(Note: Current Rosetta Inpharmatics employees are shown in boldface type.)

Hongyue Dai¹, Michael Meyer¹, Sergey Stepaniants¹, Michael Ziman, Ronald Stoughton¹

Abstract

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.

¹ Rosetta Inpharmatics
12040 115th Avenue North East
Kirkland, Washington 98034, USA.
email: ronald_stoughton@merck.com