Correlation between microarray DNA hybridization efficiency and the position of short capture probe on the target nucleic acid

BioTechniques

Volumn 39, Issue 1, 2005, Pages 89-96

  Peytavi, Régis ^a   Tang, Liu Ying ^a   Raymond, Frédéric R ^a   Boissinot, Karel ^a   Bissonnette, Luc ^a   Boissinot, Maurice ^a   Picard, François J ^a   Huletsky, Ann ^a   Ouellette, Marc ^a   Bergeron, Michel G ^a,b  

^a LAVAL UNIVERSITY   (Canada)

^b LAVAL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA HYBRIDIZATION; HYBRIDIZATION SIGNAL; NUCLEOTIDE POLYMORPHISMS; OLIGONUCLEOTIDES;

ARRAYS; CORRELATION METHODS; DNA; PARAMETER ESTIMATION;

NUCLEIC ACIDS;

NUCLEIC ACID;

ARTICLE; DNA MICROARRAY; DNA STRAND; GENE TARGETING; HYBRIDIZATION; KINETICS; POLYMERASE CHAIN REACTION; DNA PROBE; DNA SEQUENCE; EVALUATION; GENETICS; IN SITU HYBRIDIZATION; METHODOLOGY; QUALITY CONTROL; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STANDARD; STATISTICS; VALIDATION STUDY;

BENCHMARKING; DNA PROBES; IN SITU HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; STATISTICS;

EID: 24944453869     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/05391RR01     Document Type: Article

References (34)

1. Debouck, C. and RN. Goodfellow. 1999. DNA microarrays in drug discovery and development. Nat. Genet. 21:48-50.
2. Duggan, D.J., M. Bittner, Y. Chen, P. Meltzer, and J.M. Trent. 1999. Expression profiling using cDNA microarrays. Nat. Genet. 21:10-14.
3. Marton, M.J., J.L. DeRisi, H.A. Bennett, V.R. Iyer, M.R. Meyer, C.J. Roberts, R. Stoughton, J. Burchard, et al. 1998. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat. Med. 4:1293-1301.
4. Cardoso, F. 2003. Microarray technology and its effect on breast cancer (re)classification and prediction of outcome. Breast Cancer Res. 5:303-304.
5. Cromer, A., A. Carles, R. Millon, G. Ganguli, F. Chalmel, F. Lemaire, J. Young, D. Dembele, et al. 2004. Identification of genes associated with tumorigenesis and metastatic potential of hypopharyngeal cancer by microarray analysis. Oncogene 23:2484-2498.
6. Ringner, M. and C. Peterson. 2003. Microarray-based cancer diagnosis with artificial neural networks. BioTechniques 34:S30-S35.
7. Verpoorte, E. 2002. Microfluidic chips for clinical and forensic analysis. Electrophoresis 23:677-712.
8. Davies, T.A. and R. Goldschmidt. 2002. Screening of large numbers of Streptococcus pneumoniae isolates for mutations associated with fluoroquinolone resistance using an oligonucleotide probe assay. FEMS Microbiol. Lett. 217:219-224.
9. Mikhailovich, V., S. Lapa, D. Gryadunov, A. Sobolev, B. Strizhkov, N. Chernyh, O. Skotnikova, O. Irtuganova, et al. 2001. Identification of rifampin-resistant Mycobacterium tuberculosis strains by hybridization, PCR, and ligase detection reaction on oligonucleotide microchips. J. Clin. Microbiol. 39:2531-2540.
10. Stenger, D.A., J.D. Andreadis, G.J. Vora, and J.J. Pancrazio. 2002. Potential applications of DNA microarrays in biodefense-related diagnostics. Curr. Opin. Biotechnol. 13:208-212.
11. Kane, M.D., T.A. Jatkoe, C.R. Stumpf, J. Lu, J.D. Thomas, and S.J. Madore. 2000. Assessment of the sensitivity and specificity of oligonucleotide (50-mer) microarrays. Nucleic Acids Res. 28:4552-4557.
12. Wang, R.F., M.L. Beggs, L.H. Robertson, and C.E. Cerniglia. 2002. Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol. Lett. 213:175-182.
13. Urakawa, H., S. El Fantroussi, H. Smidt, J.C. Smoot, E.H. Tribou, J.J. Kelly, P.A. Noble, and D.A. Stahl. 2003. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl. Environ. Microbiol. 69:2848-2856.
14. 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.
15. Chizhikov, V., A. Rasooly, K. Chumakov, and D.D. Levy. 2001. Microarray analysis of microbial virulence factors. Appl. Environ. Microbiol. 67:3258-3263.
16. Peplies, J., F.O. Glockner, and R. Amann. 2003. Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl. Environ. Microbiol. 69:1397-1407.
17. Matveeva, O.V., S.A. Shabalina, V.A. Nemtsov, A.D. Tsodikov, R.F. Gesteland, and J.F. Atkins. 2003. Thermodynamic calculations and statistical correlations for oligoprobes design. Nucleic Acids Res. 31:4211-4217.
18. Gao, H.F., S.C. Tao, D. Wang, C. Zhang, X. Ma, J. Cheng, and Y. Zhou. 2003. Comparison of different methods for preparing single stranded DNA for oligonucleotide microarray. Anal. Lett. 33:2849-2863.
19. Tao, S.C., H.F. Gao, F. Cao, X.M. Ma, and J. Cheng. 2003. Blocking oligo-a novel approach for improving chip-based DNA hybridization efficiency. Mol. Cell. Probes 17:197-202.
20. Reyes-Lopez, M.A., A. Mendez-Tenorio, R. Maldonado-Rodriguez, M.J. Doktycz, J.T. Fleming, and K.L. Beattie. 2003. Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization. Nucleic Acids Res. 31:779-789.
21. Southern, E.M., S.C. Case-Green, J.K. Elder, M. Johnson, K.U. Mir, L. Wang, and J.C. Williams. 1994. Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res. 22:1368-1373.
22. Antipova, A.A., P. Tamayo, and T.R. Golub. 2002. A strategy for oligonucleotide microarray probe reduction. Genome Biol. 3:research0073.1- research0073.4.
23. Lockhart, D.J., H. Dong, M.C. Byrne, M.T. Follettie, M.V. Gallo, M.S. Chee, M. Mittmann, C. Wang, et al. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14:1675-1680.
24. Lane, D.R., M.J. Krug, S.F. Gonzalez, and A. Warsen. 2003. Amplicon secondary structure interferes with microarray hybridization. 103rd General Meeting of the American Society for Microbiology. Washington, DC.
25. Shi, S.J., A. Scheffer, E. Bjeldanes, M.A. Reynolds, and L.J. Arnold. 2001. DNA exhibits multi-stranded binding recognition on glass microarrays. Nucleic Acids Res. 29:4251-4256.
26. Steel, A.B., R.L. Levicky, T.M. Herne, and M.J. Tarlov. 2000. Immobilization of nucleic acids at solid surfaces: effect of oligonucleotide length on layer assembly. Biophys. J. 79:975-981.
27. Roberts, M.C., J. Sutcliffe, P. Courvalin, L.B. Jensen, J. Rood, and H. Seppala. 1999. Nomenclature for macrolide and macrolidelincosamide-streptogramin B resistance determinants. Antimicrob. Agents Chemother. 43:2823-2830.
28. Rafalski, J.A. 1988. Two strands of DNA are not equivalent as probes in hybridizations at low stringency. Anal. Biochem. 173:383-386.
29. Martineau, F., F.J. Picard, D. Ke, S. Paradis, P.H. Roy, M. Ouellette, and M.G. Bergeron. 2001. Development of a PCR assay for identification of staphylococci at genus and species levels. J. Clin. Microbiol. 39:2541-2547.
30. Bradford, P.A. 1999. Automated thermal cycling is superior to traditional methods for nucleotide sequencing of bla(SHV) genes. Antimicrob. Agents Chemother. 43:2960-2963.
31. Reynaldo, L.P., A.V. Vologodskii, B.P. Neri, and V.I. Lyamichev. 2000. The kinetics of oligonucleotide replacements. J. Mol. Biol. 297:511-520.
32. Yurke, B., A.J. Turberfield, A.P. Mills, Jr., F.C. Simmel, and J.L. Neumann. 2000. A DNA-fuelled molecular machine made of DNA. Nature 406:605-608.
33. Alberti, P. and J.L. Mergny. 2003. DNA duplex-quadruplex exchange as the basis for a nanomolecular machine. Proc. Natl. Acad. Sci. USA 100:1569-1573.
34. Lee, C.S., R.W. Davis, and N. Davidson. 1970. A physical study by electron microscopy of the terminally reptitious, circularly permuted DNA from the coliphage particles of Escherichia coli 15. J. Mol. Biol. 48:1-22.