Tentacle probes: Eliminating false positives without sacrificing sensitivity

Nucleic Acids Research

Volumn 35, Issue 10, 2007, Pages

  Satterfield, Brent C ^a,b   West, Jay A A ^b   Caplan, Michael R ^a  

^a Arizona State University   (United States)

^b Arcxis Biotechnologies   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FLUORESCENT DYE;

ACCURACY; ANALYSIS OF VARIANCE; ARTICLE; BINDING AFFINITY; BINDING KINETICS; CONTROLLED STUDY; DNA PROBE; MATHEMATICAL ANALYSIS; MICROFLUIDIC ANALYSIS; MOLECULAR BEACON; MOLECULAR INTERACTION; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; STRUCTURE ANALYSIS; CHEMISTRY; DIAGNOSTIC PROCEDURE; EVALUATION; GENETIC PROCEDURES; KINETICS; LABORATORY DIAGNOSIS; OLIGONUCLEOTIDE PROBE; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; THERMODYNAMICS;

BIOSENSING TECHNIQUES; FALSE POSITIVE REACTIONS; FLUORESCENT DYES; KINETICS; MOLECULAR DIAGNOSTIC TECHNIQUES; OLIGONUCLEOTIDE PROBES; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; THERMODYNAMICS;

EID: 34250875678     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm113     Document Type: Article

References (35)

1. Khodarev,N.N., Park,J., Kataoka,Y., Nodzenski,E., Hellman,S., Roizman,B., Weichselbaum,R.R. and Pelizzari,C.A. (2003) Receiver operating characteristic analysis: A general tool for DNA array data filtration and performance estimation. Genomics, 81, 202-209.
2. Drake,T.J. and Tan,W. (2004) Molecular beacon DNA probes and their bioanalytical applications. Appl. Spectrosc., 58, 269A-280A.
3. Marras,S.A., Tyagi,S. and Kramer,F.R. (2006) Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. Clin. Chim. Acta, 363, 48-60.
4. Marras,S.A., Kramer,F.R. and Tyagi,S. (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated uenching in oligonucleotide probes. Nucleic Acids Res., 30, e122.
5. Yao,Y., Nellaker,C. and Karlsson,H. (2006) Evaluation of minor groove binding probe and Taqman probe PCR assays: Influence of mismatches and template complexity on quantification. Mol. Cell. Probes., 20, 311-316.
6. Iqbal,S.S., Mayo,M.W., Bruno,J.G., Bronk,B.V., Batt,C.A. and Chambers,J.P. (2000) A review of molecular recognition technologies for detection of biological threat agents. Biosens. Bioelectron., 15, 549-578.
7. Call,D.R. (2005) Challenges and opportunities for pathogen detection using DNA microarrays. Crit. Rev. Microbiol., 31, 91-99.
8. Bhanot,G., Louzoun,Y., Zhu,J. and DeLisi,C. (2003) The importance of thermodynamic equilibrium for high throughput gene expression arrays. Biophys. J., 84, 124-135.
9. Peplies,J., Glockner,F.O. and Amann,R. (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl. Environ. Microbiol., 69, 1397-1407.
10. Borst,A., Box,A.T. and Fluit,A.C. (2004) False-positive results and contamination in nucleic acid amplification assays: Suggestions for a prevent and destroy strategy. Eur. J. Clin. Microbiol. Infect. Dis. 23, 289-299.
11. Draghici,S., Chen,D. and Reifman,J. (2004) Applications and challenges of DNA microarray technology in military medical research. Mil. Med. 169, 654-659.
12. Mammen,M., Choi,S. and Whitesides,G.M. (1998) Polyvalent interactions in biological systems: Implications for design and use of multivalent ligands and inhibitors. Angew. Chem. Int. Ed., 37, 2754-2794.
13. Kiessling,L.L., Gestwicki,J.E. and Strong,L.E. (2000) Synthetic multivalent ligands in the exploration of cell-surface interactions. Curr. Opin. Chem. Biol., 4, 696-703.
14. Holland,P.M., Abramson,R.D., Watson,R. and Gelfand,D.H. (1991) Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. USA, 88, 7276-7280.
15. Handl,H.L., Vagner,J., Han,H., Mash,E., Hruby,V.J. and Gillies,R.J. (2004) Hitting multiple targets with multimeric ligands. Expert Opin. Ther. Targets, 8, 565-586.
16. Caplan,M.R. and Rosca,E.V. (2005) Targeting drugs to combinations of receptors: A modeling analysis of potential specificity. Ann. Biomed. Eng., 33, 1113-1124.
17. Bates,S.R., Baldwin,D.A., Channing,A., Gifford,L.K., Hsu,A. and Lu,P. (2005) Cooperativity of paired oligonucleotide probes for microarray hybridization assays. Anal. Biochem., 342, 59-68.
18. Gentalen,E. and Chee,M. (1999) A novel method for determining linkage between DNA sequences: Hybridization to paired probe arrays. Nucleic Acids Res., 27, 1485-1491.
19. Bonnet,G., Tyagi,S., Libchaber,A. and Kramer,F.R. (1999) Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl. Acad. Sci. USA, 96, 6171-6176.
20. Tsourkas,A., Behlke,M.A., Rose,S.D. and Bao,G. (2003) Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Res. 31, 1319-1330.
21. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
22. Zarrin,F. and Dovichi,N.J. (1985) Sub-picoliter detection with the sheath flow cuvette. Anal. Chem., 57, 2690.
23. Chain,P.S., Carniel,E., Larimer,F.W., Lamerdin,J., Stoutland,P.O., Regala,W.M., Georgescu,A.M., Vergez,L.M., Land,M.L. et al. (2004) Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA, 101, 13826-13831.
24. Crothers,D.M. and Metzger,H. (1972) The influence of polyvalency on the binding properties of antibodies. Immunochemistry, 9, 341-357.
25. Kaufman,E.N. and Jain,R.K. (1992) Effect of bivalent interaction upon apparent antibody affinity: Experimental confirmation of theory using fluorescence photobleaching and implications for antibody binding assays. Cancer Res., 52, 4157-4167.
26. Dmitriev,D.A., Massino,Y.S., Segal,O.L., Smirnova,M.B., Pavlova,E.V., Gurevich,K.G., Gnedenko,O.V., Ivanov,Y.D., Kolyaskina,G.I. et al. (2002) Analysis of the binding of bispecific monoclonal antibodies with immobilized antigens (human IgG and horseradish peroxidase) using a resonant mirror biosensor. J. Immunol. Methods, 261, 103-118.
27. Dmitriev,D.A., Massino,Y.S. and Segal,O.L. (2003) Kinetic analysis of interactions between bispecific monoclonal antibodies and immobilized antigens using a resonant mirror biosensor. J. Immunol. Methods, 280, 183-202.
28. DeLisi,C. (1976) Antigen Antibody Interactions. Springer, Berlin.
29. Perelson,A.S., Goldstein,B. and Rocklin,S. (1980) Optimal strategies in immunology III. The IgM-IgG switch. J. Math. Biol., 10, 209-256.
30. Kitov,P.I. and Bundle,D.R. (2003) On the nature of the multivalency effect: A thermodynamic model. J. Am. Chem. Soc., 125, 16271-16284.
31. Huskens,J., Mulder,A., Auletta,T., Nijhuis,C.A., Ludden,M.J. and Reinhoudt,D.N. (2004) A model for describing the thermodynamics of multivalent host-guest interactions at interfaces. J. Am. Chem. Soc. 126, 6784-6797.
32. Jencks,W.P. (1981) On the attribution and additivity of binding energies. Proc. Natl. Acad. Sci. USA, 78, 4046-4050.
33. Christensen,T., Gooden,D.M., Kung,J.E. and Toone,E.J. (2003) Additivity and the physical basis of multivalency effects: A thermodynamic investigation of the calcium EDTA interaction. J. Am. Chem. Soc., 125, 7357-7366.
34. Chase,C.J., Ulrich,M.P., Wasieloski,L.P.Jr, Kondig,J.P., Garrison,J., Lindler,L.E. and Kulesh,D.A. (2005) Real-time PCR assays targeting a unique chromosomal sequence of Yersinia pestis. Clin. Chem., 51 1778-1785.
35. Hurtle,W., Bode,E., Kulesh,D.A., Kaplan,R.S., Garrison,J., Bridge,D., House,M., Frye,M.S., Loveless,B. et al. (2004) Detection of the Bacillus anthracis gyrA gene by using a minor groove binder probe. J. Clin. Microbiol., 42, 179-185.