title: Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays.
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.
authors.affiliation: Rosetta Inpharmatics, 12040 115th Avenue NE, Kirkland, WA 98034, USA.
authors.forename: Hongyue
authors.initials: H
authors.lastname: Dai
authors.forename: Michael
authors.initials: M
authors.lastname: Meyer
authors.forename: Sergey
authors.initials: S
authors.lastname: Stepaniants
authors.forename: Michael
authors.initials: M
authors.lastname: Ziman
authors.forename: Roland
authors.initials: R
authors.lastname: Stoughton
mesh_terms: D020137:Base Pair Mismatch / Q000235:genetics; D005091:Exons / Q000235:genetics; D006801:Humans; D019169:Jurkat Cells; D020014:K562 Cells; D007700:Kinetics; D008956:Models, Chemical; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012313:RNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012175:Retinoblastoma / Q000235:genetics; D012680:Sensitivity and Specificity; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D012333:RNA, Messenger; D012313:RNA