title: Towards a real-time, label-free, diamond-based DNA sensor.
abstract: Most challenging in the development of DNA sensors is the ability to distinguish between fully complementary target ssDNA (single-strand DNA) and 1-mismatch ssDNA. To deal with this problem, we performed impedance spectroscopy on DNA-functionalized nanocrystalline diamond (NCD) layers during hybridization and denaturation. In both reactions, a difference in behavior was observed for 1-mismatch target DNA and complementary target DNA in real-time. During real-time hybridization, a decrease of the impedance was observed at lower frequencies when the complementary target DNA was added, while the addition of 1-mismatch target ssDNA caused no significant change. Fitting these results to an electrical circuit demonstrates that this is correlated with a decrease of the depletion zone in the space charge region of the diamond. During real-time denaturation, differentiation between 1-mismatch and complementary target DNA was possible at higher frequencies. Denaturation of complementary DNA showed the longest exponential decay time of the impedance, while the decay time during 1-mismatch denaturation was the shortest. The real-time hybridization and denaturation experiments were carried out on different NCD samples in various buffer solutions at temperatures between 20 and 80 degrees C. It was revealed that the best results were obtained using a Microhyb hybridization buffer at 80 degrees C and 10x PCR buffer at 30 degrees C for hybridization and 0.1 M NaOH at temperatures above 40 degrees C for denaturation. We demonstrate that the combination of real-time hybridization spectra and real-time denaturation spectra yield important information on the type of target. This approach may allow a reliable identification of the mismatch sequence, which is the most biologically relevant.
authors.affiliation: Hasselt University and Transnationale Universiteit Limburg, School for Life Sciences, Biomedical Research Institute, Agoralaan, Building A, B-3590 Diepenbeek, Belgium.
authors.forename: V
authors.initials: V
authors.lastname: Vermeeren
authors.forename: N
authors.initials: N
authors.lastname: Bijnens
authors.forename: S
authors.initials: S
authors.lastname: Wenmackers
authors.forename: M
authors.initials: M
authors.lastname: Daenen
authors.forename: K
authors.initials: K
authors.lastname: Haenen
authors.forename: O A
authors.initials: OA
authors.lastname: Williams
authors.forename: M
authors.initials: M
authors.lastname: Ameloot
authors.forename: M
authors.initials: M
authors.lastname: vandeVen
authors.forename: P
authors.initials: P
authors.lastname: Wagner
authors.forename: L
authors.initials: L
authors.lastname: Michiels
mesh_terms: D001483:Base Sequence; D015374:Biosensing Techniques; D004247:DNA / Q000032:analysis*; D015342:DNA Probes; D018130:Diamond / Q000737:chemistry*; D008855:Microscopy, Electron, Scanning; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization
chemical_list: D015342:DNA Probes; D018130:Diamond; D004247:DNA