Comparison of different labeling methods for the production of labeled target DNA for microarray hybridization

Journal of Microbiological Methods

Volumn 65, Issue 1, 2006, Pages 117-126

  Franke Whittle, Ingrid H ^a,b   Klammer, Susanne H ^a   Mayrhofer, Sabine ^a   Insam, Heribert ^a,b  

^a UNIVERSITY OF INNSBRUCK   (Austria)

^b Austrian Research Studios   (Austria)

Author keywords

Hybridization; Labeling methods; Microarray

Indexed keywords

DEOXYCYTIDINE TRIPHOSPHATE; DOUBLE STRANDED DNA; PRIMER DNA; RNA 16S; SINGLE STRANDED DNA;

ARTICLE; BURKHOLDERIA CEPACIA; CHEMICAL LABELING; COMPOST; CONTROLLED STUDY; DNA MICROARRAY; FLUORESCENCE; GENE TARGETING; HYBRIDIZATION; INTERMETHOD COMPARISON; MICROORGANISM DETECTION; NONHUMAN; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SIGNAL NOISE RATIO; STAPHYLOCOCCUS AUREUS;

BURKHOLDERIA CEPACIA; CARBOCYANINES; DNA POLYMERASE I; DNA, BACTERIAL; FLUORESCENT DYES; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; STAINING AND LABELING; STAPHYLOCOCCUS AUREUS;

BURKHOLDERIA; BURKHOLDERIA CEPACIA; STAPHYLOCOCCUS AUREUS;

EID: 33644943439     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2005.06.011     Document Type: Article

References (35)

1. E.W. Alm, D.B. Oerther, N. Larsen, D.A. Stahl, and L. Raskin The oligonucleotide probe database Appl. Environ. Microbiol. 62 1996 3557 3559
2. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1991 403 410
3. R. Amann, B.J. Binder, R.J. Olson, S.W. Chisholm, R. Devereux, and D.A. Stahl Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations Appl. Environ. Microbiol. 56 1990 1919 1925
4. R.I. Amann, W. Ludwig, and K.H. Schleifer Phylogenetic identification and in situ detection of individual microbial cells without cultivation Microbiol. Rev. 59 1995 143 169
5. E.A. Barlaan, M. Sugimori, S. Furukawa, and K. Takeuchi Electronic microarray analysis of 16S rDNA amplicons for bacterial detection J. Biotechnol. 115 2005 11 21
6. D. Blaškoviè, and I. Barák Oligo-chip based detection of tick-borne bacteria FEMS Microbiol. Lett. 243 2005 473 478
7. L. Bodrossy, and A. Sessitsch Oligonucleotide microarrays in microbial diagnostics Curr. Opin. Microbiol. 7 2004 246 255
8. L. Bodrossy, N. Stralis-Pavese, J.C. Murrell, S. Radajewski, A. Weilharter, and A. Sessitsch Development and validation of a diagnostic microbial microarray for methanotrophs Environ. Microbiol. 5 2003 566 582
9. B.E.E. Buchholz-Cleven, B. Rattunde, and K.L. Straub Screening for genetic diversity of isolates of anaerobic Fe(II)-oxidizing bacteria using DGGE and whole-cell hybridization Syst. Appl. Microbiol. 20 1997 301 309
10. D.R Call, M.K. Borucki, and F.J. Loge Detection of bacterial pathogens in environmental samples using DNA microarrays J. Microbiol. Methods 53 2003 235 243
11. K.L. Cook, and G.S. Sayler Environmental application of array technology: promise, problems and practicalities Curr. Opin. Biotechnol. 14 2003 311 318
12. A. Felske, A.D.L. Akkermans, and W.M. De Vos Quantitation of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis Appl. Environ. Microbiol. 64 1998 4581 4587
13. I.H. Franke-Whittle, S.H. Klammer, and H. Insam Design and application of an oligonucleotide microarray for the investigation of compost microbial communities J. Microbiol. Methods 62 2005 37 56
14. Z. Guo, R.A. Guilfoyle, A.J. Thiel, R. Wang, and L.M. Smith Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports Nucleic Acids Res. 22 1994 5456 5465
15. D.Y. Guschin, B.K. Mobarry, D. Proudnikov, D.A. Stahl, B.E. Rittmann, and A.D. Mirzabekov Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology Appl. Environ. Microbiol. 63 1997 2397 2402
16. M. Hogardt, K. Trebesius, A.M. Geiger, M. Hornef, J. Rosenecker, and J. Heesemann Specific and rapid detection by fluorescent in situ hybridisation of bacteria in clinical samples obtained from cystic fibrosis patients J. Clin. Microbiol. 38 2000 818 825
17. H. Insam Developments in soil microbiology since the mid 1960s Geoderma 100 2001 389 402
18. S. Lane, J. Evermann, F. Loge, and D.R. Call Amplicon secondary structure prevents target hybridization to oligonucleotide microarrays Biosens. Bioelectron. 20 2004 728 735
19. B. Lievens, M. Brouwer, A.C.R.C. Vanachter, C.A. Lévesque, 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
20. W.-T. Liu, A.D. Mirzabekov, and D.A. Stahl Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach Environ. Microbiol. 3 2001 619 629
21. A. Loy, A. Lehner, N. Lee, J. Adamczyk, H. Meier, and J. Ernst Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment Appl. Environ. Microbiol. 68 2002 5064 5081
22. L. Ludwig, O. Strunk, R. Westram, L. Richter, H. Meier, and Yadhukumar ARB: a software environment for sequence data Nucleic Acids Res. 32 2004 1363 1371
23. G.J. Olsen, D.J. Lane, S.J. Giovannoni, and N.R. Pace Microbial ecology and evolution: a ribosomal RNA approach Annu. Rev. Microbiol. 40 1986 337 367
24. J. Peplies, F. Oliver Glockner, and R. Amann Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes Appl. Environ. Microbiol. 69 2003 1397 1407
25. J. Peplies, S. Chun Kwan Lau, J. Pernthaler, R. Amann, and F. Oliver Glockner Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton Environ. Microbiol. 6 2004 638 645
26. M.F. Polz, and C.M. Cavanaugh Bias in template-to-product ratios in multitemplate PCR Appl. Environ. Microbiol. 64 1998 3724 3730
27. J. Small, D.R. Call, F.J. Brockman, T.M. Straub, and D.P. Chandler Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays Appl. Environ. Microbiol. 67 2001 4708 4716
28. A. Spiro, M. Lowe, and D. Brown A bead-based method for multiplexed identification and quantification of DNA sequences using flow cytometry Appl. Environ. Microbiol. 66 2000 4258 4265
29. D.A. Stahl, B. Flesher, H.R. Mansfield, and L. Montgomery Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology Appl. Environ. Microbiol. 54 1988 1079 1084
30. G. Taroncher-Oldenburg, E.M. Griner, C.A. Francis, and B.B. Ward Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment Appl. Environ. Microbiol. 69 2003 1159 1171
31. S.M. Tiquia, L. Wu, S.C. Chong, S. Passovets, D. Xu, and Y. Xu Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples Biotechniques 36 2004 664 675
32. R.-F. Wang, M.L. Beggs, L.H. Robertson, and C.E. Cerniglia Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples FEMS Microbiol. Lett. 213 2002 175 182
33. R.-F. Wang, M.L. Beggs, B.D. Erickson, and C.E. Cerniglia DNA microarray analysis of predominant human intestinal bacteria in fecal samples Mol. Cell. Probes 18 2004 223 234
34. C.R. Woese Bacterial evolution Microbiol. Rev. 51 1987 221 271
35. D. Zheng, E.W. Alm, D.A. Stahl, and L. Raskin Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies Appl. Environ. Microbiol. 62 1996 4504 4513