Dynamic automated DNA hybridization on a CD (compact disc) fluidic platform

Abstract

A dynamic DNA hybridization microfluidic system was developed for a compact disc (CD) platform. The compact disc was used as the fluidic platform for sample and reagent manipulation using centrifugal force. Chambers for reagent storage and conduits for fluidic functions were replicated from polydimethylsiloxane (PDMS) using a SU-8 master mold fabricated by a 2-level lithography process which we developed specially for the microfluidic structures used in this work. For capture probes, we used self-assembled DNA oligonucleotide monolayers on gold pads patterned on glass slides. The PDMS flow cells were aligned with and sealed against the glass slides to form the DNA hybridization units. Hybridization was detected using an enzymatic-labeled fluorescence technique. An analytical model was introduced to quantitatively predict the accumulation of target DNA molecules. The flow-through hybridization units were tested using DNA samples (25-mers) of various concentrations down to 100 pM and passive assays (no flow) using samples of the same concentrations were performed for comparison. For the same concentration, with the same hybridization time (3 min), a fluorescence intensity increase up to threefold was observed in the flow-through hybridization unit compared to the passive hybridization assays. Furthermore, at the lowest sample concentration, the signal intensity from the passive assay is at the same level of the background while the signal from the flow-through assay is appreciably above the noise level. Besides the fast hybridization rate, the CD-based method has the potential for enabling highly automated, multiple and self-contained assays for DNA detection.