Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays

Nucleic Acids Res. 2002 Aug 15;30(16):e86. doi: 10.1093/nar/gnf085.


Hybridization kinetics were found to be significantly different for specific and non-specific binding of labeled cRNA to surface-bound oligonucleotides on microarrays. We show direct evidence that in a complex sample specific binding takes longer to reach hybridization equilibrium than the non- specific binding. We find that this property can be used to estimate and to correct for the hybridization contributed by non-specific binding. Useful applications are illustrated including the selection of superior oligonucleotides, and the reduction of false positives in exon identification.

MeSH terms

  • Base Pair Mismatch / genetics
  • Exons / genetics
  • Humans
  • Jurkat Cells
  • K562 Cells
  • Kinetics
  • Models, Chemical
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis / methods*
  • RNA / chemistry
  • RNA / genetics*
  • RNA / metabolism*
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Retinoblastoma / genetics
  • Sensitivity and Specificity
  • Substrate Specificity
  • Thermodynamics


  • RNA, Messenger
  • RNA