Flexible microarray construction and fast DNA hybridization conducted on a microfluidic chip for greenhouse plant fungal pathogen detection

Journal of Agricultural and Food Chemistry

Volumn 55, Issue 26, 2007, Pages 10509-10516

  Wang, Lin ^a   Li, Paul C H ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

DNA hybridization; Fungal pathogen; Microfluidic microarray; Single base pair difference discrimination

Indexed keywords

FUNGAL DNA;

ARTICLE; ASCOMYCETES; BOTRYTIS; DNA MICROARRAY; GENETICS; METHODOLOGY; MICROBIOLOGY; NUCLEIC ACID HYBRIDIZATION; PLANT; PLANT DISEASE;

ASCOMYCOTA; BOTRYTIS; DNA, FUNGAL; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT DISEASES; PLANTS;

BOTRYOTINIA FUCKELIANA; BOTRYOTINIA SQUAMOSA; BOTRYTIS; DIDYMELLA BRYONIAE;

EID: 38049033362     PISSN: 00218561     EISSN: None     Source Type: Journal    
DOI: 10.1021/jf0721242     Document Type: Article

References (32)

1. Paulitz, T. C.; Bélanger, R. R. Biological control in greenhouse systems. Annu. Rev. Phytopathol. 2001, 39, 103-133.
2. Jarvis, W. R. Cucumber Diseases; Agriculture Canada Publication: Harrow, Canada, 1992; p 12.
3. De Rinaldis, E., Lahm, A., Eds. DNA Microarrays: Current Applications; Horizon Bioscience: Wymondham, U.K., 2007.
4. Xu, J.; Zhu, S.; Miao, H.; Huang, W.; Qiu, M.; Huang, Y.; Fu, X.; Li, Y. Event-specific detection of seven genetically modified soybean and maizes using multiplex-PCR coupled with oligonucleotide microarray. J. Agric. Food Chem. 2007, 55, 5575-5579.
5. Bordoni, R.; Germini, A.; Mezzelani, A.; Marchelli, R.; De Bellis, G. A microarray platform for parallel detection of five transgenic events in foods; a combined Polymerase Chain Reaction-ligation detection reaction-universal array method. J. Agric. Food Chem. 2005, 53, 912-918.
6. Warsen, A. E.; Krug, M. J.; LaFrentz, S.; Stanek, D. R.; Loge, F. J.; Call, D. R. Simultaneous discrimination between 15 fish pathogens by using 16S ribosomal DNA PCR and DNA microarrays. Appl. Environ. Microbiol. 2004, 70, 4216-4221.
7. Ronning, S. B.; Rudi, K.; Berdal, K. G.; Holst-Jensen, A. Differentiation of important and closely related cereal plant species (Poaceae) in food by hybridization to an oligonucleotide array. J. Agric. Food Chem. 2005, 53, 8874-8880.
8. Campas, M.; Katakis, I. DNA biochip arraying, detection and amplification strategies. Trends Anal. Chem. 2004, 23, 49-62.
9. Bowtell, D., Sambrook, J., Eds. DNA Microarrays: A Molecular Cloning Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 2003.
10. Koch, C. A.; Li, P. C. H.; Utkhede, R. S. Evaluation of thin films of agarose on glass for hybridization of DNA to identify plant pathogens with microarray technology. Anal. Biochem. 2005, 342, 93-102.
11. Hashimoto, M.; Barany, F.; Soper, S. A. Polymerase Chain Reaction/ligase detection reaction/hybridization assays using flow-through microfluidic devices for the detection of low-abundant DNA points mutations. Biosens. Bioelectron. 2006, 21, 1915-1923.
12. Peytavi, R.; Raymond, F. R.; Gagne, D.; Picard, F. J.; Jia, G.; Zoval, J.; Madou, M.; Boissinot, K.; Boissinot, M.; Bissonnette, L.; Ouellette, M.; Bergeron, M. G. Microfluidic device for rapid (<15 min) automated microarray hybridization. Clin. Chem. 2005, 51, 1836-1844.
13. Lenigk, R.; Liu, R. H.; Athavale, M.; Chen, Z. J.; Ganser, D.; Yang, J. N.; Rauch, C.; Liu, Y. J.; Chan, B.; Yu, H. N.; Ray, M.; Marrero, R.; Grodzinski, P. Plastic biochannel hybridization devices: a new concept for microfluidic DNA arrays. Anal. Biochem. 2002, 311, 40-49.
14. Wei, C. W.; Cheng, J. Y.; Huang, C. T.; Yen, M. H.; Young, T. H. Using a microfluidic device for 1 μL DNA microarray hybridization in 500s. Nucleic Acids Res. 2005, 33, e78.
15. Liu, R. H.; Chen, H.; Luehrsen, K. R.; Ganser, D.; Weston, D.; Blackwell, J.; Grodzinski, P. Highly parallel integrated microfluidic biochannel arrays. The 14th IEEE International Conference on Micro Electro Mechanical Systems; IEEE: Piscataway, NJ, 2001; pp 439 442.
16. Lee, H. J.; Goodrich, T. T.; Corn, R. M. SPR imaging measurements of 1-D and 2-D DNA microarrays created from microfluidic channels on gold thin films. Anal. Chem. 2001, 73, 5525-5531.
17. Situma, C.; Wang, Y.; Hupert, M.; Barany, F.; McCarley, R. L.; Soper, S. A. Fabrication of DNA microarrays one poly(methyl-methacrylate) with ultraviolet patterning and microfluidics for the detection of low-abundant point mutations. Anal. Biochem. 2005, 340, 123-135.
18. Benn, J. A.; Hu, J.; Hogan, B. J.; Fry, R. C.; Samson, L. D.; Thorsen, T. Comparative modeling and analysis of microfluidic and conventional DNA microarrays. Anal. Biochem. 2006, 348, 284-293.
19. Holst-Jensen, A.; Kohn, L. M.; Schumacher, T. Nuclear rDNA phylogeny of the Sclerotiniaceae. Mycologia 1997, 89, 885-899.
20. The sequence of B′PF and BN′PF can be found in GenBank at http://www.ncbi.nlm.nih.gov.
21. Wang, H.; Li, L.; Liu, H.; Liu, Q.; Mei, Q.; Wang, Y.; Zhu, J.; He, N.; Lu, Z. Label-free hybridization detection of a single nucleotide mismatch by immobilization of molecular beacons on an agarose film. Nucleic Acids Res. 2002, 30, 1-9.
22. Duffy, D. C.; McDonald, J. C.; Schueller, O. J. A.; Whitesides, G. M. Rapid prototyping of microfluidic systems in poly(dimethylsiloxane). Anal. Chem. 1998, 70, 4974-4984.
23. Zammatteo, N.; Jeanmart, L.; Hamels, S.; Courtois, S.; Louette, P.; Hevesi, L.; Remacle, J. Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays. Anal. Biochem. 2000, 280, 143-150.
24. Le Berre, V.; Trévisiol, E.; Dagkessamanskaia, A.; Sokol, S.; Caminade, A.-M.; Majorai, J. P.; Meunier, B.; François, J. Dendrimeric coating of glass slides for sensitive DNA microarrays analysis. Nucleic Acids Res. 2003, 31, e88.
25. Lukacs, G. L.; Haggie, P.; Seksek, O.; Lechardeur, D.; Freedman, N.; Verkman, A. S. Size-dependent DNA mobility in cytoplasm and nucleus. J. Biol. Chem. 2000, 275, 1625-1629.
26. Keramas, G.; Perozziello, G.; Geschke, O.; Christensen, C. B. V. Development of a multiplex microarray microsystem. Lab Chip 2004, 4, 152-158.
27. Peterson, A. W.; Heaton, R. J.; Gadis, R. M. The effect of surface probe density on DNA hybridization. Nucleic Acids Res. 2001, 29, 5163-6168.
28. Herne, T. M.; Tarlov, M. J. Characterization of DNA probes immobilized on gold surfaces. J. Am. Chem. Soc. 1997, 119, 8916-8920.
29. Lenigk, R.; Liu, R. H.; Athavale, M.; Chen, Z.; Ganser, D.; Yang, J.; Rauch, C.; Liu, Y.; Chan, B.; Yu, H.; Ray, M.; Marrero, R.; Grodzinski, P. Plastic biochannel hybridization devices: a new concept for microfluidic DNA arrays. Anal. Biochem. 2002, 311, 40-49.
30. Hager, J. Making and using spotted DNA microarrays in an academic core laboratory. Methods Enzymol. 2006, 410, 135-168.
31. Wetmur, J. DNA probes: application of the principles of nucleic acid hybridization. Crit. Rev. Biochem. Mol. Biol. 1991, 26, 227-259.
32. Shchepinov, M. S.; Case-Green, S. C.; Southern, E. M. Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 1997, 25, 1155-1161.