Oligonucleotide microarrays: widely applied--poorly understood

Brief Funct Genomic Proteomic. 2007 Jun;6(2):141-8. doi: 10.1093/bfgp/elm014. Epub 2007 Jul 20.


Microarray technology, which has been around for almost two decades, now provides an indispensable service to the biomedical research community. Soaring demand for high-throughput screening of genes potentially associated with cancer and other diseases, as well as the increased need for identifying microorganisms, have substantially opened up the application of this technology to many fields of science, including new ones such as array-based comparisons of whole genomes. Yet, despite this significant progress, the fundamental understanding of the pillars of this technology, have been largely unexplored, in particular for oligonucleotide-based microarrays. In fact, most of the current approaches for the design of microarrays are based on 'common-sense' parameters, such as guanine-cytosine content, secondary structure, melting temperature or possibility of minimizing the effects of nonspecific hybridization. However, recent experiments suggest that these are inadequate. Here we discuss these results, which challenge the basic principles and assumptions of oligonucleotide microarray technology. It is clear that more systematic physicochemical studies will be required to better understand the hybridization and dissociation behaviour of oligonucleotides.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Animals
  • Gene Expression Profiling
  • Humans
  • Kinetics
  • Models, Biological
  • Oligonucleotide Array Sequence Analysis / methods*
  • Thermodynamics