Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes

Applied and Environmental Microbiology

Volumn 69, Issue 3, 2003, Pages 1397-1407

  Peplies, Jörg ^a   Glöckner, Frank Oliver ^a   Amann, Rudolf ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FLUORESCENCE; MOLECULES; RNA;

HYBRIDIZATION;

BACTERIA;

RNA 16S;

BACTERIAL DISEASE; DETECTION METHOD; DNA; PROBE;

ACCURACY; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM DETECTION; BINDING SITE; CONTROLLED STUDY; DATA ANALYSIS; DNA MICROARRAY; EVALUATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE TARGETING; HYBRIDIZATION; MODEL; NONHUMAN; OLIGONUCLEOTIDE PROBE; RELIABILITY; STEREOSPECIFICITY;

BACTERIA; DNA, RIBOSOMAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEAWATER; SENSITIVITY AND SPECIFICITY;

BACTERIA (MICROORGANISMS);

EID: 0037335692     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.3.1397-1407.2003     Document Type: Article

References (50)

1. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.
2. Amann, R. I. 1995. Fluorescently labelled, rRNA-targeted oligonucleotide probes in the study of microbial ecology. Mol. Ecol. 4:543-554.
3. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
4. Amann, R. I., and K.-H. Schleifer. 2001. Nucleic acid probes and their application in environmental microbiology, p. 67-82. In G. Garrity, D. R. Boone, and R. W. Castenholz (ed.), Bergey's manual of systematic bacteriology, 2nd ed., vol. 1. Springer-Verlag, New York, N.Y.
5. Bains, W., and G. C. Smith. 1988. A novel method for nucleic acid sequence determination. J. Theor. Biol. 135:303-308.
6. Beier, M., and D. Hoheisel Jörg. 1999. Versatile derivatisation of solid support media for covalent bonding on DNA-microchips. Nucleic Acids Res. 27:1970-1977.
7. Benters, R., C. M. Niemeyer, D. Drutschmann, D. Blohm, and D. Wöhrle. 2002. DNA microarrays with PAMAM dendritic linker systems. Nucleic Acids Res. 30:e10.
8. Blake, R. D., and S. G. Delcourt. 1996. Thermodynamic effects of formamide on DNA stability. Nucleic Acids Res. 24:2095-2103.
9. Breslauer, K. J., R. Frank, H. Blocker, and L. A. Marky. 1986. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83:3746-3750.
10. Brosius, J., T. J. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
11. Buchholz-Cleven, B., B. Rattunde, and K. Straub. 1997. Screening for genetic diversity of isolates of anaerobic Fe(II)-oxidizing bacteria with DGGE and whole-cell hybridization. Syst. Appl. Microbiol. 20:301-309.
12. Debouck, C., and P. N. Goodfellow. 1999. DNA microarrays in drug discovery and development. Nat. Genet. 21:48-50.
13. DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:5685-5689.
14. Drmanac, R., I. Labat, I. Brukner, and R. Crkvenjakov. 1989. Sequencing of megabase plus DNA by hybridization theory of the method. Genomics 4:114-128.
15. Eilers, H., J. Pernthaler, F. O. Glöckner, and R. Amann. 2000. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66:3044-3051.
16. Eilers, H., J. Pernthaler, J. Peplies, F. O. Glöckner, G. Gerdts, and R. Amann. 2001. Isolation of novel pelagic bacteria from the German bight and their seasonal contributions to surface picoplankton. Appl. Environ. Microbiol. 67:5134-5142.
17. Fuchs, B. M., G. Wallner, W. Beisker, I. Schwippl, W. Ludwig, and R. Amann. 1998. Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 64:4973-4982.
18. Fuchs, B. M., F. O. Glöckner, J. Wulf, and R. Amann. 2000. Unlabeled helper oligonucleotides increase the in situ accessibility of 16S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 66:3603-3607.
19. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.
20. Giuliano, L., M. De Domenico, E. De Domenico, M. G. Höffe, and M. M. Yakimov. 1999. Identification of culturable oligotrophic bacteria within naturally occurring bacterioplankton communities of the Ligurian Sea by 16S rRNA sequencing and probing. Microb. Ecol. 37:77-85.
21. Gonzalez, J. M., W. B. Whitman, R. E. Hodson, and M. A. Moran. 1996. Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture. Appl. Environ. Microbiol. 62:4433-4440.
22. Guo, Z., R. A. Guilfoyle, A. J. Thiel, R. Wang, and L. M. Smith. 1994. Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res. 22:5456-5465.
23. Gupta, P. K., J. K. Roy, and M. Prasad. 1999. DNA chips, microarrays and genomics. Curr. Sci. 77:875-884.
24. Guschin, D. Y., B. K. Mobarry, D. Proudnikov, D. A. Stahl, B. E. Rittmann, and A. D. Mirzabekov. 1997. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl. Environ. Microbiol. 63:2397-2402.
25. Hacia, J. G., L. C. Brody, M. S. Chee, S. P. A. Fodor, and F. S. Collins. 1996. Detection of heterozygous mutations in BRCA1 with high density oligonucleotide arrays and two-colour fluorescence analysis. Nat. Genet. 14:441-447.
26. Hoheisel, J. D. 1997. Oligomer-chip technology. Trends Biotechnol. 15:465-469.
27. Liu, W.-T., A. D. Mirzabekov, and D. A. Stahl. 2001. Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ. Microbiol. 3:619-629.
28. Lockhart, D. J., H. Dong, M. C. Byrne, M. T. Follettie, M. V. Gallo, M. S. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton, and E. L. Brown. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14:1675-1680.
29. Lysov, Y. P., V. L. Florentev, A. A. Khorlin, K. R. Khrapko, V. V. Shik, and A. D. Mirzabekov. 1988. Determining the nucleotide sequence of DNA by hybridization with oligonucleotides a new method. Dokl. Akad. Nauk. SSSR 303:1508-1511. (In Russian.)
30. Manz, W., R. Amann, W. Ludwig, M. Vancanneyt, and K.-H. Schleifer. 1996. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum Cytophaga-Flavobacter-Bacteroides in the natural environment. Microbiology 142:1097-1106.
31. Maskos, U., and E. M. Southern. 1992. Parallel analysis of oligodeoxyribonucleotide-oligonucleotide interactions. I. Analysis of factors influencing oligonucleotide duplex formation. Nucleic Acids Res. 20:1675-1678.
32. Maskos, U., and E. M. Southern. 1993. A study of oligonucleotide reassociation with large arrays of oligonucleotides synthesised on a glass support. Nucleic Acids Res. 21:4663-4669.
33. Mir, K. U., and E. M. Southern. 1999. Determining the influence of structure on hybridization with oligonucleotide arrays. Nat. Biotechnol. 17:788-792.
34. Neef, A. 1997. Ph.D. thesis. Technical University, Munich, Germany.
35. Niemeyer, C. M., W. Bürger, and J. Peplies. 1998. Covalent DNA-streptavidin conjugates as building blocks for novel biometallic nanostructures. Angew. Chem. Int. Ed. 37:2265-2268.
36. Niemeyer, C. M., L. Boldt, B. Ceyhan, and D. Blohm. 1999. Evaluation of single-stranded nucleic acids as carriers in the DNA-directed assembly of macromolecules. J. Biomol. Struct. Dyn. 17:527-538.
37. Pace, N. R., D. A. Stahl, D. J. Lane, and G. J. Olsen. 1986. The use of rRNA sequences to characterize natural microbial populations. Adv. Microb. Ecol. 9:1-55.
38. Pernthaler, J., F. O. Glöckner, W. Schönhuber, and R. Amann. 2001. Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. Methods Microbiol. 30:207-226.
39. Rees, W. A., T. D. Yager, J. Korte, and P. H. von Hippel. 1993. Betaine can eliminate the base pair composition dependence of DNA melting. Biochemistry 32:137-144.
40. Riccelli, P. V., F. Merante, K. T. Leung, S. Bortolin, R. L. Zastawny, R. Janeczko, and A. S. Benight. 2001. Hybridization of single-stranded DNA targets to immobilized complementary DNA probes: comparison of hairpin versus linear capture probes. Nucleic Acids Res. 29:996-1004.
41. Rudi, K., O. M. Skulberg, R. Skulberg, and K. S. Jakobsen. 2000. Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization. Appl. Environ. Microbiol. 66:4004-4011.
42. Shchepinov, M. S., S. C. Case-Green, and E. M. Southern. 1997. Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 25:1155-1161.
43. Small, J., D. R. Call, F. J. Brockman, T. M. Straub, and D. P. Chandler. 2001. Direct detection of 16S rRNA in soil extracts by with oligonucleotide microarrays. Appl. Environ. Microbiol. 67:4708-4716.
44. Southern, E., K. Mir, and M. Shchepinov. 1999. Molecular interactions on microarrays. Nat. Genet. 21:5-9.
45. Southern, E. M., U. Maskos, and J. K. Elder. 1992. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides evaluation with experimental model. Genomics 13:1008-1017.
46. Stahl, D. A., and R. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons Ltd., Chichester, United Kingdom.
47. Wahl, G. M., S. L. Berger, and A. R. Kimmel. 1987. Molecular hybridization of immobilized nucleic acids: theoretical concepts and practical considerations. Methods Enzymol. 152:399-407.
48. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63-65.
49. Williams, J. C., S. C. Case-Green, K. U. Mir, and E. M. Southern. 1994. Studies of oligonucleotide interactions by hybridisation to arrays: the influence of dangling ends on duplex yield. Nucleic Acids Res. 22:1365-1367.
50. Zubkov, M. V., B. M. Fuchs, S. D. Archer, R. P. Kiene, R. Amann, and P. H. Burkill. 2001. Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphoniopropionate in an algal bloom in the North Sea. Environ. Microbiol. 3:304-311.