title: Correlation between microarray DNA hybridization efficiency and the position of short capture probe on the target nucleic acid.
abstract: The hybridization behavior of small oligonucleotides arrayed on glass slides is currently unpredictable. In order to examine the hybridization efficiency of capture probes along target nucleic acid, 20-mer oligonucleotide probes were designed to hybridize at different distances from the 5' end of two overlapping 402- and 432-bp ermB products amplified from the target DNA. These probes were immobilized via their 5' end onto glass slides and hybridized with the two labeled products. Evaluation of the hybridization signal for each probe revealed an inverse correlation with the length of the 5' overhanging end of the captured strand and the hybridization signal intensity. Further experiments demonstrated that this phenomenon is dependent on the reassociation kinetics of the free overhanging tail of the captured DNA strand with its complementary strand. This study delineates key predictable parameters that govern the hybridization efficiency of short capture probes arrayed on glass slides. This should be most useful for designing arrays for detection of PCR products and nucleotide polymorphisms.
authors.affiliation: Centre Hospitalier Universitaire de Quebec, Sainte-Foy, Québec, Canada.
authors.forename: Régis
authors.initials: R
authors.lastname: Peytavi
authors.forename: Tang
authors.initials: T
authors.lastname: Liu-Ying
authors.forename: Frédéric R
authors.initials: FR
authors.lastname: Raymond
authors.forename: Karel
authors.initials: K
authors.lastname: Boissinot
authors.forename: Luc
authors.initials: L
authors.lastname: Bissonnette
authors.forename: Maurice
authors.initials: M
authors.lastname: Boissinot
authors.forename: François J
authors.initials: FJ
authors.lastname: Picard
authors.forename: Ann
authors.initials: A
authors.lastname: Huletsky
authors.forename: Marc
authors.initials: M
authors.lastname: Ouellette
authors.forename: Michel G
authors.initials: MG
authors.lastname: Bergeron
mesh_terms: D019985:Benchmarking / Q000379:methods*; D015342:DNA Probes / Q000235:genetics*; D017403:In Situ Hybridization / Q000379:methods* / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D013223:Statistics as Topic
chemical_list: D015342:DNA Probes