Evaluation of thin films of agarose on glass for hybridization of DNA to identify plant pathogens with microarray technology

Analytical Biochemistry

Volumn 342, Issue 1, 2005, Pages 93-102

  Koch, C A ^a,b   Li, P C H ^a   Utkhede, R S ^b  

^a SIMON FRASER UNIVERSITY   (Canada)

^b AGRICULTURE AND AGRI FOOD CANADA   (Canada)

Author keywords

Agarose substrate; Microarray

Indexed keywords

BIOCHIPS; DNA; GLASS; MICROARRAYS; OLIGONUCLEOTIDES; PROBES;

AGAROSE; BOTRYTIS CINEREA; DIDYMELLA BRYONIAE; DNA MICRO-ARRAY; HYBRIDIZATION EFFICIENCY; MICROARRAY TECHNOLOGIES; MODIFIED OLIGONUCLEOTIDES; RIGID SUBSTRATES;

POLYMERASE CHAIN REACTION;

AGAROSE; DNA; OLIGONUCLEOTIDE;

ARTICLE; BOTRYTIS CINEREA; CONTROLLED STUDY; CROSS REACTION; DNA EXTRACTION; DNA HYBRIDIZATION; DNA MICROARRAY; EVALUATION; FILM; FUNGAL PLANT DISEASE; IMMOBILIZATION; MEDICAL TECHNOLOGY; NONHUMAN; PATHOGENESIS; PLANT DISEASE; PLANT TISSUE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN MODIFICATION; SILYLATION;

BOTRYOTINIA FUCKELIANA; DIDYMELLA BRYONIAE;

EID: 20444390115     PISSN: 00032697     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ab.2005.04.010     Document Type: Article

References (23)

1. D. Volokhov, A. Rasooly, K. Chumakov, and V. Chiznikov Identification of Listeria species by microarray-based assay J. Clin. Microbiol. 40 2002 4720 4728
2. D.R. Call, M. Borucki, and F.J. Loge Detection of bacterial pathogens in environmental samples using DNA microarrays J. Microbiol. Methods 53 2003 235 243
3. S.F. Al-Khaldi, S. Martin, A. Rasooly, and J. Evans DNA microarray technology used for studying foodborne pathogens and microbial habitats:minireview J. AOAC Int. 85 2002 906 910
4. B. Lievens, M. Brouwer, A.C.R.C. Vanachter, C.A. Levesque, B.P.A. Cammue, and B.P.H.J. Thomma Design and development of a DNA array for rapid detection and identification of multiple tomato vascular wilt pathogens FEMS Microbiol. Lett. 223 2003 113 122
5. G. Yershov, V. Barsky, A. Belgovskiy, E. Kirillov, E. Kreindlin, I. Ivanov, S. Parinov, D. Guschin, A. Drobishev, S. Dubiley, and A. Mirzabekov DNA analysis and diagnostics on oligonucleotide microchips Proc. Natl. Acad. Sci. USA 93 1996 4913 4918
6. D. Guschin, G. Yershov, A. Zaslavsky, A. Gemmell, V. Shick, D. Proudnikov, P. Arenkov, and Mirzabekov Manual manufacturing of oligonucleotide, DNA, and protein microchips Anal. Biochem. 250 1997 203 211
7. A.W. Peterson, R.J. Heaton, and R.M. Georgiadis The effect of surface probe density on DNA hybridization Nucleic Acids Res. 29 2001 5163 5168
8. K. Lindroos, U. Liljedahl, M. Raitio, and A. Syvänen Minisequencing on oligonucleotide microarrays: comparison of immobilisation chemistries Nucleic Acids Res. 29 2001 e69
9. V. Afanassiev, V. Hanemann, and S. Wolfi Preparation of DNA and protein microarrays on glass slides coated with an agarose film Nucleic Acids Res. 28 2000 e66
10. M. Dufva, S. Petronis, L.B. Jensen, C. Krag, and C.B.V. Christensen Characterization of an inexpensive, nontoxic, and highly sensitive microarray substrate Biotechniques 37 2004 286 296
11. H. Wang, J. Li, H. Liu, Q. Liu, Q. Mei, Y. Wang, J. Zhu, N. He, and Z. Lu Label-free hybridization detection of a single nucleotide mismatch by immobilization of molecular beacons on an agarose film Nucleic Acids Res. 30 12 2002 e61
12. N.W. Schaad, R.D. Frederick, J. Shaw, W.L. Schneider, R. Hickson, M.D. Petrillo, and D.G. Luster Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues Annu. Rev. Phytopathol. 41 2003 305 324
13. R.R. Martin, D. James, and C.A. Levesque Impacts of molecular diagnostic technologies on plant disease management Annu. Rev. Phytopathol. 38 2000 207 239
14. N.W. Schaad, and R.D. Frederick Real-time PCR and its application for rapid plant disease diagnostics Can. J. Plant Pathol. 24 2002 250 258
15. C.A. Koch, and R.S. Utkhede Diagnosis and identification of Didymella bryoniae, causal agent of gummy stem blight of greenhouse cucumbers, using a dot blot technique J. Horticult. Sci. Biotechnol. 77 2002 62 66
16. S. Mathur, and R. Utkhede Development of a dot blot technique for rapid identification of Botrytis cinerea, the causal organism of grey mould in greenhouse tomatoes J. Horticult. Sci. Biotechnol. 77 2002 604 608
17. T.J. White, T. Bruns, S. Lee, and J. Taylor Amplification and direct sequencing of fungal, ribosomal RNA genes for phylogenetics M.A. Innis D.H. Gelfand J.J. Sninsky T.J. White PCR protocols: A guide to methods and applications 1990 Academic Press San Diego, CA 315 322
18. M. Gardes, and T.D. Bruns ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts Mol. Ecol. 2 1993 113 118
19. G. Bakkeren, J.W. Kronstad, and C.A. Levesque Comparison of AFLP fingerprints and ITS sequences as phylogenetic markers in Ustilaginomycetes Mycologia 92 2000 510 521
20. N. Zammatteo, L. Jeanmart, S. Hamels, S. Courtois, P. Louette, L. Hevesi, and J. Remacle Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays Anal. Biochem. 280 2000 143 150
21. D.R. Call, D.P. Chandler, and F. Brockman Fabrication of DNA microarrays using unmodified oligonucleotide probes Biotechniques 30 2001 368 379
22. V.E. Barsky, A.M. Kolchinsky, Y.P. Lysov, and A.D. Mirzabekov Biological microchips with hydrogel-immobilized nucleic acids, proteins, and other compounds: properties and applications in genomics Mol. Biol. 36 2002 437 455
23. V. Chizhikov, A. Rasooly, K. Chumakov, and D. Levy Microarray analysis of microbial virulence factors Appl. Environ. Microbiol. 67 2001 3258 3263