Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (105K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (67)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Mathieu-Daude, F
Right arrow Articles by McClelland, M
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Mathieu-Daude, F
Right arrow Articles by McClelland, M
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, Vol 24, Issue 11 2080-2086, Copyright © 1996 by Oxford University Press

ARTICLES

DNA rehybridization during PCR: the 'Cot effect' and its consequences

F Mathieu-Daude, J Welsh, T Vogt and M McClelland
Sidney Kimmel Cancer Center, San Diego, CA 92121, USA.

The rate of amplification of abundant PCR products generally declines faster than that of less abundant products in the same tube in the later cycles of PCR. As a consequence, differences in product abundance diminish as the number of PCR cycles increases. Rehybridization of PCR products which may interfere with primer binding or extension can explain this significant feature in late cycles. Rehybridization occurs with a half-time dependent on the reciprocal of the DNA concentration. Thus, if multiple PCR products are amplified in the same tube, reannealing occurs faster for the more abundant PCR products. In RT-PCR using an internal control, this results in a systematic bias against the more abundant of the two PCR products. In RNA fingerprinting by arbitrarily primed PCR (or differentially display of cDNAs), very large or absolute differences in the expression of a transcript between samples are preserved but smaller real differences may be gradually erased as the PCR reaction proceeds. Thus, this 'Cot effect' may systematically cause an underestimate of the true difference in starting template concentrations. However, differences in starting template concentrations will be better preserved in the less abundant PCR products. Furthermore, the slow down in amplification of abundant products will allow these rarer products to become more visible in the fingerprint which may, in turn, allow rarer cDNAs to be sampled more efficiently. In some applications, where the object is to stochiometrically amplify a mixture of nucleic acids, the bias against abundant PCR products can be partly overcome by limiting the number of PCR cycles and, thus, the concentration of the products. In other cases, abundance normalization at later cycles may be useful, such as in the production of normalized libraries.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
R. F. Thompson, M. Suzuki, K. W. Lau, and J. M. Greally
A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry
Bioinformatics, September 1, 2009; 25(17): 2164 - 2170.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
M. Nikolausz, A. Chatzinotas, A. Tancsics, G. Imfeld, and M. Kastner
Evaluation of Single-Nucleotide Primer Extension for Detection and Typing of Phylogenetic Markers Used for Investigation of Microbial Communities
Appl. Envir. Microbiol., May 1, 2009; 75(9): 2850 - 2860.
[Abstract] [Full Text] [PDF]

Home page
 Poult. Sci.Home page
A. Martynova-VanKley, A. Syvyk, I. Teplova, M. Hume, and A. Nalian
Rapid Detection of Avian Eimeria Species Using Denaturing Gradient Gel Electrophoresis
Poult. Sci., September 1, 2008; 87(9): 1707 - 1713.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. F. Thompson, M. Reimers, B. Khulan, M. Gissot, T. A. Richmond, Q. Chen, X. Zheng, K. Kim, and J. M. Greally
An analytical pipeline for genomic representations used for cytosine methylation studies
Bioinformatics, May 1, 2008; 24(9): 1161 - 1167.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
M. Haarman and J. Knol
Quantitative Real-Time PCR Analysis of Fecal Lactobacillus Species in Infants Receiving a Prebiotic Infant Formula
Appl. Envir. Microbiol., April 1, 2006; 72(4): 2359 - 2365.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Schumacher, P. Kapranov, Z. Kaminsky, J. Flanagan, A. Assadzadeh, P. Yau, C. Virtanen, N. Winegarden, J. Cheng, T. Gingeras, et al.
Microarray-based DNA methylation profiling: technology and applications
Nucleic Acids Res., January 20, 2006; 34(2): 528 - 542.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
M. Haarman and J. Knol
Quantitative Real-Time PCR Assays To Identify and Quantify Fecal Bifidobacterium Species in Infants Receiving a Prebiotic Infant Formula
Appl. Envir. Microbiol., May 1, 2005; 71(5): 2318 - 2324.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
S. Kurata, T. Kanagawa, Y. Magariyama, K. Takatsu, K. Yamada, T. Yokomaku, and Y. Kamagata
Reevaluation and Reduction of a PCR Bias Caused by Reannealing of Templates
Appl. Envir. Microbiol., December 1, 2004; 70(12): 7545 - 7549.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Chem.Home page
J. M. Rox, P. Bugert, J. Muller, A. Schorr, P. Hanfland, K. Madlener, H. Kluter, and B. Potzsch
Gene Expression Analysis in Platelets from a Single Donor: Evaluation of a PCR-Based Amplification Technique
Clin. Chem., December 1, 2004; 50(12): 2271 - 2278.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
D. A. Lipson and S. K. Schmidt
Seasonal Changes in an Alpine Soil Bacterial Community in the Colorado Rocky Mountains
Appl. Envir. Microbiol., May 1, 2004; 70(5): 2867 - 2879.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
B. Wallner, F. Piumi, G. Brem, M. Muller, and R. Achmann
Isolation of Y Chromosome-specific Microsatellites in the Horse and Cross-species Amplification in the Genus Equus
J. Hered., March 1, 2004; 95(2): 158 - 164.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
T. Lueders and M. W. Friedrich
Evaluation of PCR Amplification Bias by Terminal Restriction Fragment Length Polymorphism Analysis of Small-Subunit rRNA and mcrA Genes by Using Defined Template Mixtures of Methanogenic Pure Cultures and Soil DNA Extracts
Appl. Envir. Microbiol., January 1, 2003; 69(1): 320 - 326.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
P. C. Brzostowicz, K. L. Gibson, S. M. Thomas, M. S. Blasko, and P. E. Rouvière
Simultaneous Identification of Two Cyclohexanone Oxidation Genes from an Environmental Brevibacterium Isolate Using mRNA Differential Display
J. Bacteriol., August 1, 2000; 182(15): 4241 - 4248.
[Abstract] [Full Text]

Home page
 J. Bacteriol.Home page
N. R. Benson, R. M.-Y. Wong, and M. McClelland
Analysis of the SOS Response in Salmonella enterica Serovar Typhimurium Using RNA Fingerprinting by Arbitrarily Primed PCR
J. Bacteriol., June 15, 2000; 182(12): 3490 - 3497.
[Abstract] [Full Text]

Home page
 Proc. Natl. Acad. Sci. USAHome page
E. Dias Neto, R. Garcia Correa, S. Verjovski-Almeida, M. R. S. Briones, M. A. Nagai, W. da Silva Jr., M. A. Zago, S. Bordin, F. F. Costa, G. H. Goldman, et al.
Shotgun sequencing of the human transcriptome with ORF expressed sequence tags
PNAS, March 28, 2000; 97(7): 3491 - 3496.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
C. A. Baker, Z. Y. Lu, I. Zaitsev, and L. Manuelidis
Microglial Activation Varies in Different Models of Creutzfeldt-Jakob Disease
J. Virol., June 1, 1999; 73(6): 5089 - 5097.
[Abstract] [Full Text]

Home page
 Genome ResHome page
L. A. Haff and I. P. Smirnov
Single-Nucleotide Polymorphism Identification Assays Using a Thermostable DNA Polymerase and Delayed Extraction MALDI-TOF Mass Spectrometry
Genome Res., April 1, 1997; 7(4): 378 - 388.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.