Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (181K) 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 ISI Web of Science
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 (89)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Brownie, J.
Right arrow Articles by Little, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Brownie, J.
Right arrow Articles by Little, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, Vol 25, Issue 16 3235-3241, Copyright © 1997 by Oxford University Press

ARTICLES

The elimination of primer-dimer accumulation in PCR

J Brownie, S Shawcross, J Theaker, D Whitcombe, R Ferrie, C Newton and S Little
Zeneca Diagnostics, Gadbrook Park, Northwich, Cheshire CW9 7RA, UK.

We attempted to produce primer-dimers (PDs) from a variety of primers with differing types and extents of complementarity. Where PDs were produced they were cloned and sequenced. We were unable to produce detectable PDs either with individual primers alone or with similar sequence primers even if they had 3'complementarity. These observations led to the hypothesis that a system could be developed whereby the accumulation of PDs in a PCR may be eliminated. We demonstrate a method for the general suppression of PD formation that uses a sequence of additional nucleotides (a Tail) at the 5' ends of amplimers. Tailed amplimers are present at low concentration and only participate during early cycles of PCR. In subsequent PCR cycles, amplification is achieved using a single primer that has the same sequence as that of the Tail portion of the early cycle primers, here we refer to this as a Tag. When products are small, as with PDs, there is a high local concentration of complementary sequences derived from the Tail. This favours the annealing of the complementary ends of a single strand produced by tailed primer interactions and gives rise to 'pan-handle' structures. The formation of these outcompetes the annealing of further Tag primers thereby preventing the accumulation of non-specific PD products. This aids the design of large multiplex reactions and provides a means of detecting specific amplicons directly in the reaction vessel by using an intercalating dye.
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
 Appl. Environ. Microbiol.Home page
J. Huang, Y. Zhu, H. Wen, J. Zhang, S. Huang, J. Niu, and Q. Li
Quadruplex Real-Time PCR Assay for Detection and Identification of Vibrio cholerae O1 and O139 Strains and Determination of Their Toxigenic Potential
Appl. Envir. Microbiol., November 15, 2009; 75(22): 6981 - 6985.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
O. Peleg, G. Baneth, O. Eyal, J. Inbar, and S. Harrus
Use of Chimeric DNA-RNA Primers in Quantitative PCR for Detection of Ehrlichia canis and Babesia canis
Appl. Envir. Microbiol., October 1, 2009; 75(19): 6393 - 6398.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
S. Srivastava, A. K. Srivastava, P. Suprasanna, and S. F. D'Souza
Comparative biochemical and transcriptional profiling of two contrasting varieties of Brassica juncea L. in response to arsenic exposure reveals mechanisms of stress perception and tolerance
J. Exp. Bot., August 1, 2009; 60(12): 3419 - 3431.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
A. K. Srivastava, N. K. Ramaswamy, R. Mukopadhyaya, M. G. C. Jincy, and S. F. D'Souza
Thiourea modulates the expression and activity profile of mtATPase under salinity stress in seeds of Brassica juncea
Ann. Bot., February 1, 2009; 103(3): 403 - 410.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Chem.Home page
Q. Huang, Q. Hu, and Q. Li
Identification of 8 Foodborne Pathogens by Multicolor Combinational Probe Coding Technology in a Single Real-Time PCR
Clin. Chem., October 1, 2007; 53(10): 1741 - 1748.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J.-Y. Chun, K.-J. Kim, I.-T. Hwang, Y.-J. Kim, D.-H. Lee, I.-K. Lee, and J.-K. Kim
Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene
Nucleic Acids Res., March 19, 2007; 35(6): e40 - e40.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
B. Lin, K. M. Blaney, A. P. Malanoski, A. G. Ligler, J. M. Schnur, D. Metzgar, K. L. Russell, and D. A. Stenger
Using a Resequencing Microarray as a Multiple Respiratory Pathogen Detection Assay
J. Clin. Microbiol., February 1, 2007; 45(2): 443 - 452.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Li, Y.-C. Lin, C.-C. Wu, and H.-S. Liu
Enhancing the efficiency of a PCR using gold nanoparticles
Nucleic Acids Res., November 27, 2005; 33(21): e184 - e184.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. H. Shapero, J. Zhang, A. Loraine, W. Liu, X. Di, G. Liu, and K. W. Jones
MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays
Nucleic Acids Res., December 15, 2004; 32(22): e181 - e181.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
S. Herrera-Leon, J. R. McQuiston, M. A. Usera, P. I. Fields, J. Garaizar, and M. A. Echeita
Multiplex PCR for Distinguishing the Most Common Phase-1 Flagellar Antigens of Salmonella spp.
J. Clin. Microbiol., June 1, 2004; 42(6): 2581 - 2586.
[Abstract] [Full Text] [PDF]

Home page
 Am J Trop Med HygHome page
J. L. SMITH and D. M. FONSECA
RAPID ASSAYS FOR IDENTIFICATION OF MEMBERS OF THE CULEX (CULEX) PIPIENS COMPLEX, THEIR HYBRIDS, AND OTHER SIBLING SPECIES (DIPTERA: CULICIDAE)
Am J Trop Med Hyg, April 1, 2004; 70(4): 339 - 345.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Rudi, I. Rud, and A. Holck
A novel multiplex quantitative DNA array based PCR (MQDA-PCR) for quantification of transgenic maize in food and feed
Nucleic Acids Res., June 1, 2003; 31(11): e62 - e62.
[Abstract] [Full Text] [PDF]

Home page
 Protein Eng Des SelHome page
C. Miyazaki-Imamura, K. Oohira, R. Kitagawa, H. Nakano, T. Yamane, and H. Takahashi
Improvement of H2O2 stability of manganese peroxidase by combinatorial mutagenesis and high-throughput screening using in vitro expression with protein disulfide isomerase
Protein Eng. Des. Sel., June 1, 2003; 16(6): 423 - 428.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Chem.Home page
C. Bengra, T. E. Mifflin, Y. Khripin, P. Manunta, S. M. Williams, P. A. Jose, and R. A. Felder
Genotyping of Essential Hypertension Single-Nucleotide Polymorphisms by a Homogeneous PCR Method with Universal Energy Transfer Primers
Clin. Chem., December 1, 2002; 48(12): 2131 - 2140.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
N. E. Broude, L. Zhang, K. Woodward, D. Englert, and C. R. Cantor
Multiplex allele-specific target amplification based on PCR suppression
PNAS, January 2, 2001; 98(1): 206 - 211.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Microbiol. Rev.Home page
E. M. Elnifro, A. M. Ashshi, R. J. Cooper, and P. E. Klapper
Multiplex PCR: Optimization and Application in Diagnostic Virology
Clin. Microbiol. Rev., October 1, 2000; 13(4): 559 - 570.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
J. Yang, K. Kobayashi, Y. Iwasaki, H. Nakano, and T. Yamane
In Vitro Analysis of Roles of a Disulfide Bridge and a Calcium Binding Site in Activation of Pseudomonas sp. Strain KWI-56 Lipase
J. Bacteriol., January 15, 2000; 182(2): 295 - 302.
[Abstract] [Full Text]

Home page
 J. Histochem. Cytochem.Home page
G.J. Nuovo, R.J. Hohman, G.A. Nardone, and I.A. Nazarenko
In Situ Amplification Using Universal Energy Transfer-labeled Primers
J. Histochem. Cytochem., March 1, 1999; 47(3): 273 - 280.
[Abstract] [Full Text]

Home page
 Clin. Chem.Home page
D. Whitcombe, J. Brownie, H. L. Gillard, D. McKechnie, J. Theaker, C. R. Newton, and S. Little
A homogeneous fluorescence assay for PCR amplicons: its application to real-time, single-tube genotyping
Clin. Chem., May 1, 1998; 44(5): 918 - 923.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Chem.Home page
B. J. Del Tito Jr., H. E. Poff III, M. A. Novotny, D. M. Cartledge, R. I. Walker II, C. D. Earl, and A. L. Bailey
Automated fluorescent analysis procedure for enzymatic mutation detection
Clin. Chem., April 1, 1998; 44(4): 731 - 739.
[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.