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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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.
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.
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.
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.
Joos, B., Kuster, H., and Cone, R. (1997) Covalent attachment of hybridizable oligonucleotides to glass supports. Anal. Biochem. 247, 96–101.
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.
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.
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.
Steel, A. B., Herne, T. M., and Tarlov, M. J. (1998) Electrochemical quantitation of DNA immobilized on gold. Anal. Chem. 70, 4670–4677.
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.
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.
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.
Marie, R., Schmid, S., Johansson, A., et al. (2006) Immobilisation of DNA to polymerised SU-8 photoresist. Biosens. Bioelectron. 21, 1327–1332.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Southern, E., Mir, K., and Shchepinov, M. (1999) Molecular interactions on microarrays. Nat. Genet. 21, 5–9.
Eisen, M. B. and Brown, P. O. (1999) DNA arrays for analysis of gene expression. Methods Enzymol. 303, 179–205.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Dufva, M., Christensen, C.B.V. (2007). Optimization of Oligonucleotide DNA Microarrays. In: Rampal, J.B. (eds) Microarrays. Methods in Molecular Biology™, vol 381. Humana Press. https://doi.org/10.1007/978-1-59745-303-5_4
Download citation
DOI: https://doi.org/10.1007/978-1-59745-303-5_4
Publisher Name: Humana Press
Print ISBN: 978-1-58829-589-7
Online ISBN: 978-1-59745-303-5
eBook Packages: Springer Protocols