A model of molecular interactions on short oligonucleotide microarrays

Nat Biotechnol. 2003 Jul;21(7):818-21. doi: 10.1038/nbt836. Epub 2003 Jun 8.


High-density short oligonucleotide microarrays have become a widely used tool for measuring gene expression on a large scale. However, details of the mechanism of binding on microarrays remain unclear. Short oligonucleotide probes currently synthesized on microarrays are often ineffective as a result of limited sequence specificity or low sensitivity. Here, we describe a model of binding interactions on microarrays that reveals how probe signals depend on probe sequences and why certain probes are ineffective. The model indicates that the amount of nonspecific binding can be estimated from a simple rule. Using this model, we have developed an improved measure of gene expression for use in data analysis.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.
  • Validation Study

MeSH terms

  • Binding Sites
  • Computer Simulation
  • Gene Expression Profiling / methods*
  • Macromolecular Substances
  • Models, Chemical*
  • Models, Molecular
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotide Probes / chemistry*
  • Oligonucleotides / chemistry*
  • Quality Control
  • RNA / chemistry*


  • Macromolecular Substances
  • Oligonucleotide Probes
  • Oligonucleotides
  • RNA