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Microarrays pp 93-103 | Cite as

Optimization of Oligonucleotide DNA Microarrays

  • Martin Dufva
  • Claus B. V. Christensen
Part of the Methods in Molecular Biology™ book series (MIMB, volume 381)

Abstract

Optimization of oligonucleotide DNA microarrays is a multiparametric problem. The goal of the optimization process is to get conditions that capture target DNA with high sensitivity and selectivity. Parameters determining the performance of the microarray are spot morphology, probe and target density, background, and selectivity. More than 10 variables can be adjusted to obtain a well-optimized protocol. However, some variables only affect spot morphology and other factors affect for instance hybridization and selectivity, which can limit the optimization work considerably. This chapter suggests an outline on how an optimization procedure is made. Moreover, a simple method for absolutely quantify the number of hybridized target to the spots is given. The latter is important because it gives the possibilities to compare results with those obtained in the literature.

Key Words

DNA microarray hybridized density hybridization optimization probe density quantification spot morphology spotting 

References

  1. 1.
    Beier, M. and Hoheisel, J. D. (1999) Versatile derivatisation of solid support media for covalent bonding on DNA-microchips. Nucleic Acids Res. 27, 1970–1977.CrossRefGoogle Scholar
  2. 2.
    Britcher, L. G., Kehoe, D. C., Matisons, J. G., Smart, R. S. C., and Swincer, A. G. (1993) Silicones on glass surfaces 2: coupling agent analogs. Langmuir 9, 1609–1613.CrossRefGoogle Scholar
  3. 3.
    Guo, Z., Guilfoyle, R. A., Thiel, A. J., Wang, R., and Smith, L. M. (1994) Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res. 22, 5456–5465.CrossRefGoogle Scholar
  4. 4.
    Janolino, V. and Swaigood, H. E. (1982) Analysis and optimisation of methods using water-soluble carbidiimide for immobilization of biochemicals to porous glass. Biotechnol. Bioeng. 24, 1069–1080.CrossRefGoogle Scholar
  5. 5.
    Joos, B., Kuster, H., and Cone, R. (1997) Covalent attachment of hybridizable oligonucleotides to glass supports. Anal. Biochem. 247, 96–101.CrossRefGoogle Scholar
  6. 6.
    Rogers, Y. H., Jiang-Baucom, P., Huang, Z. J., et al. (1999) Immobilization of oligonucleotides onto a glass support via disulfide bonds: a method for preparation of DNA microarrays. Anal. Biochem. 266, 23–30.CrossRefGoogle Scholar
  7. 7.
    Chrisey, L. A., Lee, G. U., and O’Ferrall, C. E. (1996) Covalent attachment of synthetic DNA to self-assembled monolayer films. Nucleic Acids Res. 24, 3031–3039.CrossRefGoogle Scholar
  8. 8.
    Strother, T., Hamers, R. J., and Smith, L. M. (2000) Covalent attachment of oligodeoxyribonucleotides to amine-modified Si (001) surfaces. Nucleic Acids Res. 28, 3535–3541.CrossRefGoogle Scholar
  9. 9.
    Steel, A. B., Herne, T. M., and Tarlov, M. J. (1998) Electrochemical quantitation of DNA immobilized on gold. Anal. Chem. 70, 4670–4677.CrossRefGoogle Scholar
  10. 10.
    Steel, A. B., Levicky, R. L., Herne, T. M., and Tarlov, M. J. (2000) Immobilization of nucleic acids at solid surfaces: effect of oligonucleotide length on layer assembly. Biophys. J. 79, 975–981.CrossRefGoogle Scholar
  11. 11.
    Fixe, F., Dufva, M., Telleman, P., and Christensen, C. B. (2004) Functionalization of poly(methyl methacrylate) (PMMA) as a substrate for DNA microarrays. Nucleic Acids Res. 32, E9.CrossRefGoogle Scholar
  12. 12.
    Fixe, F., Dufva, M., Telleman, P., and Christensen, C. B. (2004) One-step immobilization of aminated and thiolated DNA onto poly(methylmethacrylate) (PMMA) substrates. Lab. Chip 4, 191–195.CrossRefGoogle Scholar
  13. 13.
    Marie, R., Schmid, S., Johansson, A., et al. (2006) Immobilisation of DNA to polymerised SU-8 photoresist. Biosens. Bioelectron. 21, 1327–1332.CrossRefGoogle Scholar
  14. 14.
    Vainrub, A. and Pettitt, B. M. (2002) Coulomb blockage of hybridization in two-dimensional DNA arrays. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 66, 041905.CrossRefGoogle Scholar
  15. 15.
    Dufva, M., Petronis, S., Bjerremann J. L., Krag, C., and Christensen, C. (2004) Characterization of an inexpensive, nontoxic and highly sensitive microarray substrate. Biotechniques 37, 286–296.Google Scholar
  16. 16.
    Benters, R., Niemeyer, C. M., Drutschmann, D., Blohm, D., and Wohrle, D. (2002) DNA microarrays with PAMAM dendritic linker systems. Nucleic Acids Res. 30, E10.CrossRefGoogle Scholar
  17. 17.
    Le Berre, V., Trevisiol, E., Dagkessamanskaia, A., et al. (2003) Dendrimeric coating of glass slides for sensitive DNA microarrays analysis. Nucleic Acids Res. 31, E88.CrossRefGoogle Scholar
  18. 18.
    Hughes, T. R., Mao, M., Jones, A. R., et al. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19, 342–347.CrossRefGoogle Scholar
  19. 19.
    Afanassiev, V., Hanemann, V., and Wolfl, S. (2000) Preparation of DNA and protein micro arrays on glass slides coated with an agarose film. Nucleic Acids Res. 28, E66.CrossRefGoogle Scholar
  20. 20.
    Hessner, M. J., Wang, X., Hulse, K., et al. (2003) Three color cDNA microarrays: quantitative assessment through the use of fluorescein-labeled probes. Nucleic Acids Res. 31, E14.CrossRefGoogle Scholar
  21. 21.
    Zammatteo, N., Jeanmart, L., Hamels, S., et al. (2000) Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays. Anal. Biochem. 280, 143–150.CrossRefGoogle Scholar
  22. 22.
    Shchepinov, M. S., Case-Green, S. C., and Southern, E. M. (1997) Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 25, 1155–1161.CrossRefGoogle Scholar
  23. 23.
    Keramas, G., Bang, D. D., Lund, M., et al. (2003) Development of a sensitive DNA microarray suitable for rapid detection of Campylobacter spp. Mol. Cell Probes 17, 187–196.CrossRefGoogle Scholar
  24. 24.
    Southern, E., Mir, K., and Shchepinov, M. (1999) Molecular interactions on microarrays. Nat. Genet. 21, 5–9.CrossRefGoogle Scholar
  25. 25.
    Eisen, M. B. and Brown, P. O. (1999) DNA arrays for analysis of gene expression. Methods Enzymol. 303, 179–205.CrossRefGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2007

Authors and Affiliations

  • Martin Dufva
    • 1
  • Claus B. V. Christensen
    • 1
  1. 1.Department of Micro and NanotechnologyTechnical University of DenmarkKongens LyngbyDenmark

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