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Nucleic Acids Research, 2002, Vol. 30, No. 16 e86
© 2002 Oxford University Press

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

Hongyue Dai, Michael Meyer, Sergey Stepaniants, Michael Ziman and Roland Stoughton*

Rosetta Inpharmatics, 12040 115th Avenue NE, Kirkland, WA 98034, USA

*To whom correspondence should be addressed. Tel: +1 425 823 7322; Fax: +1 425 636 6377; Email: roland_stoughton{at}merck.com

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.


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