Determinants of sensitivity and specificity in spotted DNA microarrays with unmodified oligonucleotides

Genes and Genetic Systems

Volumn 79, Issue 4, 2004, Pages 189-197

  Kucho, Ken Ichi ^a   Yoneda, Hidekatsu ^b,c   Harada, Manabu ^b,c   Ishiura, Masahiro ^a  

^a NAGOYA UNIVERSITY   (Japan)

^b Nippon Laser and Electronics Lab   (Japan)

^c Laser Techno Co Ltd   (Japan)

Author keywords

Cost effective; Cross hybridization; Microarray; Synechocystis; Unmodified oligonucleotide

Indexed keywords

DNA;

ARTICLE; BACTERIAL GENE; CHEMICAL MODIFICATION; COST EFFECTIVENESS ANALYSIS; CYANOBACTERIUM; DNA HYBRIDIZATION; DNA MICROARRAY; DNA PROBE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN PURIFICATION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SPECIES IDENTIFICATION;

BASE SEQUENCE; GENOME, BACTERIAL; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDES; RNA, BACTERIAL; SENSITIVITY AND SPECIFICITY; SYNECHOCYSTIS;

BACTERIA (MICROORGANISMS); CYANOBACTERIA; NEGIBACTERIA; SYNECHOCYSTIS;

EID: 7944220031     PISSN: 13417568     EISSN: None     Source Type: Journal    
DOI: 10.1266/ggs.79.189     Document Type: Article

References (28)

1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Beattie, W. G., Meng, L., Turner, S. L., Varma, R. S., Dao, D. D., and Beattie, K. L. (1995) Hybridization of DNA targets to glass-tethered oligonucleotide probes. Mol. Biotechnol. 4, 213-225.
3. Belosludtsev, Y., Iverson, B., Lemeshko, S., Eggers, R., Wiese, R., Lee, S., Powdrill, T., and Hogan, M. (2001) DNA microarrays based on noncovalent oligonucleotide attachment and hybridization in two dimensions. Anal. Biochem. 292, 250-256.
4. Call, D. R., Chandler, D. P., and Brockman, F. (2001) Fabrication of DNA microarrays using unmodified oligonucleotide probes. Biotechniques 30, 368-372.
5. Debouck, C., and Goodfellow, P. N. (1999) DNA microarrays in drug discovery and development. Nat. Genet. Supplement 21, 48-50.
6. DeRisi, J. L., Iyer, V. R., and Brown, P. O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
7. Duggan, D. J., Bittner, M., Chen, Y., Meltzer, P., and Trent, J. M. (1999) Expression profiling using cDNA microarrays. Nat. Genet. Supplement 21, 10-14.
8. Hihara, Y., Kamei, A., Kanehisa, M., Kaplan, A., and Ikeuchi, M. (2001) DNA microarray analysis of cyanobacterial gene expression during acclimation to high light. Plant Cell 13, 793-806.
9. Hughes, T. R., Mao, M., Jones, A. R., Burchard, J., Marton, M. J., Shannon, K. W., Lefkowitz, S. M., Ziman, M., Schelter, J. M., Meyer, M. R., Kobayashi, S., Davis, C., Dai, H., He, Y. D., Stephaniants, S. B., Cavet, G., Walker, W. L., West, A., Coffey, E., Shoemaker, D. D., Stoughton, R., Blanchard, A. P., Friend, S. H., and Linsley, P. S. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19, 342-347.
10. Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R., Armour, C. D., Bennett, H. A., Coffey, E., Dai, H., He, Y. D., Kidd, M. J., King, A. M., Meyer, M. R., Slade, D., Lum, P. Y., Stepaniants, S. B., Shoemaker, D. D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M., and Friend, S. H. (2000) Functional discovery via a compendium of expression profiles. Cell 102, 109-126.
11. Joos, B., Kuster, H., and Cone, R. (1997) Covalent attachment of hybridizable oligonucleotides to glass supports. Anal. Biochem. 247, 96-101.
12. Kane, M. D., Jatkoe, T. A., Stumpf, C. R., Lu, J., Thomas, J. D., and Madore, S. J. (2000) Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res. 28, 4552-4557.
13. Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M., Sugiura, M., Sasamoto, S., Kimura, T., Hosouchi, T., Matsuno, A., Muraki, A., Nakazaki, N., Naruo, K., Okumura, S., Shimpo, S., Takeuchi, C., Wada, T., Watanabe, A., Yamada, M., Yasuda, M., and Tabata, S. (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3, 109-136.
14. Kim, S. K., Lund, J., Kiraly, M., Duke, K., Jiang, M., Stuart, J. M., Eizinger, A., Wylie, B. N., and Davidson, G. S. (2001) A gene expression map for Caenorhabditis elegans. Science 293, 2087-2092.
15. Laub, M. T., McAdams, H. H., Feldblyum, T., Fraser, C. M., and Shapiro, L. (2000) Global analysis of the genetic network controlling a bacterial cell cycle. Science 290, 2144-2148.
16. Lipshutz, R. J., Fodor, S. P., Gingeras, T. R., and Lockhart, D. J. (1999) High density synthetic oligonucleotide arrays. Nat. Genet. Supplement 21, 20-24.
17. McDonald, M. J., and Rosbash, M. (2001) Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107, 567-578.
18. Podyminogin, M. A., Lukhtanov, E. A., and Reed, M. W. (2001) Attachment of benzaldehyde-modified oligodeoxynucleotide probes to semicarbazide-coated glass. Nucleic Acids Res. 29, 5090-5098.
19. Relogio, A., Schwager, C., Richter, A., Ansorge, W., and Valcarcel, J. (2002) Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res. 30, e51.
20. Rippka, R., Deruelles, J., Waterbury, J. B., Herdman, M., and Stanier, R. Y. (1979) Generic assignments, strain histories, and properties of pure cultures of cyanobacteria. J. Gen. Microbiol. 111, 1-61.
21. Rogers, Y. H., Jiang-Baucom, P., Huang, Z. J., Bogdanov, V., Anderson, S., and Boyce-Jacino, M. T. (1999) Immobilization of oligonucleotides onto a glass support via disulfide bonds: A method for preparation of DNA microarrays. Anal. Biochem. 266, 23-30.
22. Salih, G. F., and Jansson, C. (1997) Activation of the silent psbA1 gene in the cyanobacterium Synechocystis sp. strain 6803 produces a novel and functional D1 protein. Plant Cell 9, 869-878.
23. Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470.
24. Southern, E., Mir, K., and Shchepinov, M. (1999) Molecular interactions on microarrays. Nat. Genet. Supplement 21, 5-9.
25. Wall, L., Christiansen, T., and Orwant, J. (2002) Programming Perl Third Edition. O'Reilly and Associate, CA.
26. Wang, H. Y., Malek, R. L., Kwitek, A. E., Greene, A. S., Luu, T. V., Behbahani, B., Frank, B., Quackenbush, J., and Lee, N. H. (2003) Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. Genome Biol. 4, R5.
27. Wang, R. F., Beggs, M. L., Robertson, L. H., and Cerniglia, C. E. (2002) Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol. Lett. 213, 175-182.
28. Zammatteo, N., Jeanmart, L., Hamels, S., Courtois, S., Louette, P., Hevesi, L., and Remacle, J. (2000) Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays. Anal. Biochem. 280, 143-150.