title: Three-dimensional hydrogel structures as optical sensor arrays, for the detection of specific DNA sequences.
abstract: The fabrication and characterization of surface-attached PEG-diacrylate hydrogel structures and their application as sensing platforms for the detection of specific target sequences are reported. Hydrogel structures were formed by a photopolymerization process, using substrate-bound Eosin Y molecules for the production of free radicals. We have demonstrated that this fabrication process allows for control over hydrogel growth down to the micrometer scale. Confocal imaging revealed relatively large pore structures for 25% (v/v) PEG-diacrylate hydrogels, which appear to lie in tightly packed layers. Our data suggest that these pore structures decrease in size for hydrogels with increasing levels of PEG-diacrylate. Surface coverage values calculated for hydrogels immobilized with 21-mer DNA probe sequences were significantly higher compared to those previously reported for 2- and 3-dimensional sensing platforms, on the order of 10(16)molecules cm(-2). Used as sensing platforms in DNA hybridization assays, a detection limit of 3.9 nM was achieved for hybridization reactions between 21-mer probe and target sequences. The ability of these hydrogel sensing platforms to discriminate between wild-type and mutant allele sequences was also demonstrated, down to target concentrations of 1-2 nM. A reduction in the hybridization time down to a period of 15 min was also achieved, while still maintaining confident results, demonstrating the potential for future integration of these sensing platforms within Lab-on-Chip or diagnostic devices.
authors.affiliation: Tyndall National Institute, Lee Maltings, University College, Cork, Ireland.
authors.forename: Francine
authors.initials: F
authors.lastname: Kivlehan
authors.forename: Marta
authors.initials: M
authors.lastname: Paolucci
authors.forename: Des
authors.initials: D
authors.lastname: Brennan
authors.forename: Ioannis
authors.initials: I
authors.lastname: Ragoussis
authors.forename: Paul
authors.initials: P
authors.lastname: Galvin
mesh_terms: D001483:Base Sequence; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000235:genetics; D004247:DNA / Q000032:analysis* / Q000737:chemistry / Q000235:genetics*; D004252:DNA Mutational Analysis; D006801:Humans; D020100:Hydrogels / Q000737:chemistry; D018613:Microscopy, Confocal; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics; D055620:Optical Phenomena; D011092:Polyethylene Glycols / Q000737:chemistry; D020641:Polymorphism, Single Nucleotide; D013499:Surface Properties
chemical_list: C505032:CFTR protein, human; D020100:Hydrogels; D015345:Oligonucleotide Probes; C437167:poly(ethylene glycol)diacrylate; D019005:Cystic Fibrosis Transmembrane Conductance Regulator; D011092:Polyethylene Glycols; D004247:DNA