Tentacle Probes™: Differentiation of Difficult Single-Nucleotide Polymorphisms and Deletions by Presence or Absence of a Signal in Real-Time PCR
Abstract
Abstract Background: False-positive results are a common problem in real-time PCR identification of DNA sequences that differ from near neighbors by a single-nucleotide polymorphism (SNP) or deletion. Because of a lack of sufficient probe specificity, post-PCR analysis, such as a melting curve, is often required for mutation differentiation. Methods: Tentacle Probes™, cooperative reagents with both a capture and a detection probe based on specific cell-targeting principles, were developed as a replacement for 2 chromosomal TaqMan–minor groove binder (MGB) assays previously developed for Yersinia pestis and Bacillus anthracis detection. We compared TaqMan-MGB probes to Tentacle Probes for SNP and deletion detection based on the presence or absence of a growth curve. Results: With the TaqMan-MGB Y. pestis yp48 assays, false-positive results for Yersinia pseudotuberculosis occurred at every concentration tested, and with the TaqMan-MGB B. anthracis gyrA assays, false-positive results occurred in 21 of 29 boil preps of environmental samples of near neighbors. With Tentacle Probes no false-positive results occurred. Conclusions: The high specificity exhibited by Tentacle Probes may eliminate melting curve analysis for SNP and deletion mutation detection, allowing the diagnostic use of previously difficult targets.
- Authors:
-
- Harrington Department of Bioengineering, Arizona State University, Tempe, AZ, Arcxis Biotechnologies, Pleasanton, CA
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD
- Harrington Department of Bioengineering, Arizona State University, Tempe, AZ
- Arcxis Biotechnologies, Pleasanton, CA
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1581655
- Grant/Contract Number:
- AC05-00OR22750
- Resource Type:
- Published Article
- Journal Name:
- Clinical Chemistry
- Additional Journal Information:
- Journal Name: Clinical Chemistry Journal Volume: 53 Journal Issue: 12; Journal ID: ISSN 0009-9147
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Satterfield, Brent C., Kulesh, David A., Norwood, David A., Wasieloski, Jr, Leonard P., Caplan, Michael R., and West, Jay AA. Tentacle Probes™: Differentiation of Difficult Single-Nucleotide Polymorphisms and Deletions by Presence or Absence of a Signal in Real-Time PCR. United States: N. p., 2007.
Web. doi:10.1373/clinchem.2007.091488.
Satterfield, Brent C., Kulesh, David A., Norwood, David A., Wasieloski, Jr, Leonard P., Caplan, Michael R., & West, Jay AA. Tentacle Probes™: Differentiation of Difficult Single-Nucleotide Polymorphisms and Deletions by Presence or Absence of a Signal in Real-Time PCR. United States. https://doi.org/10.1373/clinchem.2007.091488
Satterfield, Brent C., Kulesh, David A., Norwood, David A., Wasieloski, Jr, Leonard P., Caplan, Michael R., and West, Jay AA. Sat .
"Tentacle Probes™: Differentiation of Difficult Single-Nucleotide Polymorphisms and Deletions by Presence or Absence of a Signal in Real-Time PCR". United States. https://doi.org/10.1373/clinchem.2007.091488.
@article{osti_1581655,
title = {Tentacle Probes™: Differentiation of Difficult Single-Nucleotide Polymorphisms and Deletions by Presence or Absence of a Signal in Real-Time PCR},
author = {Satterfield, Brent C. and Kulesh, David A. and Norwood, David A. and Wasieloski, Jr, Leonard P. and Caplan, Michael R. and West, Jay AA},
abstractNote = {Abstract Background: False-positive results are a common problem in real-time PCR identification of DNA sequences that differ from near neighbors by a single-nucleotide polymorphism (SNP) or deletion. Because of a lack of sufficient probe specificity, post-PCR analysis, such as a melting curve, is often required for mutation differentiation. Methods: Tentacle Probes™, cooperative reagents with both a capture and a detection probe based on specific cell-targeting principles, were developed as a replacement for 2 chromosomal TaqMan–minor groove binder (MGB) assays previously developed for Yersinia pestis and Bacillus anthracis detection. We compared TaqMan-MGB probes to Tentacle Probes for SNP and deletion detection based on the presence or absence of a growth curve. Results: With the TaqMan-MGB Y. pestis yp48 assays, false-positive results for Yersinia pseudotuberculosis occurred at every concentration tested, and with the TaqMan-MGB B. anthracis gyrA assays, false-positive results occurred in 21 of 29 boil preps of environmental samples of near neighbors. With Tentacle Probes no false-positive results occurred. Conclusions: The high specificity exhibited by Tentacle Probes may eliminate melting curve analysis for SNP and deletion mutation detection, allowing the diagnostic use of previously difficult targets.},
doi = {10.1373/clinchem.2007.091488},
journal = {Clinical Chemistry},
number = 12,
volume = 53,
place = {United States},
year = {Sat Dec 01 00:00:00 EST 2007},
month = {Sat Dec 01 00:00:00 EST 2007}
}
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Works referenced in this record:
Automated polymerase chain reaction in capillary tubes with hot air
journal, January 1989
- Wittwer, C. T.; Fillmore, G. C.; Hillyard, D. R.
- Nucleic Acids Research, Vol. 17, Issue 11
Mode of action and application of Scorpion primers to mutation detection
journal, October 2000
- Thelwell, N.
- Nucleic Acids Research, Vol. 28, Issue 19
Detection of Bacillus anthracis DNA by LightCycler PCR
journal, August 2002
- Bell, C. A.; Uhl, J. R.; Hadfield, T. L.
- Journal of Clinical Microbiology, Vol. 40, Issue 8
Diagnosis of plague and identification of virulence markers in Yersinia pestis by multiplex-PCR
journal, November 1999
- Leal, Nilma C.; Almeida, Alzira M. P. de
- Revista do Instituto de Medicina Tropical de São Paulo, Vol. 41, Issue 6
Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis
journal, September 2004
- Chain, P. S. G.; Carniel, E.; Larimer, F. W.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 38
A nested PCR method for the detection of Bacillus anthracis in environmental samples collected from former tannery sites
journal, May 1995
- Beyer, Wolfgang; Glöckner, Petra; Otto, Julia
- Microbiological Research, Vol. 150, Issue 2
Conjugative plasmid pAW63 brings new insights into the genesis of the Bacillus anthracis virulence plasmid pXO2 and of the Bacillus thuringiensis plasmid pBT9727
journal, July 2005
- Van der Auwera, Géraldine A.; Andrup, Lars; Mahillon, Jacques
- BMC Genomics, Vol. 6, Issue 1
Characterization of Bacillus anthracis-Like Bacteria Isolated from Wild Great Apes from Cote d'Ivoire and Cameroon
journal, July 2006
- Klee, S. R.; Ozel, M.; Appel, B.
- Journal of Bacteriology, Vol. 188, Issue 15
3'-Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures
journal, January 2000
- Kutyavin, I. V.
- Nucleic Acids Research, Vol. 28, Issue 2
Detection of PCR products using self-probing amplicons and fluorescence
journal, August 1999
- Whitcombe, David; Theaker, Jane; Guy, Simon P.
- Nature Biotechnology, Vol. 17, Issue 8, p. 804-807
Design and Optimization of Molecular Beacon Real-Time Polymerase Chain Reaction Assays
book, January 2005
- Vet, Jacqueline A. M.; Marras, Salvatore A. E.
- Oligonucleotide Synthesis
Nucleotide sequence comparison of homologous genomic regions from variola, monkeypox, and vaccinia viruses
journal, August 1990
- Cowley, R.; Greenaway, P. J.
- Journal of Medical Virology, Vol. 31, Issue 4
Detection of specific polymerase chain reaction product by utilizing the 5'----3' exonuclease activity of Thermus aquaticus DNA polymerase.
journal, August 1991
- Holland, P. M.; Abramson, R. D.; Watson, R.
- Proceedings of the National Academy of Sciences, Vol. 88, Issue 16, p. 7276-7280
Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes
journal, January 2006
- Marras, Salvatore A. E.; Tyagi, Sanjay; Kramer, Fred Russell
- Clinica Chimica Acta, Vol. 363, Issue 1-2
Minimizing the time required for DNA amplification by efficient heat transfer to small samples
journal, May 1990
- Wittwer, Carl T.; Fillmore, G. Chris; Garling, David J.
- Analytical Biochemistry, Vol. 186, Issue 2
Identification of capsule-forming Bacillus anthracis spores with the PCR and a novel dual-probe hybridization format.
journal, January 1994
- Reif, T. C.; Johns, M.; Pillai, S. D.
- Applied and Environmental Microbiology, Vol. 60, Issue 5
Multiplex detection of single-nucleotide variations using molecular beacons
journal, February 1999
- Marras, Salvatore A. E.; Russell Kramer, Fred; Tyagi, Sanjay
- Genetic Analysis: Biomolecular Engineering, Vol. 14, Issue 5-6
Targeting Drugs to Combinations of Receptors: A Modeling Analysis of Potential Specificity
journal, August 2005
- Caplan, Michael R.; Rosca, Elena V.
- Annals of Biomedical Engineering, Vol. 33, Issue 8
Rapid genotyping of single nucleotide polymorphisms using novel minor groove binding DNA oligonucleotides (MGB probes)
journal, April 2002
- de Kok, Jacques B.; Wiegerinck, Erwin T. G.; Giesendorf, Belinda A. J.
- Human Mutation, Vol. 19, Issue 5
Evaluation of minor groove binding probe and Taqman probe PCR assays: Influence of mismatches and template complexity on quantification
journal, October 2006
- Yao, Yuanrong; Nellåker, Christoffer; Karlsson, Håkan
- Molecular and Cellular Probes, Vol. 20, Issue 5
Tentacle probes: eliminating false positives without sacrificing sensitivity
journal, April 2007
- Satterfield, B. C.; West, J. A. A.; Caplan, M. R.
- Nucleic Acids Research, Vol. 35, Issue 10
DNA sequence conservation between the Bacillus anthracis pXO2 plasmid and genomic sequence from closely related bacteria
journal, December 2002
- Pannucci, James; Okinaka, Richard T.; Williams, Erin
- BMC Genomics, Vol. 3, Issue 1
Rapid detection of Yersinia pestis with multiplex real-time PCR assays using fluorescent hybridisation probes
journal, September 2003
- Tomaso, Herbert; Reisinger, Emil C.; Dahouk, Sascha
- FEMS Immunology & Medical Microbiology, Vol. 38, Issue 2
Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS)
journal, January 1989
- Newton, C. R.; Graham, A.; Heptinstall, L. E.
- Nucleic Acids Research, Vol. 17, Issue 7
High-Throughput SNP Allele-Frequency Determination in Pooled DNA Samples by Kinetic PCR
journal, February 2000
- Germer, S.
- Genome Research, Vol. 10, Issue 2
Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis
journal, November 1999
- Achtman, M.; Zurth, K.; Morelli, G.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 24
Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax
journal, May 2004
- Hoffmaster, A. R.; Ravel, J.; Rasko, D. A.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 22, p. 8449-8454
Bacillus anthracis pXO1 Plasmid Sequence Conservation among Closely Related Bacterial Species
journal, January 2002
- Pannucci, J.; Okinaka, R. T.; Sabin, R.
- Journal of Bacteriology, Vol. 184, Issue 1
Molecular Beacons: Probes that Fluoresce upon Hybridization
journal, March 1996
- Tyagi, Sanjay; Kramer, Fred Russell
- Nature Biotechnology, Vol. 14, Issue 3, p. 303-308
The 102-Kilobase pgm Locus of Yersinia pestis: Sequence Analysis and Comparison of Selected Regions among Different Yersinia pestis and Yersinia pseudotuberculosis Strains
journal, January 1999
- Buchrieser, Carmen; Rusniok, Christophe; Frangeul, Lionel
- Infection and Immunity, Vol. 67, Issue 9
Polyvalent Interactions in Biological Systems: Implications for Design and Use of Multivalent Ligands and Inhibitors
journal, November 1998
- Mammen, Mathai; Choi, Seok-Ki; Whitesides, George M.
- Angewandte Chemie International Edition, Vol. 37, Issue 20, p. 2754-2794
Retrospective study of a plague outbreak by multiplex-PCR
journal, November 2003
- Melo, A. C.; Almeida, A. M. P.; Leal, N. C.
- Letters in Applied Microbiology, Vol. 37, Issue 5
Real-Time PCR Assays Targeting a Unique Chromosomal Sequence of Yersinia pestis
journal, October 2005
- Chase, Catherine J.; Ulrich, Melanie P.; Wasieloski, Leonard P.
- Clinical Chemistry, Vol. 51, Issue 10
Sequence versus Structure for the Direct Detection of 16S rRNA on Planar Oligonucleotide Microarrays
journal, May 2003
- Chandler, D. P.; Newton, G. J.; Small, J. A.
- Applied and Environmental Microbiology, Vol. 69, Issue 5