title: Single-stranded DNA catalyzes hybridization of PCR-products to microarray capture probes.
abstract: Since its development, microarray technology has evolved to a standard method in the biotechnological and medical field with a broad range of applications. Nevertheless, the underlying mechanism of the hybridization process of PCR-products to microarray capture probes is still not completely understood, and several observed phenomena cannot be explained with current models. We investigated the influence of several parameters on the hybridization reaction and identified ssDNA to play a major role in the process. An increase of the ssDNA content in a hybridization reaction strongly enhanced resulting signal intensities. A strong influence could also be observed when unlabeled ssDNA was added to the hybridization reaction. A reduction of the ssDNA content resulted in a massive decrease of the hybridization efficiency. According to these data, we developed a novel model for the hybridization mechanism. This model is based on the assumption that single stranded DNA is necessary as catalyst to induce the hybridization of dsDNA. The developed hybridization model is capable of giving explanations for several yet unresolved questions regarding the functionality of microarrays. Our findings not only deepen the understanding of the hybridization process, but also have immediate practical use in data interpretation and the development of new microarrays.
authors.affiliation: Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Center North Rhine-Westphalia, Bad Oeynhausen, Germany; Department of Molecular Biotechnology, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
authors.forename: Simon
authors.initials: S
authors.lastname: Dally
authors.affiliation: Department of Molecular Biotechnology, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Rupp
authors.affiliation: Department of Molecular Biotechnology, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
authors.forename: Karin
authors.initials: K
authors.lastname: Lemuth
authors.affiliation: Department of Molecular Biotechnology, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
authors.forename: Stefan C
authors.initials: SC
authors.lastname: Hartmann
authors.affiliation: Department of Molecular Biotechnology, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
authors.forename: Ekkehard
authors.initials: E
authors.lastname: Hiller
authors.affiliation: Department of Molecular Biotechnology, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
authors.forename: Susanne M
authors.initials: SM
authors.lastname: Bailer
authors.affiliation: Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Center North Rhine-Westphalia, Bad Oeynhausen, Germany.
authors.forename: Cornelius
authors.initials: C
authors.lastname: Knabbe
authors.affiliation: Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Center North Rhine-Westphalia, Bad Oeynhausen, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Weile
mesh_terms: D055162:Biocatalysis; D004277:DNA, Single-Stranded / Q000378:metabolism*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction / Q000379:methods*
chemical_list: D004277:DNA, Single-Stranded