had variable effects. DMSO increased rates up to 33%, whereas glycerol had little effect. Betaine, formamide, and 1,2-propanediol decreased rates with increasing concentrations. Four common noncovalent DNA dyes inhibited polymerase extension. Heat-activated nucleotide analogs were 92% activated after 5 min, and hot start DNA polymerases were 73%-90% activated after 20 min. CONCLUSIONS: Simple DNAextension rate assays can be performed on real-time PCR instruments. Activity is decreased by monovalent cations,DNA dyes, and most melting temperature depressors. Rational inclusion of PCR components on the basis of their effects on polymerase extension is likely to be useful in PCR, particularly rapid-cycle or fast PCR.
Type Text
Publisher American Association for Clinical Chemistry
Volume 60
Issue 2
First Page 334
Last Page 340
Language eng
Bibliographic Citation Montgomery, J. L., & Wittwer, C. T. (2014). Influence of PCR reagents on DNA polymerase extension rates measured on real-time PCR instruments. Clinical Chemistry, 60(2), 334-40.
Rights Management (c)American Association for Clinical Chemistry ; DOI: 10.1373/clinchem.2013.212829.
Format Medium application/pdf
Format Extent 194,615 bytes
Identifier uspace,18476
ARK ark:/87278/s6mk9p13
Setname ir_uspace
Date Created 2015-02-27
Date Modified 2015-03-02
ID 712838
Reference URL https://collections.lib.utah.edu/ark:/87278/s6mk9p13
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