title: Fast-Track, One-Step E. coli Detection: A Miniaturized Hydrogel Array Permits Specific Direct PCR and DNA Hybridization while Amplification.
abstract: A timesaving and convenient method for bacterial detection based on one-step, one-tube deoxyribonucleic acid (DNA) hybridization on hydrogel array while target gene amplification is described. The hydrogel array is generated by a fast one-pot synthesis, where N,N'-dimethylacrylamide/polyethyleneglycol(PEG1900 )-bisacrylamide mixture polymerizes via radical photoinitiation by visible light within 20 min concomitant with in situ capture probe immobilization. These DNA-functionalized hydrogel droplets arrayed on a planar glass surface are placed in the polymerase chain reaction (PCR) mixture during the thermal amplification cycles. The bacterial cells can be implemented in a direct PCR reaction, omitting the need for prior template DNA extraction. The resulting fluorescence signal is immediately detectable after the end of the PCR (1 h) following one short washing step by microscopy. Therefore a valid signal can be reached within 1.5 h including 10 min for pipetting and placement of the tubes and chips. The performance of this novel hydrogel DNA array was successfully proven with varying cell numbers down to a limit of 10(1) Escherichia coli cells.
authors.affiliation: Leibniz-Institute of Photonic Technology, Jenaer BioChip Initiative, Albert-Einstein-Strasse 9, 07745, Jena, Germany.|Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Centre of Photonics, Helmholtzweg 4, 07743, Jena, Germany.|InfectoGnostics Forschungscampus Jena, Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany.
authors.forename: Antje
authors.initials: A
authors.lastname: Beyer
authors.affiliation: Leibniz-Institute of Photonic Technology, Jenaer BioChip Initiative, Albert-Einstein-Strasse 9, 07745, Jena, Germany.|InfectoGnostics Forschungscampus Jena, Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany.|Ernst-Abbe-Hochschule Jena, University of Applied Sciences, Carl-Zeiss-Promenade 2, 07745, Jena, Germany.
authors.forename: Sibyll
authors.initials: S
authors.lastname: Pollok
authors.affiliation: Leibniz-Institute of Photonic Technology, Jenaer BioChip Initiative, Albert-Einstein-Strasse 9, 07745, Jena, Germany.|InfectoGnostics Forschungscampus Jena, Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany.
authors.forename: Anne
authors.initials: A
authors.lastname: Rudloff
authors.affiliation: Leibniz-Institute of Photonic Technology, Jenaer BioChip Initiative, Albert-Einstein-Strasse 9, 07745, Jena, Germany.|Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Centre of Photonics, Helmholtzweg 4, 07743, Jena, Germany.|InfectoGnostics Forschungscampus Jena, Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany.
authors.forename: Dana
authors.initials: D
authors.lastname: Cialla-May
authors.affiliation: Leibniz-Institute of Photonic Technology, Jenaer BioChip Initiative, Albert-Einstein-Strasse 9, 07745, Jena, Germany. karina.weber@ipht-jena.de.|Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Centre of Photonics, Helmholtzweg 4, 07743, Jena, Germany. karina.weber@ipht-jena.de.|InfectoGnostics Forschungscampus Jena, Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany. karina.weber@ipht-jena.de.
authors.forename: Karina
authors.initials: K
authors.lastname: Weber
authors.affiliation: Leibniz-Institute of Photonic Technology, Jenaer BioChip Initiative, Albert-Einstein-Strasse 9, 07745, Jena, Germany.|Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Centre of Photonics, Helmholtzweg 4, 07743, Jena, Germany.|InfectoGnostics Forschungscampus Jena, Zentrum für Angewandte Forschung, Philosophenweg 7, 07743, Jena, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Popp
mesh_terms: D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics*; D004587:Electrophoresis, Agar Gel; D004926:Escherichia coli / Q000235:genetics* / Q000302:isolation & purification*; D005453:Fluorescence; D020136:Hydrogel, Polyethylene Glycol Dimethacrylate / Q000737:chemistry*; D008904:Miniaturization / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*
chemical_list: D004269:DNA, Bacterial; D020136:Hydrogel, Polyethylene Glycol Dimethacrylate
keywords: combined direct PCR; functional hydrogel interface; functionalization of polymers; one pot radical polymerization