Skip to main content

DNA Microarrays: An Introduction to the Technology

  • Protocol
Microchip Methods in Diagnostics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 509))

Summary

DNA microarrays allow the comprehensive genetic analysis of an organism or a sample. They are based on probes, which are immobilized in an ordered two-dimensional pattern on substrates, such as nylon membranes or glass slides. Probes are either spotted cDNAs or oligonucleotides and are designed to be specific for an organism, a gene, a genetic variant (mutation or polymorphism), or intergenic regions. Thus, they can be used for example for genotyping, expression analysis, or studies of protein–DNA interactions, and in the biomedical field they allow the detection of pathogens, antibiotic resistances, gene mutations and polymorphisms, and pathogenic states and can guide therapy. Microarrays, which cover the whole genome of an organism, are as well available as those which are focussed on genes related to a certain diagnostic application.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Lipshutz, R.J., Fodor, S.P.A., Gingeras, T.R. ,Lockhart, D.J. (1999) High density synthetic oligonucleotide arrays, Nat. Genet. 21 Suppl. 1, 20–24

    Article  CAS  Google Scholar 

  2. Brown, P.O., Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays, Nat. Genet. 21 Suppl. 1, 33–37

    Article  CAS  Google Scholar 

  3. Jordan, B.R. (2001) DNA Microarrays: Gene expression applications, Springer, Berlin

    Google Scholar 

  4. Perreten, V., Vorlet-Fawer, L., Slickers, P., Ehricht, R., Kuhnert, P., Frey, F. (2005) Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria, J. Clin. Microbiol. 43, 2291–2302

    Article  CAS  Google Scholar 

  5. Tempfer, C.B., Riener, E.K., Hefler, L.A., Huber, J.C., Muendlein, A. (2004) DNA microarray-based single nucleotide polymorphisms may be useful for assessing the risks and benefits of hormone therapy, Fertil. Steril 82, 132–137

    Article  CAS  Google Scholar 

  6. Hoheisel, J.D. (2006) Microarray technology: Beyond transcript profiling and genotype analysis, Nat. Rev. Genet. 7, 200–210

    Article  CAS  Google Scholar 

  7. Bulyck, M.L. (2006) DNA microarray technologies for measuring protein-DNA interactions, Curr. Opin. Biotechnol. 17, 422–430

    Article  Google Scholar 

  8. Hudson, M.E., Snyder, M. (2006) Highthroughput methods for regulatory element discovery, BioTechniques 41, 673–681

    Article  CAS  Google Scholar 

  9. Lee, M., Trent, J.M., Bittner, M.L. (2007) Optimization of oligonucleotide microarray fabricated by spotting 65-mer, Anal. Bio-chem. 368, 61–69

    CAS  Google Scholar 

  10. Ehrenreich, A. (2006) DNA microarray technology for the microbiologist: An overview, Appl. Microbiol. Biotechnol. 73, 255–273

    Article  CAS  Google Scholar 

  11. Kane, M.D., Jatkoe, T.A., Stumpf, C.R., Lu, J., Thomas, J.D., Madore, S.J. (2000) Assessment of the sensitivity and specificty of oli-gonucleotide (50mer) microarrays, Nucleic Acids Res. 28, 4552–4557

    Article  CAS  Google Scholar 

  12. Watts, H.J., Yeung, D., Parkes, H. (1995) Real-time detection and quantification of DNA hybridization by an optical biosensor, Anal. Chem. 67, 4283–4289

    Article  CAS  Google Scholar 

  13. Persson, B., Stenhag, K., Nilsson, P., Larsson, A., Uhlán, M., Nygren, P.A. (1997) Analysis of nucleotide probe affinities using surface plasmon resonance: A means for mutational scanning, Anal. Biochem. 246, 34–44

    Article  CAS  Google Scholar 

  14. Dorris, D.R., Nguyen, A., Gieser, L., Lockner, R., Lublinsky, A., Patterson, M., Touma, E., Sendera, T.J., Elghanian, R., Mazumder, A. (2003) Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios, BMC Biotechnol. 3, 6

    Article  Google Scholar 

  15. ÓMeara, D., Ahmadian, A., Odeberg, J., Lunde- berg, J. (2002) SNP typing by apyrase-mediated allele-specific primer extension on DNA micro-arrays, Nucleic Acids Res. 30, e75

    Article  Google Scholar 

  16. Relogio, A., Schwager, C., Richter, A., Ansorge, W., Valcarcel, J. (2002) Optimization of oligonucleotide-based DNA microar-rays, Nucleic Acids Res. 30, e51

    Article  Google Scholar 

  17. Peterson, A.W., Heaton, R.J., Georgiadis, R.M. (2001) The effect of surface probe density on DNA hybridisation, Nucleic Acids Res. 29, 5163–5168

    Article  CAS  Google Scholar 

  18. Campas, M., Katakis, I. (2004) DNA biochip arraying, detection and amplification strategies, Trends Anal. Chem. 23, 49–62

    Article  CAS  Google Scholar 

  19. Zammatteo, N., Jeanmart, L., Hamels, S., Courtois, S., Louette, P., Hevesi, L., Remacle, J. (2000) Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays, Anal. Biochem. 280, 143–150

    Article  CAS  Google Scholar 

  20. Pease, A.C., Solas, D., Sullivan, E.J., Cronin, M.T., Holmes, C.P., Fodor, S.P.A. (1994) Light-generated oligonucleotide arrays for rapid DNA sequence analysis Proc. Natl. Acad. Sci. 91, 5022–5026

    Article  CAS  Google Scholar 

  21. Weiler, J., Hoheisel, J.D. (1996) Combining the preparation of oligonucleotide arrays and synthesis of high-quality primers, Anal. Bio-chem. 243, 218–227

    CAS  Google Scholar 

  22. Blanchard, A.P., Kaiser, R.J., Hood, L.E. (1996) High-density oligonucleotide arrays, Biosens. Bioelectr. 11, 687–690

    Article  CAS  Google Scholar 

  23. Bier, F.F., Kleinjung, F., Scheller, F.W. (1997) Real-time measurment of nucleic-acid hybridisation using evanescent-wave sensors: Steps towards the genosensor, Sens Actuators B 38/39, 78–82

    Article  Google Scholar 

  24. Taton, T.A., Mirkin, C.A., Letsinger, R.L. (2000) Scanometric DNA Array detection with nanoparticle probes, Science 289, 1757–1760

    Article  CAS  Google Scholar 

  25. Brazma et al. (2001) Minimum information about a microarray experiment (MIAME) – Toward standards for microarray data, Nat. Genet. 29, 365–371

    Article  Google Scholar 

  26. Wang, X.W., Zhang, L., Jin, L.Q., Jin, M., Shen, Z.Q., An, S., Chao, F.H., Li, J.W. (2007) Development and application of an oligonucleotide microarray for the detection of food-borne bacterial pathogens, Appl. Microbiol. Biotechnol. 76, 225–233

    Article  CAS  Google Scholar 

  27. Leinberger, D.M., Schumacher, U., Autenrieth, I.B., Bachmann, T.T. (2005) Development of a DNA microarray for detection and identification of fungal pathogens in invasive mycoses, J. Clin. Microbiol. 43, 4943–4952

    Article  CAS  Google Scholar 

  28. Hacia, J.G. (1999) Resequencing and mutational analysis using oligonucleotide microar-rays, Nat. Genet. 21 Suppl. 1, 42–47

    Article  CAS  Google Scholar 

  29. Hughes, T.R., et al. (2000) Functional discovery via a compendium of expression profiles, Cell 102, 109–126

    Article  CAS  Google Scholar 

  30. Hamadeh, H.K., Afshari, C.A. (2004) Toxicogenomics Principles and Applications, Wiley, New Jersey 31. Members of the toxicogenomics research consortium (2005) Standardizing global gene expression analysis between laboratories and across platforms, Nat. Methods 2, 1–6

    Google Scholar 

  31. Members of the toxicogenomics research consortium (2005) Standardizing global gene expression analysis between laboratories and across platforms, Nat. Methods 2, 1–6

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Bilitewski, U. (2009). DNA Microarrays: An Introduction to the Technology. In: Bilitewski, U. (eds) Microchip Methods in Diagnostics. Methods in Molecular Biology™, vol 509. Humana Press. https://doi.org/10.1007/978-1-59745-372-1_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-372-1_1

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-955-0

  • Online ISBN: 978-1-59745-372-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics